Daily Papers

Large language models (LLMs) show promise for molecular optimization, but aligning them with selective and competing drug-design constraints remains challenging. We propose C-Moral, a reinforcement learning post-training framework for controllable multi-objective molecular optimization. C-Moral combines group-based relative optimization, property score alignment for heterogeneous objectives, and continuous non-linear reward aggregation to improve stability across competing properties. Experiments on the C-MuMOInstruct benchmark show that C-Moral consistently outperforms state-of-the-art models across both in-domain and out-of-domain settings, achieving the best Success Optimized Rate (SOR) of 48.9% on IND tasks and 39.5% on OOD tasks, while largely preserving scaffold similarity. These results suggest that RL post-training is an effective way to align molecular language models with continuous molecular design objectives. Our code and models are publicly available at https://github.com/Rwigie/C-MORAL.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.

Modern coding scaffolds turn LLMs into capable software agents, but their ability to follow scaffold-specified instructions remains under-examined, especially when constraints are heterogeneous and persist across interactions. To fill this gap, we introduce OctoBench, which benchmarks scaffold-aware instruction following in repository-grounded agentic coding. OctoBench includes 34 environments and 217 tasks instantiated under three scaffold types, and is paired with 7,098 objective checklist items. To disentangle solving the task from following the rules, we provide an automated observation-and-scoring toolkit that captures full trajectories and performs fine-grained checks. Experiments on eight representative models reveal a systematic gap between task-solving and scaffold-aware compliance, underscoring the need for training and evaluation that explicitly targets heterogeneous instruction following. We release the benchmark to support reproducible benchmarking and to accelerate the development of more scaffold-aware coding agents.

In this paper, we propose a new class of metric for table structure recognition (TSR) evaluation, called grid table similarity (GriTS). Unlike prior metrics, GriTS evaluates the correctness of a predicted table directly in its natural form as a matrix. To create a similarity measure between matrices, we generalize the two-dimensional largest common substructure (2D-LCS) problem, which is NP-hard, to the 2D most similar substructures (2D-MSS) problem and propose a polynomial-time heuristic for solving it. This algorithm produces both an upper and a lower bound on the true similarity between matrices. We show using evaluation on a large real-world dataset that in practice there is almost no difference between these bounds. We compare GriTS to other metrics and empirically validate that matrix similarity exhibits more desirable behavior than alternatives for TSR performance evaluation. Finally, GriTS unifies all three subtasks of cell topology recognition, cell location recognition, and cell content recognition within the same framework, which simplifies the evaluation and enables more meaningful comparisons across different types of TSR approaches. Code will be released at https://github.com/microsoft/table-transformer.

Detecting code clones is relevant to software maintenance and code refactoring. This challenge still presents unresolved cases, mainly when structural similarity does not reflect functional equivalence, though recent code models show promise. Therefore, this research aims to systematically measure the performance of several newly introduced small code models in classifying code pairs as clones or non-clones. The evaluation is based on five datasets: BigCloneBench, CodeJam, Karnalim, POJ104, and PoolC, as well as six code models: CodeBERT, GraphCodeBERT, Salesforce T5, UniXCoder, PLBART, and Polycoder. Most models performed well across standard metrics, including accuracy, precision, recall, and F1-score. However, a marginal fraction of clones remains challenging to detect, especially when the code looks similar but performs different operations. The source code that illustrates our approach is available at: https://github.com/jorge-martinez-gil/small-code-models

This paper introduces a public dataset of 1.4 million procedurally-generated bicycle designs represented parametrically, as JSON files, and as rasterized images. The dataset is created through the use of a rendering engine which harnesses the BikeCAD software to generate vector graphics from parametric designs. This rendering engine is discussed in the paper and also released publicly alongside the dataset. Though this dataset has numerous applications, a principal motivation is the need to train cross-modal predictive models between parametric and image-based design representations. For example, we demonstrate that a predictive model can be trained to accurately estimate Contrastive Language-Image Pretraining (CLIP) embeddings from a parametric representation directly. This allows similarity relations to be established between parametric bicycle designs and text strings or reference images. Trained predictive models are also made public. The dataset joins the BIKED dataset family which includes thousands of mixed-representation human-designed bicycle models and several datasets quantifying design performance. The code and dataset can be found at: https://github.com/Lyleregenwetter/BIKED_multimodal/tree/main

LLM-based coding agents can localize bugs, generate patches, and run tests with diminishing human oversight, yet the scaffolding code that surrounds the language model (the control loop, tool definitions, state management, and context strategy) remains poorly understood. Existing surveys classify agents by abstract capabilities (tool use, planning, reflection) that cannot distinguish between architecturally distinct systems, and trajectory studies observe what agents do without examining the scaffold code that determines why. This paper presents a source-code-level architectural taxonomy derived from analysis of 13 open-source coding agent scaffolds at pinned commit hashes. Each agent is characterized across 12 dimensions organized into three layers: control architecture, tool and environment interface, and resource management. The analysis reveals that scaffold architectures resist discrete classification: control strategies range from fixed pipelines to Monte Carlo Tree Search, tool counts range from 0 to 37, and context compaction spans seven distinct strategies. Five loop primitives (ReAct, generate-test-repair, plan-execute, multi-attempt retry, tree search) function as composable building blocks that agents layer in different combinations; 11 of 13 agents compose multiple primitives rather than relying on a single control structure. Dimensions converge where external constraints dominate (tool capability categories, edit formats, execution isolation) and diverge where open design questions remain (context compaction, state management, multi-model routing). All taxonomic claims are grounded in file paths and line numbers, providing a reusable reference for researchers studying agent behavior and practitioners designing new scaffolds.

We present a method for estimating neural scenes representations of objects given only a single image. The core of our method is the estimation of a geometric scaffold for the object and its use as a guide for the reconstruction of the underlying radiance field. Our formulation is based on a generative process that first maps a latent code to a voxelized shape, and then renders it to an image, with the object appearance being controlled by a second latent code. During inference, we optimize both the latent codes and the networks to fit a test image of a new object. The explicit disentanglement of shape and appearance allows our model to be fine-tuned given a single image. We can then render new views in a geometrically consistent manner and they represent faithfully the input object. Additionally, our method is able to generalize to images outside of the training domain (more realistic renderings and even real photographs). Finally, the inferred geometric scaffold is itself an accurate estimate of the object's 3D shape. We demonstrate in several experiments the effectiveness of our approach in both synthetic and real images.

Modern image generators produce strikingly realistic images, where only artifacts like distorted hands or warped objects reveal their synthetic origin. Detecting these artifacts is essential: without detection, we cannot benchmark generators or train reward models to improve them. Current detectors fine-tune VLMs on tens of thousands of labeled images, but this is expensive to repeat whenever generators evolve or new artifact types emerge. We show that pretrained VLMs already encode the knowledge needed to detect artifacts - with the right scaffolding, this capability can be unlocked using only a few hundred labeled examples per artifact category. Our system, ArtifactLens, achieves state-of-the-art on five human artifact benchmarks (the first evaluation across multiple datasets) while requiring orders of magnitude less labeled data. The scaffolding consists of a multi-component architecture with in-context learning and text instruction optimization, with novel improvements to each. Our methods generalize to other artifact types - object morphology, animal anatomy, and entity interactions - and to the distinct task of AIGC detection.

Inference-time steering enables pretrained diffusion/flow models to be adapted to new tasks without retraining. A widely used approach is the ratio-of-densities method, which defines a time-indexed target path by reweighting probability-density trajectories from multiple models with positive, or in some cases, negative exponents. This construction, however, harbors a critical and previously unformalized failure mode: Marginal Path Collapse, where intermediate densities become non-normalizable even though endpoints remain valid. Collapse arises systematically when composing heterogeneous models trained on different noise schedules or datasets, including a common setting in molecular design where de-novo, conformer, and pocket-conditioned models must be combined for tasks such as flexible-pose scaffold decoration. We provide a novel and complete solution for the problem. First, we derive a simple path existence criterion that predicts exactly when collapse occurs from noise schedules and exponents alone. Second, we introduce Adaptive path Correction with Exponents (ACE), which extends Feynman-Kac steering to time-varying exponents and guarantees a valid probability path. On a synthetic 2D benchmark and on flexible-pose scaffold decoration, ACE eliminates collapse and enables high-guidance compositional generation, improving distributional and docking metrics over constant-exponent baselines and even specialized task-specific scaffold decoration models. Our work turns ratio-of-densities steering with heterogeneous experts from an unstable heuristic into a reliable tool for controllable generation.

BigCloneBench is a well-known and widely used large-scale dataset for the evaluation of recall of clone detection tools. It has been beneficial for research on clone detection and has become a standard in evaluating the performance of clone detection tools. More recently, it has also been widely used as a dataset to evaluate machine learning approaches to semantic clone detection or code similarity detection for functional or semantic similarity. This paper demonstrates that BigCloneBench is problematic to use as ground truth for learning or evaluating semantic code similarity, and highlights the aspects of BigCloneBench that affect the ground truth quality. A manual investigation of a statistically significant random sample of 406 Weak Type-3/Type-4 clone pairs revealed that 93% of them do not have a similar functionality and are therefore mislabelled. In a literature review of 179 papers that use BigCloneBench as a dataset, we found 139 papers that used BigCloneBench to evaluate semantic clone detection and where the results are threatened in their validity by the mislabelling. As such, these papers often report high F1 scores (e.g., above 0.9), which indicates overfitting to dataset-specific artefacts rather than genuine semantic similarity detection. We emphasise that using BigCloneBench remains valid for the intended purpose of evaluating syntactic or textual clone detection of Type-1, Type-2, and Type-3 clones. We acknowledge the important contributions of BigCloneBench to two decades of traditional clone detection research. However, the usage of BigCloneBench beyond the intended purpose without careful consideration of its limitations has led to misleading results and conclusions, and potentially harmed the field of semantic clone detection.

As models and data scale, independently trained networks often induce analogous notions of similarity. But, matching similarities is weaker than establishing an explicit correspondence between the representation spaces, especially for multimodal models, where consistency must hold not only within each modality, but also for the learned image-text coupling. We therefore ask: given two independently trained multimodal contrastive models (with encoders (f, g) and (f,g)) -- trained on different distributions and with different architectures -- does a systematic geometric relationship exist between their embedding spaces? If so, what form does it take, and does it hold uniformly across modalities? In this work, we show that across model families such as CLIP, SigLIP, and FLAVA, this geometric relationship is well approximated by an orthogonal map (up to a global mean shift), i.e., there exists an orthogonal map Q where Q^top Q = I such that f(x)approx Q f(x) for paired images x. Strikingly, the same Q simultaneously aligns the text encoders i.e., g(y)approx Q g(y) for texts y. Theoretically, we prove that if the multimodal kernel agrees across models on a small anchor set i.e. langle f(x), g(y)rangle approx langle f(x), g(y)rangle, then the two models must be related by a single orthogonal map Q and the same Q maps images and text across models. More broadly, this finding enables backward-compatible model upgrades, avoiding costly re-embedding, and has implications for the privacy of learned representations. Our project page: https://canonical-multimodal.github.io/

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

In recent years, many deep neural architectures have been developed for image classification. Whether they are similar or dissimilar and what factors contribute to their (dis)similarities remains curious. To address this question, we aim to design a quantitative and scalable similarity measure between neural architectures. We propose Similarity by Attack Transferability (SAT) from the observation that adversarial attack transferability contains information related to input gradients and decision boundaries widely used to understand model behaviors. We conduct a large-scale analysis on 69 state-of-the-art ImageNet classifiers using our proposed similarity function to answer the question. Moreover, we observe neural architecture-related phenomena using model similarity that model diversity can lead to better performance on model ensembles and knowledge distillation under specific conditions. Our results provide insights into why developing diverse neural architectures with distinct components is necessary.

Graph similarity computation (GSC) is to calculate the similarity between one pair of graphs, which is a fundamental problem with fruitful applications in the graph community. In GSC, graph edit distance (GED) and maximum common subgraph (MCS) are two important similarity metrics, both of which are NP-hard to compute. Instead of calculating the exact values, recent solutions resort to leveraging graph neural networks (GNNs) to learn data-driven models for the estimation of GED and MCS. Most of them are built on components involving node-level interactions crossing graphs, which engender vast computation overhead but are of little avail in effectiveness. In the paper, we present GraSP, a simple yet effective GSC approach for GED and MCS prediction. GraSP achieves high result efficacy through several key instruments: enhanced node features via positional encoding and a GNN model augmented by a gating mechanism, residual connections, as well as multi-scale pooling. Theoretically, GraSP can surpass the 1-WL test, indicating its high expressiveness. Empirically, extensive experiments comparing GraSP against 10 competitors on multiple widely adopted benchmark datasets showcase the superiority of GraSP over prior arts in terms of both effectiveness and efficiency. The code is available at https://github.com/HaoranZ99/GraSP.

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

Coding agents, autonomous systems that use large language models (LLMs) to resolve software engineering tasks, rely on agentic scaffolding: a middleware layer in between a developer and a large language model that orchestrates system prompts, tool execution, context management, and iterative reasoning loops. While these scaffoldings evolve at extreme velocities, no study has examined how this evolution affects agent quality (i.e., effectiveness and efficiency) over time. Practitioners regularly report quality regressions after scaffolding updates, yet consistently attribute them to the underlying model rather than the scaffolding itself. In this paper, we address this gap by conducting the first controlled longitudinal study that isolates the scaffolding's contribution. Unlike prior work that fixes the scaffolding and varies the model, we fix the model and vary only the scaffolding, evaluating 35 sequential releases to measure their impact on agent effectiveness and efficiency. We first empirically study the development and release evolution of five major open-source scaffoldings (i.e., Codex, Qwen Code, Gemini, OpenCode, and OpenHands), revealing extreme release velocities exceeding two releases per day and thousands of issues within months. We then perform a controlled deep dive into 35 sequential releases of the Qwen Code CLI, evaluating each against 50 stratified SWE-bench Verified tasks while holding the underlying LLM constant. We trace the resulting quality fluctuations to specific development patterns and architectural components, and illustrate our findings with concrete qualitative evidence linking individual pull requests to measured quality shifts.

Several recent advances in AI systems (e.g., Tree-of-Thoughts and Program-Aided Language Models) solve problems by providing a "scaffolding" program that structures multiple calls to language models to generate better outputs. A scaffolding program is written in a programming language such as Python. In this work, we use a language-model-infused scaffolding program to improve itself. We start with a seed "improver" that improves an input program according to a given utility function by querying a language model several times and returning the best solution. We then run this seed improver to improve itself. Across a small set of downstream tasks, the resulting improved improver generates programs with significantly better performance than its seed improver. Afterward, we analyze the variety of self-improvement strategies proposed by the language model, including beam search, genetic algorithms, and simulated annealing. Since the language models themselves are not altered, this is not full recursive self-improvement. Nonetheless, it demonstrates that a modern language model, GPT-4 in our proof-of-concept experiments, is capable of writing code that can call itself to improve itself. We critically consider concerns around the development of self-improving technologies and evaluate the frequency with which the generated code bypasses a sandbox.

Assessing similarity in source code has gained significant attention in recent years due to its importance in software engineering tasks such as clone detection and code search and recommendation. This work presents a comparative analysis of unsupervised similarity measures for identifying source code clone detection. The goal is to overview the current state-of-the-art techniques, their strengths, and weaknesses. To do that, we compile the existing unsupervised strategies and evaluate their performance on a benchmark dataset to guide software engineers in selecting appropriate methods for their specific use cases. The source code of this study is available at https://github.com/jorge-martinez-gil/codesim

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

We study neural network loss landscapes through the lens of mode connectivity, the observation that minimizers of neural networks retrieved via training on a dataset are connected via simple paths of low loss. Specifically, we ask the following question: are minimizers that rely on different mechanisms for making their predictions connected via simple paths of low loss? We provide a definition of mechanistic similarity as shared invariances to input transformations and demonstrate that lack of linear connectivity between two models implies they use dissimilar mechanisms for making their predictions. Relevant to practice, this result helps us demonstrate that naive fine-tuning on a downstream dataset can fail to alter a model's mechanisms, e.g., fine-tuning can fail to eliminate a model's reliance on spurious attributes. Our analysis also motivates a method for targeted alteration of a model's mechanisms, named connectivity-based fine-tuning (CBFT), which we analyze using several synthetic datasets for the task of reducing a model's reliance on spurious attributes.

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

We propose a method to estimate the mechanical parameters of fabrics using a casual capture setup with a depth camera. Our approach enables to create mechanically-correct digital representations of real-world textile materials, which is a fundamental step for many interactive design and engineering applications. As opposed to existing capture methods, which typically require expensive setups, video sequences, or manual intervention, our solution can capture at scale, is agnostic to the optical appearance of the textile, and facilitates fabric arrangement by non-expert operators. To this end, we propose a sim-to-real strategy to train a learning-based framework that can take as input one or multiple images and outputs a full set of mechanical parameters. Thanks to carefully designed data augmentation and transfer learning protocols, our solution generalizes to real images despite being trained only on synthetic data, hence successfully closing the sim-to-real loop.Key in our work is to demonstrate that evaluating the regression accuracy based on the similarity at parameter space leads to an inaccurate distances that do not match the human perception. To overcome this, we propose a novel metric for fabric drape similarity that operates on the image domain instead on the parameter space, allowing us to evaluate our estimation within the context of a similarity rank. We show that out metric correlates with human judgments about the perception of drape similarity, and that our model predictions produce perceptually accurate results compared to the ground truth parameters.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

Similarity metrics such as representational similarity analysis (RSA) and centered kernel alignment (CKA) have been used to compare layer-wise representations between neural networks. However, these metrics are confounded by the population structure of data items in the input space, leading to spuriously high similarity for even completely random neural networks and inconsistent domain relations in transfer learning. We introduce a simple and generally applicable fix to adjust for the confounder with covariate adjustment regression, which retains the intuitive invariance properties of the original similarity measures. We show that deconfounding the similarity metrics increases the resolution of detecting semantically similar neural networks. Moreover, in real-world applications, deconfounding improves the consistency of representation similarities with domain similarities in transfer learning, and increases correlation with out-of-distribution accuracy.

Foundation models rely on large-scale web-crawled datasets, which frequently contain noisy data, biases, and irrelevant content. Existing data selection techniques typically use human heuristics, downstream evaluation datasets, or specialized scoring models, and can overlook samples' utility in the training process. Instead, we propose a new approach, Mimic Score, a data quality metric that uses a pretrained reference model as a guide to assess the usefulness of data samples for training a new model. It relies on the alignment between the gradient of the new model parameters and the vector pointing toward the reference model in weight space. Samples that misalign with this direction are considered low-value and can be filtered out. Motivated by the Mimic score, we develop Grad-Mimic, a data selection framework that identifies and prioritizes useful samples, automating the selection process to create effective filters. Empirically, using Mimic scores to guide model training results in consistent performance gains across six image datasets and enhances the performance of CLIP models. Moreover, Mimic scores and their associated filters improve upon existing filtering methods and offer accurate estimation of dataset quality.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Observational studies can yield clinically actionable evidence at scale, but executing them on real-world databases is open-ended and requires coherent decisions across cohort construction, analysis, and reporting. Prior evaluations of LLM agents emphasize isolated steps or single answers, missing the integrity and internal structure of the resulting evidence bundle. To address this gap, we introduce RWE-bench, a benchmark grounded in MIMIC-IV and derived from peer-reviewed observational studies. Each task provides the corresponding study protocol as the reference standard, requiring agents to execute experiments in a real database and iteratively generate tree-structured evidence bundles. We evaluate six LLMs (three open-source, three closed-source) under three agent scaffolds using both question-level correctness and end-to-end task metrics. Across 162 tasks, task success is low: the best agent reaches 39.9%, and the best open-source model reaches 30.4%. Agent scaffolds also matter substantially, causing over 30% variation in performance metrics. Furthermore, we implement an automated cohort evaluation method to rapidly localize errors and identify agent failure modes. Overall, the results highlight persistent limitations in agents' ability to produce end-to-end evidence bundles, and efficient validation remains an important direction for future work. Code and data are available at https://github.com/somewordstoolate/RWE-bench.

We present Muses, the first training-free method for fantastic 3D creature generation in a feed-forward paradigm. Previous methods, which rely on part-aware optimization, manual assembly, or 2D image generation, often produce unrealistic or incoherent 3D assets due to the challenges of intricate part-level manipulation and limited out-of-domain generation. In contrast, Muses leverages the 3D skeleton, a fundamental representation of biological forms, to explicitly and rationally compose diverse elements. This skeletal foundation formalizes 3D content creation as a structure-aware pipeline of design, composition, and generation. Muses begins by constructing a creatively composed 3D skeleton with coherent layout and scale through graph-constrained reasoning. This skeleton then guides a voxel-based assembly process within a structured latent space, integrating regions from different objects. Finally, image-guided appearance modeling under skeletal conditions is applied to generate a style-consistent and harmonious texture for the assembled shape. Extensive experiments establish Muses' state-of-the-art performance in terms of visual fidelity and alignment with textual descriptions, and potential on flexible 3D object editing. Project page: https://luhexiao.github.io/Muses.github.io/.

Many learning algorithms such as kernel machines, nearest neighbors, clustering, or anomaly detection, are based on the concept of 'distance' or 'similarity'. Before similarities are used for training an actual machine learning model, we would like to verify that they are bound to meaningful patterns in the data. In this paper, we propose to make similarities interpretable by augmenting them with an explanation in terms of input features. We develop BiLRP, a scalable and theoretically founded method to systematically decompose similarity scores on pairs of input features. Our method can be expressed as a composition of LRP explanations, which were shown in previous works to scale to highly nonlinear functions. Through an extensive set of experiments, we demonstrate that BiLRP robustly explains complex similarity models, e.g. built on VGG-16 deep neural network features. Additionally, we apply our method to an open problem in digital humanities: detailed assessment of similarity between historical documents such as astronomical tables. Here again, BiLRP provides insight and brings verifiability into a highly engineered and problem-specific similarity model.

Representational similarity analysis and related methods compare the internal geometries of neural networks, but they measure only alignment between spaces, leaving a blind spot -- whether a representation's structure is reliably recoverable, not merely similar. We introduce geometric stability, a distinct axis, and Shesha, a metric that quantifies it from a single representation by correlating dissimilarity matrices built from complementary random halves of the feature dimensions. Unlike CKA and Procrustes distance, Shesha is provably non-invariant to orthogonal rotations of the feature basis. This is by design: the basis is privileged for learned models, since probes, patching, and steering act on coordinates, and a rotation-invariant metric cannot see whether the targeted structure survives them. A double dissociation isolates the mechanism -- removing the top principal component collapses CKA while Shesha holds, whereas rotating a representation into its eigenbasis, which preserves the spectrum and CKA exactly, collapses Shesha. Across 2,463 encoder configurations in seven domains, the metrics are redundant under geometry-preserving transforms and anti-correlate under compression (ρ=-0.47). Across 170 vision models spanning 6 clean and 38 corruption-shifted datasets, DINOv2 ranks first or second in transferability on three of six clean datasets yet bottom-quartile in stability on five, an isolated dissociation rather than a trade-off.

We propose SADGE, a quantitative similarity metric that predicts the performance of synthetic image datasets for common computer vision tasks without downstream model training. Estimating whether a synthetic dataset will lead to a model that performs well on real-world data remains a bottleneck in model development. Existing evaluation metrics (e.g., PSNR, FID, CLIP) primarily measure semantic alignment between real and synthetic images (Appearance Similarity Score). Less commonly, structural similarity between images is considered to assess the domain gap (Geometric Similarity Score). However, to the best of our knowledge there exists no studies that evaluate which similarity metric is the best downstream predictor for a given synthetic dataset. In this paper, we show over a wide variety of different synthetic datasets and downstream tasks that neither appearance nor geometry alone can reliably predict downstream performance; rather, it is their non-linear interplay that dictates synthetic data utility. Specifically, we measure how commonly used Appearance and Geometric Similarity metrics computed between synthetic and real images correlate with downstream performance in object detection, semantic segmentation, and pose estimation. Across five public synthetic-to-real benchmark families and 15 dataset-level variants (79k image pairs), SADGE achieves the strongest association with downstream transfer performance under both linear and rank-based criteria, reaching Pearson r=0.88 and Spearman rho=0.77. We compute for each combination of geometry-based methods and appearance-based approaches SADGE scores across all benchmark families. The best configuration is obtained by fusing DINOv3 appearance similarity with MASt3R geometric consistency through a constrained bilinear interaction, outperforming both the strongest geometry-only baseline and the strongest appearance-only baseline .

Foundation features from self-supervised vision models and text-to-image diffusion models have proven effective for semantic correspondence estimation. However, because these features are learned primarily from 2D image objectives, they lack explicit 3D awareness and often confuse symmetric object sides, repeated parts, and visually similar structures that are distinct in 3D. We introduce a 3D-aware post-training framework that goes beyond available 2D foundation features by incorporating priors from 3D foundation models. Given an image, our method uses SAM3D to estimate object geometry and pose, and refines the pose through render-and-compare optimization. Subsequently, we render PartField descriptors from the reconstructed geometry into the image plane based on the estimated object pose. The resulting geometry-aware feature maps complement DINO and Stable Diffusion features, while geodesic distances on the reconstructed shapes enable reliable filtering of candidate correspondences. We use the filtered matches as supervision to train a lightweight adapter on top of DINO and Stable Diffusion for semantic correspondence. In contrast to prior post-training approaches that require pose annotations and rely on coarse spherical geometry, our method automatically obtains instance-specific 3D structure and uses it to guide correspondence learning. Experiments show that our approach improves semantic correspondence over the prior methods while reducing manual geometric supervision. Code and model can be found at https:/github.com/GenIntel/3D-SC.

Neural rendering methods have significantly advanced photo-realistic 3D scene rendering in various academic and industrial applications. The recent 3D Gaussian Splatting method has achieved the state-of-the-art rendering quality and speed combining the benefits of both primitive-based representations and volumetric representations. However, it often leads to heavily redundant Gaussians that try to fit every training view, neglecting the underlying scene geometry. Consequently, the resulting model becomes less robust to significant view changes, texture-less area and lighting effects. We introduce Scaffold-GS, which uses anchor points to distribute local 3D Gaussians, and predicts their attributes on-the-fly based on viewing direction and distance within the view frustum. Anchor growing and pruning strategies are developed based on the importance of neural Gaussians to reliably improve the scene coverage. We show that our method effectively reduces redundant Gaussians while delivering high-quality rendering. We also demonstrates an enhanced capability to accommodate scenes with varying levels-of-detail and view-dependent observations, without sacrificing the rendering speed.

Recently, deep learning techniques have shown great success in automatic code generation. Inspired by the code reuse, some researchers propose copy-based approaches that can copy the content from similar code snippets to obtain better performance. Practically, human developers recognize the content in the similar code that is relevant to their needs, which can be viewed as a code sketch. The sketch is further edited to the desired code. However, existing copy-based approaches ignore the code sketches and tend to repeat the similar code without necessary modifications, which leads to generating wrong results. In this paper, we propose a sketch-based code generation approach named SkCoder to mimic developers' code reuse behavior. Given a natural language requirement, SkCoder retrieves a similar code snippet, extracts relevant parts as a code sketch, and edits the sketch into the desired code. Our motivations are that the extracted sketch provides a well-formed pattern for telling models "how to write". The post-editing further adds requirement-specific details to the sketch and outputs the complete code. We conduct experiments on two public datasets and a new dataset collected by this work. We compare our approach to 20 baselines using 5 widely used metrics. Experimental results show that (1) SkCoder can generate more correct programs, and outperforms the state-of-the-art - CodeT5-base by 30.30%, 35.39%, and 29.62% on three datasets. (2) Our approach is effective to multiple code generation models and improves them by up to 120.1% in Pass@1. (3) We investigate three plausible code sketches and discuss the importance of sketches. (4) We manually evaluate the generated code and prove the superiority of our SkCoder in three aspects.

Humans are the bottleneck in building and improving AI. Both the models and the agents that wrap them are written, tuned, and corrected by people. The long-horizon goal of an AI that can figure out how to improve itself remains open. Two largely disjoint research lines attack this bottleneck. The harness-update school has a meta-agent rewrite the scaffold of a task-specific agent (its tools, prompts, retry logic, and search procedure) while the model weights are held fixed. The test-time training school uses hand-written RL pipelines to update the model's own weights on task feedback while the harness is held fixed. These two silos operate in isolation. We propose SIA, a self-improving loop in which a language-model agent (the Feedback-Agent) updates both the harness and the weights of a task-specific agent. We evaluate across three contrasting domains: Chinese legal charge classification, low-level GPU kernel optimisation, and single-cell RNA denoising. Combining both levers outperforms scaffold iteration alone on all three benchmarks. The gains are 56.6% on LawBench, 91.9% runtime reduction on GPU kernels, and 502% on denoising over the initial baseline. Harness updates make the model agentic, shaping how it searches and acts, while weight updates build the domain intuition that no prompt or scaffold can instil.

Many tasks revolve around editing a document, whether code or text. We formulate the revision similarity problem to unify a wide range of machine learning evaluation problems whose goal is to assess a revision to an existing document. We observe that revisions usually change only a small portion of an existing document, so the existing document and its immediate revisions share a majority of their content. We formulate five adequacy criteria for revision similarity measures, designed to align them with human judgement. We show that popular pairwise measures, like BLEU, fail to meet these criteria, because their scores are dominated by the shared content. They report high similarity between two revisions when humans would assess them as quite different. This is a fundamental flaw we address. We propose a novel static measure, Excision Score (ES), which computes longest common subsequence (LCS) to remove content shared by an existing document with the ground truth and predicted revisions, before comparing only the remaining divergent regions. This is analogous to a surgeon creating a sterile field to focus on the work area. We use approximation to speed the standard cubic LCS computation to quadratic. In code-editing evaluation, where static measures are often used as a cheap proxy for passing tests, we demonstrate that ES surpasses existing measures. When aligned with test execution on HumanEvalFix, ES improves over its nearest competitor, SARI, by 12% Pearson correlation and by >21% over standard measures like BLEU. The key criterion is invariance to shared context; when we perturb HumanEvalFix with increased shared context, ES' improvement over SARI increases to 20% and >30% over standard measures. ES also handles other corner cases that other measures do not, such as correctly aligning moved code blocks, and appropriately rewarding matching insertions or deletions.

Benchmarks are often used as a standard to understand LLM capabilities in different domains. However, aggregate benchmark scores provide limited insight into compositional skill gaps of LLMs and how to improve them. To make these weaknesses visible, we propose Scaffolded Task Design (STaD) framework. STaD generates controlled variations of benchmark tasks based on the concept of scaffolding, which introduces structured, incremental support in a step-by-step manner. Rather than inspecting failures individually, this approach enables systematic and scalable probing of model behavior by identifying the specific reasoning skill compositions they lack. Treating the LLM as a black box, our experiments on six models of varying sizes reveal multiple failure points in three reasoning benchmarks and highlight each model's unique and distinct skill gaps.

This paper presents a novel approach for source code similarity detection that integrates an additional output feature into the classification process with the goal of improving model performance. Our approach is based on the GraphCodeBERT model, extended with a custom output feature layer and a concatenation mechanism for improved feature representation. The model was trained and evaluated, achieving promising results in terms of precision, recall, and f-measure. The implementation details, including model architecture and training strategies are discussed. The source code that illustrates our approach can be downloaded from https://www.github.com/jorge-martinez-gil/graphcodebert-feature-integration.

Native 3D generative models have achieved remarkable fidelity and speed, yet they suffer from a critical limitation: inability to prescribe precise structural articulations, where precise structural control within the native 3D space remains underexplored. This paper proposes SK-Adapter, a simple and yet highly efficient and effective framework that unlocks precise skeletal manipulation for native 3D generation. Moving beyond text or image prompts, which can be ambiguous for precise structure, we treat the 3D skeleton as a first-class control signal. SK-Adapter is a lightweight structural adapter network that encodes joint coordinates and topology into learnable tokens, which are injected into the frozen 3D generation backbone via cross-attention. This smart design allows the model to not only effectively "attend" to specific 3D structural constraints but also preserve its original generative priors. To bridge the data gap, we contribute Objaverse-TMS dataset, a large-scale dataset of 24k text-mesh-skeleton pairs. Extensive experiments confirm that our method achieves robust structural control while preserving the geometry and texture quality of the foundation model, significantly outperforming existing baselines. Furthermore, we extend this capability to local 3D editing, enabling the region specific editing of existing assets with skeletal guidance, which is unattainable by previous methods. Project Page: https://sk-adapter.github.io/

Code clones are pairs of code snippets that implement similar functionality. Clone detection is a fundamental branch of automatic source code comprehension, having many applications in refactoring recommendation, plagiarism detection, and code summarization. A particularly interesting case of clone detection is the detection of semantic clones, i.e., code snippets that have the same functionality but significantly differ in implementation. A promising approach to detecting semantic clones is contrastive learning (CL), a machine learning paradigm popular in computer vision but not yet commonly adopted for code processing. Our work aims to evaluate the most popular CL algorithms combined with three source code representations on two tasks. The first task is code clone detection, which we evaluate on the POJ-104 dataset containing implementations of 104 algorithms. The second task is plagiarism detection. To evaluate the models on this task, we introduce CodeTransformator, a tool for transforming source code. We use it to create a dataset that mimics plagiarised code based on competitive programming solutions. We trained nine models for both tasks and compared them with six existing approaches, including traditional tools and modern pre-trained neural models. The results of our evaluation show that proposed models perform diversely in each task, however the performance of the graph-based models is generally above the others. Among CL algorithms, SimCLR and SwAV lead to better results, while Moco is the most robust approach. Our code and trained models are available at https://doi.org/10.5281/zenodo.6360627, https://doi.org/10.5281/zenodo.5596345.

Federated learning is a powerful paradigm for large-scale machine learning, but it faces significant challenges due to unreliable network connections, slow communication, and substantial data heterogeneity across clients. FedAvg and SCAFFOLD are two prominent algorithms to address these challenges. In particular, FedAvg employs multiple local updates before communicating with a central server, while SCAFFOLD maintains a control variable on each client to compensate for ``client drift'' in its local updates. Various methods have been proposed to enhance the convergence of these two algorithms, but they either make impractical adjustments to the algorithmic structure or rely on the assumption of bounded data heterogeneity. This paper explores the utilization of momentum to enhance the performance of FedAvg and SCAFFOLD. When all clients participate in the training process, we demonstrate that incorporating momentum allows FedAvg to converge without relying on the assumption of bounded data heterogeneity even using a constant local learning rate. This is novel and fairly surprising as existing analyses for FedAvg require bounded data heterogeneity even with diminishing local learning rates. In partial client participation, we show that momentum enables SCAFFOLD to converge provably faster without imposing any additional assumptions. Furthermore, we use momentum to develop new variance-reduced extensions of FedAvg and SCAFFOLD, which exhibit state-of-the-art convergence rates. Our experimental results support all theoretical findings.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation models is identifying the recipes for scaling the model. In this work, we present SeedFold, a folding model that successfully scales up the model capacity. Our contributions are threefold: first, we identify an effective width-scaling strategy for the Pairformer to increase representation capacity; second, we introduce a novel linear triangular attention that reduces computational complexity to enable efficient scaling; finally, we construct a large-scale distillation dataset to substantially enlarge the training set. Experiments on FoldBench show that SeedFold outperforms AlphaFold3 on most protein-related tasks.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

In contrastive learning, two views of an original image, generated by different augmentations, are considered a positive pair, and their similarity is required to be high. Similarly, two views of distinct images form a negative pair, with encouraged low similarity. Typically, a single similarity measure, provided by a lone projection head, evaluates positive and negative sample pairs. However, due to diverse augmentation strategies and varying intra-sample similarity, views from the same image may not always be similar. Additionally, owing to inter-sample similarity, views from different images may be more akin than those from the same image. Consequently, enforcing high similarity for positive pairs and low similarity for negative pairs may be unattainable, and in some cases, such enforcement could detrimentally impact performance. To address this challenge, we propose using multiple projection heads, each producing a distinct set of features. Our pre-training loss function emerges from a solution to the maximum likelihood estimation over head-wise posterior distributions of positive samples given observations. This loss incorporates the similarity measure over positive and negative pairs, each re-weighted by an individual adaptive temperature, regulated to prevent ill solutions. Our approach, Adaptive Multi-Head Contrastive Learning (AMCL), can be applied to and experimentally enhances several popular contrastive learning methods such as SimCLR, MoCo, and Barlow Twins. The improvement remains consistent across various backbones and linear probing epochs, and becomes more significant when employing multiple augmentation methods.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

We present a novel generative 3D modeling system, coined CraftsMan, which can generate high-fidelity 3D geometries with highly varied shapes, regular mesh topologies, and detailed surfaces, and, notably, allows for refining the geometry in an interactive manner. Despite the significant advancements in 3D generation, existing methods still struggle with lengthy optimization processes, irregular mesh topologies, noisy surfaces, and difficulties in accommodating user edits, consequently impeding their widespread adoption and implementation in 3D modeling software. Our work is inspired by the craftsman, who usually roughs out the holistic figure of the work first and elaborates the surface details subsequently. Specifically, we employ a 3D native diffusion model, which operates on latent space learned from latent set-based 3D representations, to generate coarse geometries with regular mesh topology in seconds. In particular, this process takes as input a text prompt or a reference image and leverages a powerful multi-view (MV) diffusion model to generate multiple views of the coarse geometry, which are fed into our MV-conditioned 3D diffusion model for generating the 3D geometry, significantly improving robustness and generalizability. Following that, a normal-based geometry refiner is used to significantly enhance the surface details. This refinement can be performed automatically, or interactively with user-supplied edits. Extensive experiments demonstrate that our method achieves high efficacy in producing superior-quality 3D assets compared to existing methods. HomePage: https://craftsman3d.github.io/, Code: https://github.com/wyysf-98/CraftsMan

Large Language Models (LLMs) have demonstrated impressive capabilities in a wide range of code generation tasks. However, generating code for certain domains remains challenging. One such domain is Computer-Aided Design (CAD) program, where the goal is to produce scripted parametric models that define object geometry for precise design and manufacturing applications. A key challenge in LLM-based CAD program generation is the limited geometric complexity of generated shapes compared to those found in real-world industrial designs. This shortfall is in part due to the lack of diversity in the available CAD program training data. To address this, we propose a novel data augmentation paradigm that prompts an LLM to generate CAD programs conditioned on a reference surface program and a modeling procedure - an idea inspired by practices in industrial design. By varying the reference surface using a collection of organic shapes, our method enriches the geometric distribution of generated CAD models. In particular, it introduces edges and faces defined by spline-based curvature, which are typically missing or underrepresented in existing open-source CAD program datasets. Experiments show that our method produces CAD samples with significantly greater geometric diversity and a higher resemblance to industry-grade CAD designs in terms of the proportion of organic shape primitives. This enhancement makes our CAD data augmentation approach a useful tool for training LLMs and other deep learning models in CAD generation.

Computer-Aided Design (CAD) powers modern engineering, yet producing high-quality parts still demands substantial expert effort. Many AI systems tackle CAD reverse engineering, but most are single-pass and miss fine geometric details. In contrast, human engineers compare the input shape with the reconstruction and iteratively modify the design based on remaining discrepancies. Agent-based methods mimic this loop with frozen VLMs, but weak 3D grounding of current foundation models limits reliability and efficiency. We introduce CADReasoner, a model trained to iteratively refine its prediction using geometric discrepancy between the input and the predicted shape. The model outputs a runnable CadQuery Python program whose rendered mesh is fed back at the next step. CADReasoner fuses multi-view renders and point clouds as complementary modalities. To bridge the realism gap, we propose a scan-simulation protocol applied during both training and evaluation. Across DeepCAD, Fusion 360, and MCB benchmarks, CADReasoner attains state-of-the-art results on clean and scan-sim tracks.

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks that lack stochastic layers) or averaged responses (e.g., trial-averaged firing rates in biological data). However, these measures of _deterministic_ representational similarity ignore the scale and geometric structure of noise, both of which play important roles in neural computation. To rectify this, we generalize previously proposed shape metrics (Williams et al. 2021) to quantify differences in _stochastic_ representations. These new distances satisfy the triangle inequality, and thus can be used as a rigorous basis for many supervised and unsupervised analyses. Leveraging this novel framework, we find that the stochastic geometries of neurobiological representations of oriented visual gratings and naturalistic scenes respectively resemble untrained and trained deep network representations. Further, we are able to more accurately predict certain network attributes (e.g. training hyperparameters) from its position in stochastic (versus deterministic) shape space.

Materials discovery and design aim to find compositions and structures with desirable properties over highly complex and diverse physical spaces. Traditional solutions, such as high-throughput simulations or machine learning, often rely on complex descriptors, which hinder generalizability and transferability across different material systems. Moreover, These descriptors may inadequately represent macro-scale material properties, which are influenced by structural imperfections and compositional variations in real-world samples, thus limiting their practical applicability. To address these challenges, we propose DARWIN 1.5, the largest open-source large language model tailored for materials science. By leveraging natural language as input, DARWIN eliminates the need for task-specific descriptors and enables a flexible, unified approach to material property prediction and discovery. Our approach integrates 6M material domain papers and 21 experimental datasets from 49,256 materials across modalities while enabling cross-task knowledge transfer. The enhanced model achieves up to 59.1% improvement in prediction accuracy over the base LLaMA-7B architecture and outperforms SOTA machine learning approaches across 8 materials design tasks. These results establish LLMs as a promising foundation for developing versatile and scalable models in materials science.

Measuring the similarity of the internal representations of deep neural networks is an important and challenging problem. Model stitching has been proposed as a possible approach, where two half-networks are connected by mapping the output of the first half-network to the input of the second one. The representations are considered functionally similar if the resulting stitched network achieves good task-specific performance. The mapping is normally created by training an affine stitching layer on the task at hand while freezing the two half-networks, a method called task loss matching. Here, we argue that task loss matching may be very misleading as a similarity index. For example, it can indicate very high similarity between very distant layers, whose representations are known to have different functional properties. Moreover, it can indicate very distant layers to be more similar than architecturally corresponding layers. Even more surprisingly, when comparing layers within the same network, task loss matching often indicates that some layers are more similar to a layer than itself. We argue that the main reason behind these problems is that task loss matching tends to create out-of-distribution representations to improve task-specific performance. We demonstrate that direct matching (when the mapping minimizes the distance between the stitched representations) does not suffer from these problems. We compare task loss matching, direct matching, and well-known similarity indices such as CCA and CKA. We conclude that direct matching strikes a good balance between the structural and functional requirements for a good similarity index.

Outfits in online fashion data are composed of items of many different types (e.g. top, bottom, shoes) that share some stylistic relationship with one another. A representation for building outfits requires a method that can learn both notions of similarity (for example, when two tops are interchangeable) and compatibility (items of possibly different type that can go together in an outfit). This paper presents an approach to learning an image embedding that respects item type, and jointly learns notions of item similarity and compatibility in an end-to-end model. To evaluate the learned representation, we crawled 68,306 outfits created by users on the Polyvore website. Our approach obtains 3-5% improvement over the state-of-the-art on outfit compatibility prediction and fill-in-the-blank tasks using our dataset, as well as an established smaller dataset, while supporting a variety of useful queries.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

This paper introduces a new benchmark for large-scale image similarity detection. This benchmark is used for the Image Similarity Challenge at NeurIPS'21 (ISC2021). The goal is to determine whether a query image is a modified copy of any image in a reference corpus of size 1~million. The benchmark features a variety of image transformations such as automated transformations, hand-crafted image edits and machine-learning based manipulations. This mimics real-life cases appearing in social media, for example for integrity-related problems dealing with misinformation and objectionable content. The strength of the image manipulations, and therefore the difficulty of the benchmark, is calibrated according to the performance of a set of baseline approaches. Both the query and reference set contain a majority of "distractor" images that do not match, which corresponds to a real-life needle-in-haystack setting, and the evaluation metric reflects that. We expect the DISC21 benchmark to promote image copy detection as an important and challenging computer vision task and refresh the state of the art. Code and data are available at https://github.com/facebookresearch/isc2021

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

We introduce ISO-Bench, a benchmark for coding agents to test their capabilities on real-world inference optimization tasks. These tasks were taken from vLLM and SGLang, two of the most popular LLM serving frameworks. Each task provides an agent with a codebase and bottleneck description, whereby the agent must produce an optimization patch evaluated against expert human solutions. We curated 54 tasks from merged pull requests with measurable performance improvements. While existing benchmarks heavily use runtime-based metrics, such approaches can be gamed to pass tests without capturing the actual intent of the code changes. Therefore, we combine both hard (execution-based) and soft (LLM-based) metrics to show that both are necessary for complete evaluation. While evaluating both closed and open-source coding agents, we find no single agent dominates across codebases. Surprisingly, agents often identify correct bottlenecks but fail to execute working solutions. We also show that agents with identical underlying models differ substantially, suggesting scaffolding is as important as the model.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

DNA foundation models have become transformative tools in bioinformatics and healthcare applications. Trained on vast genomic datasets, these models can be used to generate sequence embeddings, dense vector representations that capture complex genomic information. These embeddings are increasingly being shared via Embeddings-as-a-Service (EaaS) frameworks to facilitate downstream tasks, while supposedly protecting the privacy of the underlying raw sequences. However, as this practice becomes more prevalent, the security of these representations is being called into question. This study evaluates the resilience of DNA foundation models to model inversion attacks, whereby adversaries attempt to reconstruct sensitive training data from model outputs. In our study, the model's output for reconstructing the DNA sequence is a zero-shot embedding, which is then fed to a decoder. We evaluated the privacy of three DNA foundation models: DNABERT-2, Evo 2, and Nucleotide Transformer v2 (NTv2). Our results show that per-token embeddings allow near-perfect sequence reconstruction across all models. For mean-pooled embeddings, reconstruction quality degrades as sequence length increases, though it remains substantially above random baselines. Evo 2 and NTv2 prove to be most vulnerable, especially for shorter sequences with reconstruction similarities > 90%, while DNABERT-2's BPE tokenization provides the greatest resilience. We found that the correlation between embedding similarity and sequence similarity was a key predictor of reconstruction success. Our findings emphasize the urgent need for privacy-aware design in genomic foundation models prior to their widespread deployment in EaaS settings. Training code, model weights and evaluation pipeline are released on: https://github.com/not-a-feature/DNA-Embedding-Inversion.

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fr\'echet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. Code is available online at https://github.com/httk/wyckoffdiff

Data-driven surrogate models are an alternative to numerical homogenization of heterogeneous materials. In this contribution, a supervised learning approach is presented for predicting effective Lamé parameters of hyperelastic composites from low-dimensional microstructural descriptors. The data set is based on previously published numerical homogenization results for ensembles of two-phase stochastic microstructures generated by planar Boolean models, covering variations of inclusion shape, phase contrast, and area fraction; see Brändel, Brands, Maike, Rheinbach, Schröder, Schwarz and Stoyan (2022). A neural network is trained on combinations of scalar and curve-valued statistical descriptors, including the area fraction, a derived scalar shape descriptor τ, the two-point correlation function S_2(r), and the lineal-path function ell(z). Additional data representing limiting cases of the parameter space are incorporated to stabilize training and improve extrapolation behavior. The surrogate is evaluated by leave-one-grain-type-out cross-validation in order to assess generalization to unseen grain geometries. Numerical results demonstrate that additional descriptors can reduce relative errors. A predictor trained with τ and S_2(r) provides a compact representation with good quantitative accuracy and regular dense response behavior. Adding the lineal-path function ell(z) further reduces the error at the available data points, indicating that it is a promising additional descriptor; however, dense post-training response evaluations show that improved pointwise accuracy does not automatically guarantee physically admissible behavior between sampled parameter values. This motivates future work on physically constrained surrogate models, loss formulations, bounded output parametrizations, and a more systematic representation of curve-valued geometric descriptors.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

We present CrochetBench, a benchmark for evaluating the ability of multimodal large language models to perform fine-grained, low-level procedural reasoning in the domain of crochet. Unlike prior benchmarks that focus on high-level description or visual question answering, CrochetBench shifts the emphasis from describing to doing: models are required to recognize stitches, select structurally appropriate instructions, and generate compilable crochet procedures. We adopt the CrochetPARADE DSL as our intermediate representation, enabling structural validation and functional evaluation via execution. The benchmark covers tasks including stitch classification, instruction grounding, and both natural language and image-to-DSL translation. Across all tasks, performance sharply declines as the evaluation shifts from surface-level similarity to executable correctness, exposing limitations in long-range symbolic reasoning and 3D-aware procedural synthesis. CrochetBench offers a new lens for assessing procedural competence in multimodal models and highlights the gap between surface-level understanding and executable precision in real-world creative domains. Code is available at https://github.com/Peiyu-Georgia-Li/crochetBench.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

Humans are good at recomposing novel objects, i.e. they can identify commonalities between unknown objects from general structure to finer detail, an ability difficult to replicate by machines. We propose a framework, ISCO, to recompose an object using 3D superquadrics as semantic parts directly from 2D views without training a model that uses 3D supervision. To achieve this, we optimize the superquadric parameters that compose a specific instance of the object, comparing its rendered 3D view and 2D image silhouette. Our ISCO framework iteratively adds new superquadrics wherever the reconstruction error is high, abstracting first coarse regions and then finer details of the target object. With this simple coarse-to-fine inductive bias, ISCO provides consistent superquadrics for related object parts, despite not having any semantic supervision. Since ISCO does not train any neural network, it is also inherently robust to out-of-distribution objects. Experiments show that, compared to recent single instance superquadrics reconstruction approaches, ISCO provides consistently more accurate 3D reconstructions, even from images in the wild. Code available at https://github.com/ExplainableML/ISCO .

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in molecular chemistry. This study presents the most extensive comparison of such models to date, evaluating 25 models across 25 datasets. Under a fair comparison framework, we assess models spanning various modalities, architectures, and pretraining strategies. Using a dedicated hierarchical Bayesian statistical testing model, we arrive at a surprising result: nearly all neural models show negligible or no improvement over the baseline ECFP molecular fingerprint. Only the CLAMP model, which is also based on molecular fingerprints, performs statistically significantly better than the alternatives. These findings raise concerns about the evaluation rigor in existing studies. We discuss potential causes, propose solutions, and offer practical recommendations.

Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical space. Yet, the lack of standardized evaluation frameworks makes it challenging to evaluate, compare, and further develop these ML models meaningfully. In this work, we introduce LeMat-GenBench, a unified benchmark for generative models of crystalline materials, supported by a set of evaluation metrics designed to better inform model development and downstream applications. We release both an open-source evaluation suite and a public leaderboard on Hugging Face, and benchmark 12 recent generative models. Results reveal that an increase in stability leads to a decrease in novelty and diversity on average, with no model excelling across all dimensions. Altogether, LeMat-GenBench establishes a reproducible and extensible foundation for fair model comparison and aims to guide the development of more reliable, discovery-oriented generative models for crystalline materials.

The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify their activation scores to interact with the model. However, these concepts are at the image level, which hinders the model from pinpointing the exact patches the concepts are activated. Alternatively, prototype-based methods learn representations from training image patches and compare these with test image patches, using the similarity scores for final class prediction. However, interpreting the underlying concepts of these patches can be challenging and often necessitates post-hoc guesswork. To address this issue, this paper introduces the novel Concept-based Similarity Reasoning network (CSR), which offers (i) patch-level prototype with intrinsic concept interpretation, and (ii) spatial interactivity. First, the proposed CSR provides localized explanation by grounding prototypes of each concept on image regions. Second, our model introduces novel spatial-level interaction, allowing doctors to engage directly with specific image areas, making it an intuitive and transparent tool for medical imaging. CSR improves upon prior state-of-the-art interpretable methods by up to 4.5\% across three biomedical datasets. Our code is released at https://github.com/tadeephuy/InteractCSR.

The aim of this article is to introduce a new methodology for constructing morphings between shapes that have identical topology. This morphing is obtained by deforming a reference shape, through the resolution of a sequence of linear elasticity equations, onto the target shape. In particular, our approach does not assume any knowledge of a boundary parametrization. Furthermore, we demonstrate how constraints can be imposed on specific points, lines and surfaces in the reference domain to ensure alignment with their counterparts in the target domain after morphing. Additionally, we show how the proposed methodology can be integrated in an offline and online paradigm, which is useful in reduced-order modeling scenarii involving variable shapes. This framework facilitates the efficient computation of the morphings in various geometric configurations, thus improving the versatility and applicability of the approach. The methodology is illustrated on the regression problem of the drag and lift coefficients of airfoils of non-parameterized variable shapes.

Computer-aided design (CAD) is the digital construction of 2D and 3D objects, and is central to a wide range of engineering and manufacturing applications like automobile and aviation. Despite its importance, CAD modeling remains largely a time-intensive, manual task. Recent works have attempted to automate this process with small transformer-based models and handcrafted CAD sequence representations. However, there has been little effort to leverage the potential of large language models (LLMs) for sequential CAD design. In this work, we introduce a new large-scale dataset of more than 170k CAD models annotated with high-quality, human-like descriptions generated with our pipeline based on GPT-4.1. Using this dataset, we fine-tune powerful code-LLMs to generate CAD sequences represented in a JSON-based format from natural language descriptions, demonstrating the viability and effectiveness of this approach for text-conditioned CAD generation. Because simple metrics often fail to reflect the quality of generated objects, we introduce geometric and topological metrics based on sphericity, mean curvature, and Euler characteristic to provide richer structural insights. Our experiments and ablation studies on both synthetic and human-annotated data demonstrate that CADmium is able to automate CAD design, drastically speeding up the design of new objects. The dataset, code, and fine-tuned models are available online.

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.

We introduce the problem of material-aware part grouping in untextured meshes. Many real-world shapes, such as scales of pinecones or windows of buildings, contain repeated structures that share the same material but exhibit geometric variations. When assigning materials to such meshes, these repeated parts often require piece-by-piece manual identification and selection, which is tedious and time-consuming. To address this, we propose Material Magic Wand, a tool that allows artists to select part groups based on their estimated material properties -- when one part is selected, our algorithm automatically retrieves all other parts likely to share the same material. The key component of our approach is a part encoder that generates a material-aware embedding for each 3D part, accounting for both local geometry and global context. We train our model with a supervised contrastive loss that brings embeddings of material-consistent parts closer while separating those of different materials; therefore, part grouping can be achieved by retrieving embeddings that are close to the embedding of the selected part. To benchmark this task, we introduce a curated dataset of 100 shapes with 241 part-level queries. We verify the effectiveness of our method through extensive experiments and demonstrate its practical value in an interactive material assignment application.

Multimodal large language models can write code to produce complex programs as well as use programs to do 3D modeling, which opens up a new avenue for 3D generation powered by their priors, world knowledge and reasoning. Yet existing benchmarks rarely evaluate 3D modeling through code. Such modeling demands more than runnable code: from a text or visual specification, a model must generate a parametric 3D program that is geometrically precise, semantically aligned and assembly-consistent. We introduce P3D-Bench, a benchmark for parametric 3D generation. Unlike a 3D mesh, a parametric 3D program exposes explicit dimensions, construction operations and part relations, revealing whether a model recovers a design's structure, not just its appearance. Under a unified protocol, P3D-Bench covers three task families (Text-to-3D, Image-to-3D and Assembly-3D) and scores each output for executability, geometric fidelity, topology, text-grounded constraints, multiview semantic alignment and part-level structure. We evaluate frontier MLLMs and text-only LLMs on 400 text cases, 400 image cases and 203 annotated assemblies, with domain-specific models as reference points. Our extensive evaluation yields three findings. First, assemblies are the hardest setting, where models still fail to compose multiple parts into a coherent structure. Second, models can often recover the global shape and semantic identity of the target object, yet fail to reproduce the precise parametric geometry specified by the input. Third, part-level modeling remains weak on assemblies, where models recover neither the geometry of each part nor the right number of parts. These results position P3D-Bench as a benchmark for evaluating precise parametric geometry and part-level structure in parametric 3D generation.

We consider the visual disambiguation task of determining whether a pair of visually similar images depict the same or distinct 3D surfaces (e.g., the same or opposite sides of a symmetric building). Illusory image matches, where two images observe distinct but visually similar 3D surfaces, can be challenging for humans to differentiate, and can also lead 3D reconstruction algorithms to produce erroneous results. We propose a learning-based approach to visual disambiguation, formulating it as a binary classification task on image pairs. To that end, we introduce a new dataset for this problem, Doppelgangers, which includes image pairs of similar structures with ground truth labels. We also design a network architecture that takes the spatial distribution of local keypoints and matches as input, allowing for better reasoning about both local and global cues. Our evaluation shows that our method can distinguish illusory matches in difficult cases, and can be integrated into SfM pipelines to produce correct, disambiguated 3D reconstructions. See our project page for our code, datasets, and more results: http://doppelgangers-3d.github.io/.

Cancer is the second leading cause of death, with chemotherapy as one of the primary forms of treatment. As a result, researchers are turning to drug combination therapy to decrease drug resistance and increase efficacy. Current methods of drug combination screening, such as in vivo and in vitro, are inefficient due to stark time and monetary costs. In silico methods have become increasingly important for screening drugs, but current methods are inaccurate and generalize poorly to unseen anticancer drugs. In this paper, I employ a geometric deep-learning model utilizing a graph attention network that is equivariant to 3D rotations, translations, and reflections with structural motifs. Additionally, the gene expression of cancer cell lines is utilized to classify synergistic drug combinations specific to each cell line. I compared the proposed geometric deep learning framework to current state-of-the-art (SOTA) methods, and the proposed model architecture achieved greater performance on all 12 benchmark tasks performed on the DrugComb dataset. Specifically, the proposed framework outperformed other SOTA methods by an accuracy difference greater than 28%. Based on these results, I believe that the equivariant graph attention network's capability of learning geometric data accounts for the large performance improvements. The model's ability to generalize to foreign drugs is thought to be due to the structural motifs providing a better representation of the molecule. Overall, I believe that the proposed equivariant geometric deep learning framework serves as an effective tool for virtually screening anticancer drug combinations for further validation in a wet lab environment. The code for this work is made available online at: https://github.com/WeToTheMoon/EGAT_DrugSynergy.

Small-molecule identification from tandem mass spectrometry (MS/MS) remains a bottleneck in untargeted settings where spectral libraries are incomplete. While deep learning offers a solution, current approaches typically fall into two extremes: explicit generative models that construct molecular graphs atom-by-atom, or joint contrastive models that learn cross-modal subspaces from scratch. We introduce SpecBridge, a novel implicit alignment framework that treats structure identification as a geometric alignment problem. SpecBridge fine-tunes a self-supervised spectral encoder (DreaMS) to project directly into the latent space of a frozen molecular foundation model (ChemBERTa), and then performs retrieval by cosine similarity to a fixed bank of precomputed molecular embeddings. Across MassSpecGym, Spectraverse, and MSnLib benchmarks, SpecBridge improves top-1 retrieval accuracy by roughly 20-25% relative to strong neural baselines, while keeping the number of trainable parameters small. These results suggest that aligning to frozen foundation models is a practical, stable alternative to designing new architectures from scratch. The code for SpecBridge is released at https://github.com/HassounLab/SpecBridge.

Competitive programming benchmarks are widely used in scenarios such as programming contests and large language model assessments. However, the growing presence of duplicate or highly similar problems raises concerns not only about competition fairness, but also about the validity of competitive programming as a benchmark for model evaluation. In this paper, we propose a new problem -- similar question retrieval -- to address this issue. Due to the lack of both data and models, solving this problem is challenging. To this end, we introduce CPRet, a retrieval-oriented benchmark suite for competitive programming, covering four retrieval tasks: two code-centric (i.e., Text-to-Code and Code-to-Code) and two newly proposed problem-centric tasks (i.e., Problem-to-Duplicate and Simplified-to-Full), built from a combination of automatically crawled problem-solution data and manually curated annotations. Our contribution includes both high-quality training data and temporally separated test sets for reliable evaluation. In addition, we develop two task-specialized retrievers based on this dataset: CPRetriever-Code, trained with a novel Group-InfoNCE loss for problem-code alignment, and CPRetriever-Prob, fine-tuned for identifying problem-level similarity. Both models achieve strong results and are open-sourced for local use. Finally, we analyze LiveCodeBench and find that high-similarity problems inflate model pass rates and reduce differentiation, underscoring the need for similarity-aware evaluation in future benchmarks. Code and data are available at: https://github.com/coldchair/CPRet

Similarity between training examples is used to curate pretraining datasets for language models by many methods -- for diversification and to select examples similar to high-quality data. However, similarity is typically measured with off-the-shelf embedding models that are generic or trained for tasks such as retrieval. This paper introduces a framework to analyze the suitability of embedding models specifically for data curation in the language model pretraining setting. We quantify the correlation between similarity in the embedding space to similarity in pretraining loss between different training examples, and how diversifying in the embedding space affects pretraining quality. We analyze a variety of embedding models in our framework, with experiments using the Pile dataset for pretraining a 1.7B parameter decoder-only language model. We find that the embedding models we consider are all useful for pretraining data curation. Moreover, a simple approach of averaging per-token embeddings proves to be surprisingly competitive with more sophisticated embedding models -- likely because the latter are not designed specifically for pretraining data curation. Indeed, we believe our analysis and evaluation framework can serve as a foundation for the design of embedding models that specifically reason about similarity in pretraining datasets.

3D shape completion from point clouds is a challenging task, especially from scans of real-world objects. Considering the paucity of 3D shape ground truths for real scans, existing works mainly focus on benchmarking this task on synthetic data, e.g. 3D computer-aided design models. However, the domain gap between synthetic and real data limits the generalizability of these methods. Thus, we propose a new task, SCoDA, for the domain adaptation of real scan shape completion from synthetic data. A new dataset, ScanSalon, is contributed with a bunch of elaborate 3D models created by skillful artists according to scans. To address this new task, we propose a novel cross-domain feature fusion method for knowledge transfer and a novel volume-consistent self-training framework for robust learning from real data. Extensive experiments prove our method is effective to bring an improvement of 6%~7% mIoU.

The democratization of machine learning systems has made the process of fine-tuning accessible to practitioners, leading to a wide range of open-source models fine-tuned on specialized tasks and datasets. Recent work has proposed to merge such models to combine their functionalities. However, prior approaches are usually restricted to models that are fine-tuned from the same base model. Furthermore, the final merged model is typically required to be of the same size as the original models. In this work, we propose a new two-step algorithm to merge models -- termed PLeaS -- which relaxes these constraints. First, leveraging the Permutation symmetries inherent in the two models, PLeaS partially matches nodes in each layer by maximizing alignment. Next, PLeaS computes the weights of the merged model as a layer-wise Least Squares solution to minimize the approximation error between the features of the merged model and the permuted features of the original models. PLeaS allows a practitioner to merge two models sharing the same architecture into a single performant model of a desired size, even when the two original models are fine-tuned from different base models. We also demonstrate how our method can be extended to address a challenging scenario where no data is available from the fine-tuning domains. We demonstrate our method to merge ResNet and ViT models trained with shared and different label spaces, and show improvement over the state-of-the-art merging methods of up to 15 percentage points for the same target compute while merging models trained on DomainNet and fine-grained classification tasks. Our code is open-sourced at https://github.com/SewoongLab/PLeaS-Merging .

3D shape modeling is labor-intensive, time-consuming, and requires years of expertise. To facilitate 3D shape modeling, we propose a 3D shape generation network that takes a 3D VR sketch as a condition. We assume that sketches are created by novices without art training and aim to reconstruct geometrically realistic 3D shapes of a given category. To handle potential sketch ambiguity, our method creates multiple 3D shapes that align with the original sketch's structure. We carefully design our method, training the model step-by-step and leveraging multi-modal 3D shape representation to support training with limited training data. To guarantee the realism of generated 3D shapes we leverage the normalizing flow that models the distribution of the latent space of 3D shapes. To encourage the fidelity of the generated 3D shapes to an input sketch, we propose a dedicated loss that we deploy at different stages of the training process. The code is available at https://github.com/Rowl1ng/3Dsketch2shape.

Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development. These methods are evaluated on different SAbDab snapshots, non-overlapping test sets, and incompatible metrics, and the literature fragments the design problem into numerous sub-tasks with no common definition. We introduce Chimera-Bench (CDR Modeling with Epitope-guided Redesign), a unified benchmark built around a single canonical task: epitope-conditioned CDR sequence-structure co-design. Chimera-Bench provides (1) a curated, deduplicated dataset of 2,922 antibody-antigen complexes with epitope and paratope annotations; (2) three biologically motivated splits testing generalization to unseen epitopes, unseen antigen folds, and prospective temporal targets; and (3) a comprehensive evaluation protocol with five metric groups including novel epitope-specificity measures. We benchmark representative methods spanning different generative paradigms and report results across all splits. Chimera-Bench is the largest dataset of its kind for the antibody design problem, allowing the community to develop and test novel methods and evaluate their generalizability. The source code and data are available at: https://github.com/mansoor181/chimera-bench.git

It has been observed that representations learned by distinct neural networks conceal structural similarities when the models are trained under similar inductive biases. From a geometric perspective, identifying the classes of transformations and the related invariances that connect these representations is fundamental to unlocking applications, such as merging, stitching, and reusing different neural modules. However, estimating task-specific transformations a priori can be challenging and expensive due to several factors (e.g., weights initialization, training hyperparameters, or data modality). To this end, we introduce a versatile method to directly incorporate a set of invariances into the representations, constructing a product space of invariant components on top of the latent representations without requiring prior knowledge about the optimal invariance to infuse. We validate our solution on classification and reconstruction tasks, observing consistent latent similarity and downstream performance improvements in a zero-shot stitching setting. The experimental analysis comprises three modalities (vision, text, and graphs), twelve pretrained foundational models, nine benchmarks, and several architectures trained from scratch.

Artificial intelligence is transforming computational materials science, improving the prediction of material properties, and accelerating the discovery of novel materials. Recently, publicly available material data repositories have grown rapidly. This growth encompasses not only more materials, but also a greater variety and quantity of their associated properties. Existing machine learning efforts in materials science focus primarily on single-modality tasks, i.e., relationships between materials and a single physical property, thus not taking advantage of the rich and multimodal set of material properties. Here, we introduce Multimodal Learning for Materials (MultiMat), which enables self-supervised multi-modality training of foundation models for materials. We demonstrate our framework's potential using data from the Materials Project database on multiple axes: (i) MultiMat achieves state-of-the-art performance for challenging material property prediction tasks; (ii) MultiMat enables novel and accurate material discovery via latent space similarity, enabling screening for stable materials with desired properties; and (iii) MultiMat encodes interpretable emergent features that may provide novel scientific insights.

Great progress has been made in estimating 3D human pose and shape from images and video by training neural networks to directly regress the parameters of parametric human models like SMPL. However, existing body models have simplified kinematic structures that do not correspond to the true joint locations and articulations in the human skeletal system, limiting their potential use in biomechanics. On the other hand, methods for estimating biomechanically accurate skeletal motion typically rely on complex motion capture systems and expensive optimization methods. What is needed is a parametric 3D human model with a biomechanically accurate skeletal structure that can be easily posed. To that end, we develop SKEL, which re-rigs the SMPL body model with a biomechanics skeleton. To enable this, we need training data of skeletons inside SMPL meshes in diverse poses. We build such a dataset by optimizing biomechanically accurate skeletons inside SMPL meshes from AMASS sequences. We then learn a regressor from SMPL mesh vertices to the optimized joint locations and bone rotations. Finally, we re-parametrize the SMPL mesh with the new kinematic parameters. The resulting SKEL model is animatable like SMPL but with fewer, and biomechanically-realistic, degrees of freedom. We show that SKEL has more biomechanically accurate joint locations than SMPL, and the bones fit inside the body surface better than previous methods. By fitting SKEL to SMPL meshes we are able to "upgrade" existing human pose and shape datasets to include biomechanical parameters. SKEL provides a new tool to enable biomechanics in the wild, while also providing vision and graphics researchers with a better constrained and more realistic model of human articulation. The model, code, and data are available for research at https://skel.is.tue.mpg.de..

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Human perception of similarity across uni- and multimodal inputs is highly complex, making it challenging to develop automated metrics that accurately mimic it. General purpose vision-language models, such as CLIP and large multi-modal models (LMMs), can be applied as zero-shot perceptual metrics, and several recent works have developed models specialized in narrow perceptual tasks. However, the extent to which existing perceptual metrics align with human perception remains unclear. To investigate this question, we introduce UniSim-Bench, a benchmark encompassing 7 multi-modal perceptual similarity tasks, with a total of 25 datasets. Our evaluation reveals that while general-purpose models perform reasonably well on average, they often lag behind specialized models on individual tasks. Conversely, metrics fine-tuned for specific tasks fail to generalize well to unseen, though related, tasks. As a first step towards a unified multi-task perceptual similarity metric, we fine-tune both encoder-based and generative vision-language models on a subset of the UniSim-Bench tasks. This approach yields the highest average performance, and in some cases, even surpasses taskspecific models. Nevertheless, these models still struggle with generalization to unseen tasks, highlighting the ongoing challenge of learning a robust, unified perceptual similarity metric capable of capturing the human notion of similarity. The code and models are available at https://github.com/SaraGhazanfari/UniSim.

With the advent of AI agents, automatic scientific discovery has become a tenable goal. Many recent works scaffold agentic systems that can perform machine learning research, but don't offer a principled way to train such agents -- and current LLMs often generate plausible-looking but ineffective ideas. To make progress on training agents that can learn from doing, we provide a novel synthetic environment generation pipeline targeting machine learning agents. Our pipeline automatically synthesizes machine learning challenges compatible with the SWE-agent framework, covering topic sampling, dataset proposal, and code generation. The resulting synthetic tasks are 1) grounded in real machine learning datasets, because the proposed datasets are verified against the Huggingface API and are 2) verified for higher quality with a self-debugging loop. To validate the effectiveness of our synthetic tasks, we tackle MLGym, a benchmark for machine learning tasks. From the synthetic tasks, we sample trajectories from a teacher model (GPT-5), then use the trajectories to train a student model (Qwen3-4B and Qwen3-8B). The student models trained with our synthetic tasks achieve improved performance on MLGym, raising the AUP metric by 9% for Qwen3-4B and 12% for Qwen3-8B.

Empirically validating new 3D-printing related algorithms and implementations requires testing data representative of inputs encountered in the wild. An ideal benchmarking dataset should not only draw from the same distribution of shapes people print in terms of class (e.g., toys, mechanisms, jewelry), representation type (e.g., triangle soup meshes) and complexity (e.g., number of facets), but should also capture problems and artifacts endemic to 3D printing models (e.g., self-intersections, non-manifoldness). We observe that the contextual and geometric characteristics of 3D printing models differ significantly from those used for computer graphics applications, not to mention standard models (e.g., Stanford bunny, Armadillo, Fertility). We present a new dataset of 10,000 models collected from an online 3D printing model-sharing database. Via analysis of both geometric (e.g., triangle aspect ratios, manifoldness) and contextual (e.g., licenses, tags, classes) characteristics, we demonstrate that this dataset represents a more concise summary of real-world models used for 3D printing compared to existing datasets. To facilitate future research endeavors, we also present an online query interface to select subsets of the dataset according to project-specific characteristics. The complete dataset and per-model statistical data are freely available to the public.

Learning 3D shape representation with dense correspondence for deformable objects is a fundamental problem in computer vision. Existing approaches often need additional annotations of specific semantic domain, e.g., skeleton poses for human bodies or animals, which require extra annotation effort and suffer from error accumulation, and they are limited to specific domain. In this paper, we propose a novel self-supervised approach to learn neural implicit shape representation for deformable objects, which can represent shapes with a template shape and dense correspondence in 3D. Our method does not require the priors of skeleton and skinning weight, and only requires a collection of shapes represented in signed distance fields. To handle the large deformation, we constrain the learned template shape in the same latent space with the training shapes, design a new formulation of local rigid constraint that enforces rigid transformation in local region and addresses local reflection issue, and present a new hierarchical rigid constraint to reduce the ambiguity due to the joint learning of template shape and correspondences. Extensive experiments show that our model can represent shapes with large deformations. We also show that our shape representation can support two typical applications, such as texture transfer and shape editing, with competitive performance. The code and models are available at https://iscas3dv.github.io/deformshape

We present Diff3F as a simple, robust, and class-agnostic feature descriptor that can be computed for untextured input shapes (meshes or point clouds). Our method distills diffusion features from image foundational models onto input shapes. Specifically, we use the input shapes to produce depth and normal maps as guidance for conditional image synthesis. In the process, we produce (diffusion) features in 2D that we subsequently lift and aggregate on the original surface. Our key observation is that even if the conditional image generations obtained from multi-view rendering of the input shapes are inconsistent, the associated image features are robust and, hence, can be directly aggregated across views. This produces semantic features on the input shapes, without requiring additional data or training. We perform extensive experiments on multiple benchmarks (SHREC'19, SHREC'20, FAUST, and TOSCA) and demonstrate that our features, being semantic instead of geometric, produce reliable correspondence across both isometric and non-isometrically related shape families. Code is available via the project page at https://diff3f.github.io/

Universal machine learning force fields (UMLFFs) promise to revolutionize materials science by enabling rapid atomistic simulations across the periodic table. However, their evaluation has been limited to computational benchmarks that may not reflect real-world performance. Here, we present UniFFBench, a comprehensive framework for evaluating UMLFFs against experimental measurements of ~1,500 carefully curated mineral structures spanning diverse chemical environments, bonding types, structural complexity, and elastic properties. Our systematic evaluation of six state-of-the-art UMLFFs reveals a substantial reality gap: models achieving impressive performance on computational benchmarks often fail when confronted with experimental complexity. Even the best-performing models exhibit higher density prediction error than the threshold required for practical applications. Most strikingly, we observe disconnects between simulation stability and mechanical property accuracy, with prediction errors correlating with training data representation rather than the modeling method. These findings demonstrate that while current computational benchmarks provide valuable controlled comparisons, they may overestimate model reliability when extrapolated to experimentally complex chemical spaces. Altogether, UniFFBench establishes essential experimental validation standards and reveals systematic limitations that must be addressed to achieve truly universal force field capabilities.

When robots learn reward functions using high capacity models that take raw state directly as input, they need to both learn a representation for what matters in the task -- the task ``features" -- as well as how to combine these features into a single objective. If they try to do both at once from input designed to teach the full reward function, it is easy to end up with a representation that contains spurious correlations in the data, which fails to generalize to new settings. Instead, our ultimate goal is to enable robots to identify and isolate the causal features that people actually care about and use when they represent states and behavior. Our idea is that we can tune into this representation by asking users what behaviors they consider similar: behaviors will be similar if the features that matter are similar, even if low-level behavior is different; conversely, behaviors will be different if even one of the features that matter differs. This, in turn, is what enables the robot to disambiguate between what needs to go into the representation versus what is spurious, as well as what aspects of behavior can be compressed together versus not. The notion of learning representations based on similarity has a nice parallel in contrastive learning, a self-supervised representation learning technique that maps visually similar data points to similar embeddings, where similarity is defined by a designer through data augmentation heuristics. By contrast, in order to learn the representations that people use, so we can learn their preferences and objectives, we use their definition of similarity. In simulation as well as in a user study, we show that learning through such similarity queries leads to representations that, while far from perfect, are indeed more generalizable than self-supervised and task-input alternatives.

Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research. For such structures, the topology is their most important characteristic; particularly preserving connectedness: in the case of vascular networks, missing a connected vessel entirely alters the blood-flow dynamics. We introduce a novel similarity measure termed centerlineDice (short clDice), which is calculated on the intersection of the segmentation masks and their (morphological) skeleta. We theoretically prove that clDice guarantees topology preservation up to homotopy equivalence for binary 2D and 3D segmentation. Extending this, we propose a computationally efficient, differentiable loss function (soft-clDice) for training arbitrary neural segmentation networks. We benchmark the soft-clDice loss on five public datasets, including vessels, roads and neurons (2D and 3D). Training on soft-clDice leads to segmentation with more accurate connectivity information, higher graph similarity, and better volumetric scores.

The procure to pay process (P2P) in large enterprises is a back-end business process which deals with the procurement of products and services for enterprise operations. Procurement is done by issuing purchase orders to impaneled vendors and invoices submitted by vendors are paid after they go through a rigorous validation process. Agents orchestrating P2P process often encounter the problem of matching a product or service descriptions in the invoice to those in purchase order and verify if the ordered items are what have been supplied or serviced. For example, the description in the invoice and purchase order could be TRES 739mL CD KER Smooth and TRES 0.739L CD KER Smth which look different at word level but refer to the same item. In a typical P2P process, agents are asked to manually select the products which are similar before invoices are posted for payment. This step in the business process is manual, repetitive, cumbersome, and costly. Since descriptions are not well-formed sentences, we cannot apply existing semantic and syntactic text similarity approaches directly. In this paper, we present two approaches to solve the above problem using various types of available agent's recorded feedback data. If the agent's feedback is in the form of a relative ranking between descriptions, we use similarity ranking algorithm. If the agent's feedback is absolute such as match or no-match, we use classification similarity algorithm. We also present the threats to the validity of our approach and present a possible remedy making use of product taxonomy and catalog. We showcase the comparative effectiveness and efficiency of the proposed approaches over many benchmarks and real-world data sets.

We present Shap-MeD, a text-to-3D object generative model specialized in the biomedical domain. The objective of this study is to develop an assistant that facilitates the 3D modeling of medical objects, thereby reducing development time. 3D modeling in medicine has various applications, including surgical procedure simulation and planning, the design of personalized prosthetic implants, medical education, the creation of anatomical models, and the development of research prototypes. To achieve this, we leverage Shap-e, an open-source text-to-3D generative model developed by OpenAI, and fine-tune it using a dataset of biomedical objects. Our model achieved a mean squared error (MSE) of 0.089 in latent generation on the evaluation set, compared to Shap-e's MSE of 0.147. Additionally, we conducted a qualitative evaluation, comparing our model with others in the generation of biomedical objects. Our results indicate that Shap-MeD demonstrates higher structural accuracy in biomedical object generation.

Traditional document similarity measures provide a coarse-grained distinction between similar and dissimilar documents. Typically, they do not consider in what aspects two documents are similar. This limits the granularity of applications like recommender systems that rely on document similarity. In this paper, we extend similarity with aspect information by performing a pairwise document classification task. We evaluate our aspect-based document similarity for research papers. Paper citations indicate the aspect-based similarity, i.e., the section title in which a citation occurs acts as a label for the pair of citing and cited paper. We apply a series of Transformer models such as RoBERTa, ELECTRA, XLNet, and BERT variations and compare them to an LSTM baseline. We perform our experiments on two newly constructed datasets of 172,073 research paper pairs from the ACL Anthology and CORD-19 corpus. Our results show SciBERT as the best performing system. A qualitative examination validates our quantitative results. Our findings motivate future research of aspect-based document similarity and the development of a recommender system based on the evaluated techniques. We make our datasets, code, and trained models publicly available.

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

This paper presents a new approach for code similarity on High Level programs. Our technique is based on Fast Dynamic Time Warping, that builds a warp path or points relation with local restrictions. The source code is represented into Time Series using the operators inside programming languages that makes possible the comparison. This makes possible subsequence detection that represent similar code instructions. In contrast with other code similarity algorithms, we do not make features extraction. The experiments show that two source codes are similar when their respective Time Series are similar.

Assessing the degree of similarity of code fragments is crucial for ensuring software quality, but it remains challenging due to the need to capture the deeper semantic aspects of code. Traditional syntactic methods often fail to identify these connections. Recent advancements have addressed this challenge, though they frequently sacrifice interpretability. To improve this, we present an approach aiming to improve the transparency of the similarity assessment by using GraphCodeBERT, which enables the identification of semantic relationships between code fragments. This approach identifies similar code fragments and clarifies the reasons behind that identification, helping developers better understand and trust the results. The source code for our implementation is available at https://www.github.com/jorge-martinez-gil/graphcodebert-interpretability.

Work in psychology has highlighted that the geometric model of similarity standard in deep learning is not psychologically plausible because its metric properties such as symmetry do not align with human perception. In contrast, Tversky (1977) proposed an axiomatic theory of similarity based on a representation of objects as sets of features, and their similarity as a function of common and distinctive features. However, this model has not been used in deep learning before, partly due to the challenge of incorporating discrete set operations. We develop a differentiable parameterization of Tversky's similarity that is learnable through gradient descent, and derive neural network building blocks such as the Tversky projection layer, which unlike the linear projection layer can model non-linear functions such as XOR. Through experiments with image recognition and language modeling, we show that the Tversky projection layer is a beneficial replacement for the linear projection layer, which employs geometric similarity. On the NABirds image classification task, a frozen ResNet-50 adapted with a Tversky projection layer achieves a 24.7% relative accuracy improvement over the linear layer adapter baseline. With Tversky projection layers, GPT-2's perplexity on PTB decreases by 7.5%, and its parameter count by 34.8%. Finally, we propose a unified interpretation of both projection layers as computing similarities of input stimuli to learned prototypes, for which we also propose a novel visualization technique highlighting the interpretability of Tversky projection layers. Our work offers a new paradigm for thinking about the similarity model implicit in deep learning, and designing networks that are interpretable under an established theory of psychological similarity.

Schema matching -- the task of finding matches between attributes across disparate data sources with different tables and hierarchies -- is critical for creating interoperable machine learning (ML)-ready data. Addressing this fundamental data-centric problem has wide implications, especially in domains like healthcare, finance and e-commerce -- but also has the potential to benefit ML models more generally, by increasing the data available for ML model training. However, schema matching is a challenging ML task due to structural/hierarchical and semantic heterogeneity between different schemas. Previous ML approaches to automate schema matching have either required significant labeled data for model training, which is often unrealistic or suffer from poor zero-shot performance. To this end, we propose Matchmaker - a compositional language model program for schema matching, comprised of candidate generation, refinement and confidence scoring. Matchmaker also self-improves in a zero-shot manner without the need for labeled demonstrations via a novel optimization approach, which constructs synthetic in-context demonstrations to guide the language model's reasoning process. Empirically, we demonstrate on real-world medical schema matching benchmarks that Matchmaker outperforms previous ML-based approaches, highlighting its potential to accelerate data integration and interoperability of ML-ready data.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Transfer learning is crucial for medical imaging, yet the selection of source datasets - which can impact the generalizability of algorithms, and thus patient outcomes - often relies on researchers' intuition rather than systematic principles. This study investigates these decisions through a task-based survey with machine learning practitioners. Unlike prior work that benchmarks models and experimental setups, we take a human-centered HCI perspective on how practitioners select source datasets. Our findings indicate that choices are task-dependent and influenced by community practices, dataset properties, and computational (data embedding), or perceived visual or semantic similarity. However, similarity ratings and expected performance are not always aligned, challenging a traditional "more similar is better" view. Participants often used ambiguous terminology, which suggests a need for clearer definitions and HCI tools to make them explicit and usable. By clarifying these heuristics, this work provides practical insights for more systematic source selection in transfer learning.

We present a sketch-based CAD modeling system, where users create objects incrementally by sketching the desired shape edits, which our system automatically translates to CAD operations. Our approach is motivated by the close similarities between the steps industrial designers follow to draw 3D shapes, and the operations CAD modeling systems offer to create similar shapes. To overcome the strong ambiguity with parsing 2D sketches, we observe that in a sketching sequence, each step makes sense and can be interpreted in the context of what has been drawn before. In our system, this context corresponds to a partial CAD model, inferred in the previous steps, which we feed along with the input sketch to a deep neural network in charge of interpreting how the model should be modified by that sketch. Our deep network architecture then recognizes the intended CAD operation and segments the sketch accordingly, such that a subsequent optimization estimates the parameters of the operation that best fit the segmented sketch strokes. Since there exists no datasets of paired sketching and CAD modeling sequences, we train our system by generating synthetic sequences of CAD operations that we render as line drawings. We present a proof of concept realization of our algorithm supporting four frequently used CAD operations. Using our system, participants are able to quickly model a large and diverse set of objects, demonstrating Sketch2CAD to be an alternate way of interacting with current CAD modeling systems.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>99.0%/97.3%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

Recent studies have shown that CLIP model's adversarial robustness in zero-shot classification tasks can be enhanced by adversarially fine-tuning its image encoder with adversarial examples (AEs), which are generated by minimizing the cosine similarity between images and a hand-crafted template (e.g., ''A photo of a {label}''). However, it has been shown that the cosine similarity between a single image and a single hand-crafted template is insufficient to measure the similarity for image-text pairs. Building on this, in this paper, we find that the AEs generated using cosine similarity may fail to fool CLIP when the similarity metric is replaced with semantically enriched alternatives, making the image encoder fine-tuned with these AEs less robust. To overcome this issue, we first propose a semantic-ensemble attack to generate semantic-aware AEs by minimizing the average similarity between the original image and an ensemble of refined textual descriptions. These descriptions are initially generated by a foundation model to capture core semantic features beyond hand-crafted templates and are then refined to reduce hallucinations. To this end, we propose Semantic-aware Adversarial Fine-Tuning (SAFT), which fine-tunes CLIP's image encoder with semantic-aware AEs. Extensive experiments show that SAFT outperforms current methods, achieving substantial improvements in zero-shot adversarial robustness across 16 datasets. Our code is available at: https://github.com/tmlr-group/SAFT.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

Learning compatible representations enables the interchangeable use of semantic features as models are updated over time. This is particularly relevant in search and retrieval systems where it is crucial to avoid reprocessing of the gallery images with the updated model. While recent research has shown promising empirical evidence, there is still a lack of comprehensive theoretical understanding about learning compatible representations. In this paper, we demonstrate that the stationary representations learned by the d-Simplex fixed classifier optimally approximate compatibility representation according to the two inequality constraints of its formal definition. This not only establishes a solid foundation for future works in this line of research but also presents implications that can be exploited in practical learning scenarios. An exemplary application is the now-standard practice of downloading and fine-tuning new pre-trained models. Specifically, we show the strengths and critical issues of stationary representations in the case in which a model undergoing sequential fine-tuning is asynchronously replaced by downloading a better-performing model pre-trained elsewhere. Such a representation enables seamless delivery of retrieval service (i.e., no reprocessing of gallery images) and offers improved performance without operational disruptions during model replacement. Code available at: https://github.com/miccunifi/iamcl2r.

We study the problem of (learning) algorithm comparison, where the goal is to find differences between models trained with two different learning algorithms. We begin by formalizing this goal as one of finding distinguishing feature transformations, i.e., input transformations that change the predictions of models trained with one learning algorithm but not the other. We then present ModelDiff, a method that leverages the datamodels framework (Ilyas et al., 2022) to compare learning algorithms based on how they use their training data. We demonstrate ModelDiff through three case studies, comparing models trained with/without data augmentation, with/without pre-training, and with different SGD hyperparameters. Our code is available at https://github.com/MadryLab/modeldiff .

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis procedures from scientific literature as structured data. However, existing studies often rely on rigid, domain-specific schemas with predefined fields for structuring synthesis procedures or assume that synthesis procedures are linear sequences of operations, which limits their ability to capture the structural complexity of real-world procedures. To address these limitations, we adopt PROV-DM, an international standard for provenance information, which supports flexible, graph-based modeling of procedures. We present MatPROV, a dataset of PROV-DM-compliant synthesis procedures extracted from scientific literature using large language models. MatPROV captures structural complexities and causal relationships among materials, operations, and conditions through visually intuitive directed graphs. This representation enables machine-interpretable synthesis knowledge, opening opportunities for future research such as automated synthesis planning and optimization.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

The capability of accurately determining code similarity is crucial in many tasks related to software development. For example, it might be essential to identify code duplicates for performing software maintenance. This research introduces a novel ensemble learning approach for code similarity assessment, combining the strengths of multiple unsupervised similarity measures. The key idea is that the strengths of a diverse set of similarity measures can complement each other and mitigate individual weaknesses, leading to improved performance. Preliminary results show that while Transformers-based CodeBERT and its variant GraphCodeBERT are undoubtedly the best option in the presence of abundant training data, in the case of specific small datasets (up to 500 samples), our ensemble achieves similar results, without prejudice to the interpretability of the resulting solution, and with a much lower associated carbon footprint due to training. The source code of this novel approach can be downloaded from https://github.com/jorge-martinez-gil/ensemble-codesim.