Daily Papers

The integration of Large Language Models (LLMs) into software engineering has revolutionized code generation, enabling unprecedented productivity through promptware and autonomous AI agents. However, this transformation introduces significant risks, including insecure code generation, hallucinated outputs, irreversible actions, and a lack of transparency and accountability. Incidents like the Replit database deletion underscore the urgent need for robust safety and governance mechanisms. This paper comprehensively analyzes the inherent challenges of LLM-assisted code generation, such as vulnerability inheritance, overtrust, misinterpretation, and the absence of standardized validation and rollback protocols. To address these, we propose the SAFE-AI Framework, a holistic approach emphasizing Safety, Auditability, Feedback, and Explainability. The framework integrates guardrails, sandboxing, runtime verification, risk-aware logging, human-in-the-loop systems, and explainable AI techniques to mitigate risks while fostering trust and compliance. We introduce a novel taxonomy of AI behaviors categorizing suggestive, generative, autonomous, and destructive actions to guide risk assessment and oversight. Additionally, we identify open problems, including the lack of standardized benchmarks for code specific hallucinations and autonomy levels, and propose future research directions for hybrid verification, semantic guardrails, and proactive governance tools. Through detailed comparisons of autonomy control, prompt engineering, explainability, and governance frameworks, this paper provides a roadmap for responsible AI integration in software engineering, aligning with emerging regulations like the EU AI Act and Canada's AIDA to ensure safe, transparent, and accountable AI-driven development.

Fleets of robo-taxis offering on-demand transportation services, commonly known as Autonomous Mobility-on-Demand (AMoD) systems, hold significant promise for societal benefits, such as reducing pollution, energy consumption, and urban congestion. However, orchestrating these systems at scale remains a critical challenge, with existing coordination algorithms often failing to exploit the systems' full potential. This work introduces a novel decision-making framework that unites mathematical modeling with data-driven techniques. In particular, we present the AMoD coordination problem through the lens of reinforcement learning and propose a graph network-based framework that exploits the main strengths of graph representation learning, reinforcement learning, and classical operations research tools. Extensive evaluations across diverse simulation fidelities and scenarios demonstrate the flexibility of our approach, achieving superior system performance, computational efficiency, and generalizability compared to prior methods. Finally, motivated by the need to democratize research efforts in this area, we release publicly available benchmarks, datasets, and simulators for network-level coordination alongside an open-source codebase designed to provide accessible simulation platforms and establish a standardized validation process for comparing methodologies. Code available at: https://github.com/StanfordASL/RL4AMOD

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

Lung cancer remains the leading cause of cancer-related mortality worldwide, and early detection through low-dose computed tomography (LDCT) has shown significant promise in reducing death rates. With the growing integration of artificial intelligence (AI) into medical imaging, the development and evaluation of robust AI models require access to large, well-annotated datasets. In this study, we introduce the utility of Duke Lung Cancer Screening (DLCS) Dataset, the largest open-access LDCT dataset with over 2,000 scans and 3,000 expert-verified nodules. We benchmark deep learning models for both 3D nodule detection and lung cancer classification across internal and external datasets including LUNA16, LUNA25, and NLST-3D+. For detection, we develop two MONAI-based RetinaNet models (DLCSDmD and LUNA16-mD), evaluated using the Competition Performance Metric (CPM). For classification, we compare five models, including state-of-the-art pretrained models (Models Genesis, Med3D), a selfsupervised foundation model (FMCB), a randomly initialized ResNet50, and proposed a novel Strategic Warm-Start++ (SWS++) model. SWS++ uses curated candidate patches to pretrain a classification backbone within the same detection pipeline, enabling task-relevant feature learning. Our models demonstrated strong generalizability, with SWS++ achieving comparable or superior performance to existing foundational models across multiple datasets (AUC: 0.71 to 0.90). All code, models, and data are publicly released to promote reproducibility and collaboration. This work establishes a standardized benchmarking resource for lung cancer AI research, supporting future efforts in model development, validation, and clinical translation.

In recent years, the intersection of Natural Language Processing (NLP) and public health has opened innovative pathways for investigating various domains, including chronic pain in textual datasets. Despite the promise of NLP in chronic pain, the literature is dispersed across various disciplines, and there is a need to consolidate existing knowledge, identify knowledge gaps in the literature, and inform future research directions in this emerging field. This review aims to investigate the state of the research on NLP-based interventions designed for chronic pain research. A search strategy was formulated and executed across PubMed, Web of Science, IEEE Xplore, Scopus, and ACL Anthology to find studies published in English between 2014 and 2024. After screening 132 papers, 26 studies were included in the final review. Key findings from this review underscore the significant potential of NLP techniques to address pressing challenges in chronic pain research. The past 10 years in this field have showcased the utilization of advanced methods (transformers like RoBERTa and BERT) achieving high-performance metrics (e.g., F1>0.8) in classification tasks, while unsupervised approaches like Latent Dirichlet Allocation (LDA) and k-means clustering have proven effective for exploratory analyses. Results also reveal persistent challenges such as limited dataset diversity, inadequate sample sizes, and insufficient representation of underrepresented populations. Future research studies should explore multimodal data validation systems, context-aware mechanistic modeling, and the development of standardized evaluation metrics to enhance reproducibility and equity in chronic pain research.

Constructing large-scale datasets for the GitHub issue resolution task is crucial for both training and evaluating the software engineering capabilities of Large Language Models (LLMs). However, the traditional process for creating such benchmarks is notoriously challenging and labor-intensive, particularly in the stages of setting up evaluation environments, grading test outcomes, and validating task instances. In this paper, we propose SWE-Factory, an automated pipeline designed to address these challenges. To tackle these issues, our pipeline integrates three core automated components. First, we introduce SWE-Builder, a multi-agent system that automates evaluation environment construction, which employs four specialized agents that work in a collaborative, iterative loop and leverages an environment memory pool to enhance efficiency. Second, we introduce a standardized, exit-code-based grading method that eliminates the need for manually writing custom parsers. Finally, we automate the fail2pass validation process using these reliable exit code signals. Experiments on 671 issues across four programming languages show that our pipeline can effectively construct valid task instances; for example, with GPT-4.1-mini, our SWE-Builder constructs 269 valid instances at 0.045 per instance, while with Gemini-2.5-flash, it achieves comparable performance at the lowest cost of 0.024 per instance. We also demonstrate that our exit-code-based grading achieves 100% accuracy compared to manual inspection, and our automated fail2pass validation reaches a precision of 0.92 and a recall of 1.00. We hope our automated pipeline will accelerate the collection of large-scale, high-quality GitHub issue resolution datasets for both training and evaluation. Our code and datasets are released at https://github.com/DeepSoftwareAnalytics/swe-factory.

Human evaluation is critical for validating the performance of text-to-image generative models, as this highly cognitive process requires deep comprehension of text and images. However, our survey of 37 recent papers reveals that many works rely solely on automatic measures (e.g., FID) or perform poorly described human evaluations that are not reliable or repeatable. This paper proposes a standardized and well-defined human evaluation protocol to facilitate verifiable and reproducible human evaluation in future works. In our pilot data collection, we experimentally show that the current automatic measures are incompatible with human perception in evaluating the performance of the text-to-image generation results. Furthermore, we provide insights for designing human evaluation experiments reliably and conclusively. Finally, we make several resources publicly available to the community to facilitate easy and fast implementations.

To address overfitting and enhance model generalization in gastroenterological polyp size assessment, our study introduces Feature-Selection Gates (FSG) or Hard-Attention Gates (HAG) alongside Gradient Routing (GR) for dynamic feature selection. This technique aims to boost Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) by promoting sparse connectivity, thereby reducing overfitting and enhancing generalization. HAG achieves this through sparsification with learnable weights, serving as a regularization strategy. GR further refines this process by optimizing HAG parameters via dual forward passes, independently from the main model, to improve feature re-weighting. Our evaluation spanned multiple datasets, including CIFAR-100 for a broad impact assessment and specialized endoscopic datasets (REAL-Colon, Misawa, and SUN) focusing on polyp size estimation, covering over 200 polyps in more than 370,000 frames. The findings indicate that our HAG-enhanced networks substantially enhance performance in both binary and triclass classification tasks related to polyp sizing. Specifically, CNNs experienced an F1 Score improvement to 87.8% in binary classification, while in triclass classification, the ViT-T model reached an F1 Score of 76.5%, outperforming traditional CNNs and ViT-T models. To facilitate further research, we are releasing our codebase, which includes implementations for CNNs, multistream CNNs, ViT, and HAG-augmented variants. This resource aims to standardize the use of endoscopic datasets, providing public training-validation-testing splits for reliable and comparable research in gastroenterological polyp size estimation. The codebase is available at github.com/cosmoimd/feature-selection-gates.

In August 2025, OpenAI released GPT-OSS models, its first open weight large language models since GPT-2 in 2019, comprising two mixture of experts architectures with 120B and 20B parameters. We evaluated both variants against six contemporary open source large language models ranging from 14.7B to 235B parameters, representing both dense and sparse designs, across ten benchmarks covering general knowledge, mathematical reasoning, code generation, multilingual understanding, and conversational ability. All models were tested in unquantised form under standardised inference settings, with statistical validation using McNemars test and effect size analysis. Results show that gpt-oss-20B consistently outperforms gpt-oss-120B on several benchmarks, such as HumanEval and MMLU, despite requiring substantially less memory and energy per response. Both models demonstrate mid-tier overall performance within the current open source landscape, with relative strength in code generation and notable weaknesses in multilingual tasks. These findings provide empirical evidence that scaling in sparse architectures may not yield proportional performance gains, underscoring the need for further investigation into optimisation strategies and informing more efficient model selection for future open source deployments.