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Oct 28

Crafting Distribution Shifts for Validation and Training in Single Source Domain Generalization

Single-source domain generalization attempts to learn a model on a source domain and deploy it to unseen target domains. Limiting access only to source domain data imposes two key challenges - how to train a model that can generalize and how to verify that it does. The standard practice of validation on the training distribution does not accurately reflect the model's generalization ability, while validation on the test distribution is a malpractice to avoid. In this work, we construct an independent validation set by transforming source domain images with a comprehensive list of augmentations, covering a broad spectrum of potential distribution shifts in target domains. We demonstrate a high correlation between validation and test performance for multiple methods and across various datasets. The proposed validation achieves a relative accuracy improvement over the standard validation equal to 15.4% or 1.6% when used for method selection or learning rate tuning, respectively. Furthermore, we introduce a novel family of methods that increase the shape bias through enhanced edge maps. To benefit from the augmentations during training and preserve the independence of the validation set, a k-fold validation process is designed to separate the augmentation types used in training and validation. The method that achieves the best performance on the augmented validation is selected from the proposed family. It achieves state-of-the-art performance on various standard benchmarks. Code at: https://github.com/NikosEfth/crafting-shifts

  • 3 authors
·
Sep 29, 2024

SecBench: A Comprehensive Multi-Dimensional Benchmarking Dataset for LLMs in Cybersecurity

Evaluating Large Language Models (LLMs) is crucial for understanding their capabilities and limitations across various applications, including natural language processing and code generation. Existing benchmarks like MMLU, C-Eval, and HumanEval assess general LLM performance but lack focus on specific expert domains such as cybersecurity. Previous attempts to create cybersecurity datasets have faced limitations, including insufficient data volume and a reliance on multiple-choice questions (MCQs). To address these gaps, we propose SecBench, a multi-dimensional benchmarking dataset designed to evaluate LLMs in the cybersecurity domain. SecBench includes questions in various formats (MCQs and short-answer questions (SAQs)), at different capability levels (Knowledge Retention and Logical Reasoning), in multiple languages (Chinese and English), and across various sub-domains. The dataset was constructed by collecting high-quality data from open sources and organizing a Cybersecurity Question Design Contest, resulting in 44,823 MCQs and 3,087 SAQs. Particularly, we used the powerful while cost-effective LLMs to (1). label the data and (2). constructing a grading agent for automatic evaluation of SAQs. Benchmarking results on 16 SOTA LLMs demonstrate the usability of SecBench, which is arguably the largest and most comprehensive benchmark dataset for LLMs in cybersecurity. More information about SecBench can be found at our website, and the dataset can be accessed via the artifact link.

  • 8 authors
·
Dec 30, 2024

MMLU-CF: A Contamination-free Multi-task Language Understanding Benchmark

Multiple-choice question (MCQ) datasets like Massive Multitask Language Understanding (MMLU) are widely used to evaluate the commonsense, understanding, and problem-solving abilities of large language models (LLMs). However, the open-source nature of these benchmarks and the broad sources of training data for LLMs have inevitably led to benchmark contamination, resulting in unreliable evaluation results. To alleviate this issue, we propose a contamination-free and more challenging MCQ benchmark called MMLU-CF. This benchmark reassesses LLMs' understanding of world knowledge by averting both unintentional and malicious data leakage. To avoid unintentional data leakage, we source data from a broader domain and design three decontamination rules. To prevent malicious data leakage, we divide the benchmark into validation and test sets with similar difficulty and subject distributions. The test set remains closed-source to ensure reliable results, while the validation set is publicly available to promote transparency and facilitate independent verification. Our evaluation of mainstream LLMs reveals that the powerful GPT-4o achieves merely a 5-shot score of 73.4% and a 0-shot score of 71.9% on the test set, which indicates the effectiveness of our approach in creating a more rigorous and contamination-free evaluation standard. The GitHub repository is available at https://github.com/microsoft/MMLU-CF and the dataset refers to https://huggingface.co/datasets/microsoft/MMLU-CF.

  • 11 authors
·
Dec 19, 2024

WxC-Bench: A Novel Dataset for Weather and Climate Downstream Tasks

High-quality machine learning (ML)-ready datasets play a foundational role in developing new artificial intelligence (AI) models or fine-tuning existing models for scientific applications such as weather and climate analysis. Unfortunately, despite the growing development of new deep learning models for weather and climate, there is a scarcity of curated, pre-processed machine learning (ML)-ready datasets. Curating such high-quality datasets for developing new models is challenging particularly because the modality of the input data varies significantly for different downstream tasks addressing different atmospheric scales (spatial and temporal). Here we introduce WxC-Bench (Weather and Climate Bench), a multi-modal dataset designed to support the development of generalizable AI models for downstream use-cases in weather and climate research. WxC-Bench is designed as a dataset of datasets for developing ML-models for a complex weather and climate system, addressing selected downstream tasks as machine learning phenomenon. WxC-Bench encompasses several atmospheric processes from meso-beta (20 - 200 km) scale to synoptic scales (2500 km), such as aviation turbulence, hurricane intensity and track monitoring, weather analog search, gravity wave parameterization, and natural language report generation. We provide a comprehensive description of the dataset and also present a technical validation for baseline analysis. The dataset and code to prepare the ML-ready data have been made publicly available on Hugging Face -- https://huggingface.co/datasets/nasa-impact/WxC-Bench

  • 13 authors
·
Dec 3, 2024

Model Evaluation, Model Selection, and Algorithm Selection in Machine Learning

The correct use of model evaluation, model selection, and algorithm selection techniques is vital in academic machine learning research as well as in many industrial settings. This article reviews different techniques that can be used for each of these three subtasks and discusses the main advantages and disadvantages of each technique with references to theoretical and empirical studies. Further, recommendations are given to encourage best yet feasible practices in research and applications of machine learning. Common methods such as the holdout method for model evaluation and selection are covered, which are not recommended when working with small datasets. Different flavors of the bootstrap technique are introduced for estimating the uncertainty of performance estimates, as an alternative to confidence intervals via normal approximation if bootstrapping is computationally feasible. Common cross-validation techniques such as leave-one-out cross-validation and k-fold cross-validation are reviewed, the bias-variance trade-off for choosing k is discussed, and practical tips for the optimal choice of k are given based on empirical evidence. Different statistical tests for algorithm comparisons are presented, and strategies for dealing with multiple comparisons such as omnibus tests and multiple-comparison corrections are discussed. Finally, alternative methods for algorithm selection, such as the combined F-test 5x2 cross-validation and nested cross-validation, are recommended for comparing machine learning algorithms when datasets are small.

  • 1 authors
·
Nov 13, 2018

SecCodePLT: A Unified Platform for Evaluating the Security of Code GenAI

Existing works have established multiple benchmarks to highlight the security risks associated with Code GenAI. These risks are primarily reflected in two areas: a model potential to generate insecure code (insecure coding) and its utility in cyberattacks (cyberattack helpfulness). While these benchmarks have made significant strides, there remain opportunities for further improvement. For instance, many current benchmarks tend to focus more on a model ability to provide attack suggestions rather than its capacity to generate executable attacks. Additionally, most benchmarks rely heavily on static evaluation metrics, which may not be as precise as dynamic metrics such as passing test cases. Conversely, expert-verified benchmarks, while offering high-quality data, often operate at a smaller scale. To address these gaps, we develop SecCodePLT, a unified and comprehensive evaluation platform for code GenAIs' risks. For insecure code, we introduce a new methodology for data creation that combines experts with automatic generation. Our methodology ensures the data quality while enabling large-scale generation. We also associate samples with test cases to conduct code-related dynamic evaluation. For cyberattack helpfulness, we set up a real environment and construct samples to prompt a model to generate actual attacks, along with dynamic metrics in our environment. We conduct extensive experiments and show that SecCodePLT outperforms the state-of-the-art (SOTA) benchmark CyberSecEval in security relevance. Furthermore, it better identifies the security risks of SOTA models in insecure coding and cyberattack helpfulness. Finally, we apply SecCodePLT to the SOTA code agent, Cursor, and, for the first time, identify non-trivial security risks in this advanced coding agent.

  • 7 authors
·
Oct 14, 2024 2

CodeDPO: Aligning Code Models with Self Generated and Verified Source Code

Code generation models have shown significant potential for programming tasks. However, existing training methods like supervised fine-tuning face key limitations: they do not effectively teach models to prioritize correct over incorrect solutions in ambiguous situations, nor do they effectively optimize the runtime efficiency of the generated code. To address these challenges, we propose CodeDPO, a framework that integrates preference learning into code generation to improve two key code preference factors: code correctness and efficiency. CodeDPO employs a novel dataset construction method, utilizing a self-generation-and-validation mechanism that simultaneously generates and evaluates code and test cases. The underlying assumption is that test cases executable by multiple code snippets provide more reliable validation, and code that passes more tests is more likely to be correct. Through this self-validation process, our PageRank-inspired algorithm iteratively updates the ranking score of each code snippet, ultimately creating a code preference optimization dataset based on correctness and efficiency. CodeDPO is flexible and scalable, generating diverse preference optimization data without depending on external resources. Through comprehensive evaluations of five widely used benchmarks, CodeDPO demonstrates significant improvements in correctness and efficiency compared to existing methods. Our experiments prove that CodeDPO enhances the capabilities of LLMs in code generation and provides a robust foundation for conducting code preference optimization in more complex and challenging real-world scenarios.

  • 8 authors
·
Oct 7, 2024

MIGRATION-BENCH: Repository-Level Code Migration Benchmark from Java 8

With the rapid advancement of powerful large language models (LLMs) in recent years, a wide range of software engineering tasks can now be addressed using LLMs, significantly enhancing productivity and scalability. Numerous benchmark datasets have been developed to evaluate the coding capabilities of these models, while they primarily focus on problem-solving and issue-resolution tasks. In contrast, we introduce a new coding benchmark MIGRATION-BENCH with a distinct focus: code migration. MIGRATION-BENCH aims to serve as a comprehensive benchmark for migration from Java 8 to the latest long-term support (LTS) versions (Java 17, 21), MIGRATION-BENCH includes a full dataset and its subset selected with 5,102 and 300 repositories respectively. Selected is a representative subset curated for complexity and difficulty, offering a versatile resource to support research in the field of code migration. Additionally, we provide a comprehensive evaluation framework to facilitate rigorous and standardized assessment of LLMs on this challenging task. We further propose SD-Feedback and demonstrate that LLMs can effectively tackle repository-level code migration to Java 17. For the selected subset with Claude-3.5-Sonnet-v2, SD-Feedback achieves 62.33% and 27.00% success rate (pass@1) for minimal and maximal migration respectively. The benchmark dataset and source code are available at: https://huggingface.co/collections/AmazonScience and https://github.com/amazon-science/self_debug respectively.

  • 11 authors
·
May 14 2

Neural Theorem Proving: Generating and Structuring Proofs for Formal Verification

Formally verifying properties of software code has been a highly desirable task, especially with the emergence of LLM-generated code. In the same vein, they provide an interesting avenue for the exploration of formal verification and mechanistic interpretability. Since the introduction of code-specific models, despite their successes in generating code in Lean4 and Isabelle, the task of generalized theorem proving still remains far from being fully solved and will be a benchmark for reasoning capability in LLMs. In this work, we introduce a framework that generates whole proofs in a formal language to be used within systems that utilize the power of built-in tactics and off-the-shelf automated theorem provers. Our framework includes 3 components: generating natural language statements of the code to be verified, an LLM that generates formal proofs for the given statement, and a module employing heuristics for building the final proof. To train the LLM, we employ a 2-stage fine-tuning process, where we first use SFT-based training to enable the model to generate syntactically correct Isabelle code and then RL-based training that encourages the model to generate proofs verified by a theorem prover. We validate our framework using the miniF2F-test benchmark and the Isabelle proof assistant and design a use case to verify the correctness of the AWS S3 bucket access policy code. We also curate a dataset based on the FVEL\textnormal{ER} dataset for future training tasks.

  • 3 authors
·
Apr 23

CompassVerifier: A Unified and Robust Verifier for LLMs Evaluation and Outcome Reward

Answer verification is crucial not only for evaluating large language models (LLMs) by matching their unstructured outputs against standard answers, but also serves as the reward model to guide LLM optimization. Most evaluation frameworks rely on regularized matching or employ general LLMs for answer verification, which demands extensive, repetitive customization for regex rules or evaluation prompts. Two fundamental limitations persist in current methodologies: 1) the absence of comprehensive benchmarks that systematically evaluate verification capabilities across different LLMs; and 2) the nascent stage of verifier development, where existing approaches lack both the robustness to handle complex edge cases and the generalizability across different domains. In this work, we develop CompassVerifier, an accurate and robust lightweight verifier model for evaluation and outcome reward. It demonstrates multi-domain competency spanning math, knowledge, and diverse reasoning tasks, with the capability to process various answer types, including multi-subproblems, formulas, and sequence answers, while effectively identifying abnormal/invalid responses. We introduce VerifierBench benchmark comprising model outputs collected from multiple data sources, augmented through manual analysis of metaerror patterns to enhance CompassVerifier. We anticipate that CompassVerifier and VerifierBench will facilitate answer verification, evaluation protocols, and reinforcement learning research. Code and dataset are available at https://github.com/open-compass/CompassVerifier.

Merlin: A Vision Language Foundation Model for 3D Computed Tomography

Over 85 million computed tomography (CT) scans are performed annually in the US, of which approximately one quarter focus on the abdomen. Given the current radiologist shortage, there is a large impetus to use artificial intelligence to alleviate the burden of interpreting these complex imaging studies. Prior state-of-the-art approaches for automated medical image interpretation leverage vision language models (VLMs). However, current medical VLMs are generally limited to 2D images and short reports, and do not leverage electronic health record (EHR) data for supervision. We introduce Merlin - a 3D VLM that we train using paired CT scans (6+ million images from 15,331 CTs), EHR diagnosis codes (1.8+ million codes), and radiology reports (6+ million tokens). We evaluate Merlin on 6 task types and 752 individual tasks. The non-adapted (off-the-shelf) tasks include zero-shot findings classification (31 findings), phenotype classification (692 phenotypes), and zero-shot cross-modal retrieval (image to findings and image to impressions), while model adapted tasks include 5-year disease prediction (6 diseases), radiology report generation, and 3D semantic segmentation (20 organs). We perform internal validation on a test set of 5,137 CTs, and external validation on 7,000 clinical CTs and on two public CT datasets (VerSe, TotalSegmentator). Beyond these clinically-relevant evaluations, we assess the efficacy of various network architectures and training strategies to depict that Merlin has favorable performance to existing task-specific baselines. We derive data scaling laws to empirically assess training data needs for requisite downstream task performance. Furthermore, unlike conventional VLMs that require hundreds of GPUs for training, we perform all training on a single GPU.

  • 31 authors
·
Jun 10, 2024

VERINA: Benchmarking Verifiable Code Generation

Large language models (LLMs) are increasingly integrated in software development, but ensuring correctness in LLM-generated code remains challenging and often requires costly manual review. Verifiable code generation -- jointly generating code, specifications, and proofs of code-specification alignment -- offers a promising path to address this limitation and further unleash LLMs' benefits in coding. Yet, there exists a significant gap in evaluation: current benchmarks often lack support for end-to-end verifiable code generation. In this paper, we introduce Verina (Verifiable Code Generation Arena), a high-quality benchmark enabling a comprehensive and modular evaluation of code, specification, and proof generation as well as their compositions. Verina consists of 189 manually curated coding tasks in Lean, with detailed problem descriptions, reference implementations, formal specifications, and extensive test suites. Our extensive evaluation of state-of-the-art LLMs reveals significant challenges in verifiable code generation, especially in proof generation, underscoring the need for improving LLM-based theorem provers in verification domains. The best model, OpenAI o4-mini, generates only 61.4% correct code, 51.0% sound and complete specifications, and 3.6% successful proofs, with one trial per task. We hope Verina will catalyze progress in verifiable code generation by providing a rigorous and comprehensive benchmark. We release our dataset on https://huggingface.co/datasets/sunblaze-ucb/verina and our evaluation code on https://github.com/sunblaze-ucb/verina.

  • 6 authors
·
May 29

LLMxCPG: Context-Aware Vulnerability Detection Through Code Property Graph-Guided Large Language Models

Software vulnerabilities present a persistent security challenge, with over 25,000 new vulnerabilities reported in the Common Vulnerabilities and Exposures (CVE) database in 2024 alone. While deep learning based approaches show promise for vulnerability detection, recent studies reveal critical limitations in terms of accuracy and robustness: accuracy drops by up to 45% on rigorously verified datasets, and performance degrades significantly under simple code modifications. This paper presents LLMxCPG, a novel framework integrating Code Property Graphs (CPG) with Large Language Models (LLM) for robust vulnerability detection. Our CPG-based slice construction technique reduces code size by 67.84 to 90.93% while preserving vulnerability-relevant context. Our approach's ability to provide a more concise and accurate representation of code snippets enables the analysis of larger code segments, including entire projects. This concise representation is a key factor behind the improved detection capabilities of our method, as it can now identify vulnerabilities that span multiple functions. Empirical evaluation demonstrates LLMxCPG's effectiveness across verified datasets, achieving 15-40% improvements in F1-score over state-of-the-art baselines. Moreover, LLMxCPG maintains high performance across function-level and multi-function codebases while exhibiting robust detection efficacy under various syntactic code modifications.

Refining Focus in AI for Lung Cancer: Comparing Lesion-Centric and Chest-Region Models with Performance Insights from Internal and External Validation

Background: AI-based classification models are essential for improving lung cancer diagnosis. However, the relative performance of lesion-level versus chest-region models in internal and external datasets remains unclear. Purpose: This study evaluates the performance of lesion-level and chest-region models for lung cancer classification, comparing their effectiveness across internal Duke Lung Nodule Dataset 2024 (DLND24) and external (LUNA16, NLST) datasets, with a focus on subgroup analyses by demographics, histology, and imaging characteristics. Materials and Methods: Two AI models were trained: one using lesion-centric patches (64,64,64) and the other using chest-region patches (512,512,8). Internal validation was conducted on DLND24, while external validation utilized LUNA16 and NLST datasets. The models performances were assessed using AUC-ROC, with subgroup analyses for demographic, clinical, and imaging factors. Statistical comparisons were performed using DeLongs test. Gradient-based visualizations and probability distribution were further used for analysis. Results: The lesion-level model consistently outperformed the chest-region model across datasets. In internal validation, the lesion-level model achieved an AUC of 0.71(CI: 0.61-0.81), compared to 0.68(0.57-0.77) for the chest-region model. External validation showed similar trends, with AUCs of 0.90(0.87-0.92) and 0.81(0.79-0.82) on LUNA16 and NLST, respectively. Subgroup analyses revealed significant advantages for lesion-level models in certain histological subtypes (adenocarcinoma) and imaging conditions (CT manufacturers). Conclusion: Lesion-level models demonstrate superior classification performance, especially for external datasets and challenging subgroups, suggesting their clinical utility for precision lung cancer diagnostics.

  • 1 authors
·
Nov 25, 2024

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise--the disagreement between model and metric defined candidate rankings--minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries

  • 10 authors
·
May 12, 2023 1

VeriCoder: Enhancing LLM-Based RTL Code Generation through Functional Correctness Validation

Recent advances in Large Language Models (LLMs) have sparked growing interest in applying them to Electronic Design Automation (EDA) tasks, particularly Register Transfer Level (RTL) code generation. While several RTL datasets have been introduced, most focus on syntactic validity rather than functional validation with tests, leading to training examples that compile but may not implement the intended behavior. We present VERICODER, a model for RTL code generation fine-tuned on a dataset validated for functional correctness. This fine-tuning dataset is constructed using a novel methodology that combines unit test generation with feedback-directed refinement. Given a natural language specification and an initial RTL design, we prompt a teacher model (GPT-4o-mini) to generate unit tests and iteratively revise the RTL design based on its simulation results using the generated tests. If necessary, the teacher model also updates the tests to ensure they comply with the natural language specification. As a result of this process, every example in our dataset is functionally validated, consisting of a natural language description, an RTL implementation, and passing tests. Fine-tuned on this dataset of over 125,000 examples, VERICODER achieves state-of-the-art metrics in functional correctness on VerilogEval and RTLLM, with relative gains of up to 71.7% and 27.4% respectively. An ablation study further shows that models trained on our functionally validated dataset outperform those trained on functionally non-validated datasets, underscoring the importance of high-quality datasets in RTL code generation.

  • 8 authors
·
Apr 22

Design of Negative Sampling Strategies for Distantly Supervised Skill Extraction

Skills play a central role in the job market and many human resources (HR) processes. In the wake of other digital experiences, today's online job market has candidates expecting to see the right opportunities based on their skill set. Similarly, enterprises increasingly need to use data to guarantee that the skills within their workforce remain future-proof. However, structured information about skills is often missing, and processes building on self- or manager-assessment have shown to struggle with issues around adoption, completeness, and freshness of the resulting data. Extracting skills is a highly challenging task, given the many thousands of possible skill labels mentioned either explicitly or merely described implicitly and the lack of finely annotated training corpora. Previous work on skill extraction overly simplifies the task to an explicit entity detection task or builds on manually annotated training data that would be infeasible if applied to a complete vocabulary of skills. We propose an end-to-end system for skill extraction, based on distant supervision through literal matching. We propose and evaluate several negative sampling strategies, tuned on a small validation dataset, to improve the generalization of skill extraction towards implicitly mentioned skills, despite the lack of such implicit skills in the distantly supervised data. We observe that using the ESCO taxonomy to select negative examples from related skills yields the biggest improvements, and combining three different strategies in one model further increases the performance, up to 8 percentage points in RP@5. We introduce a manually annotated evaluation benchmark for skill extraction based on the ESCO taxonomy, on which we validate our models. We release the benchmark dataset for research purposes to stimulate further research on the task.

  • 5 authors
·
Sep 13, 2022

SecReEvalBench: A Multi-turned Security Resilience Evaluation Benchmark for Large Language Models

The increasing deployment of large language models in security-sensitive domains necessitates rigorous evaluation of their resilience against adversarial prompt-based attacks. While previous benchmarks have focused on security evaluations with limited and predefined attack domains, such as cybersecurity attacks, they often lack a comprehensive assessment of intent-driven adversarial prompts and the consideration of real-life scenario-based multi-turn attacks. To address this gap, we present SecReEvalBench, the Security Resilience Evaluation Benchmark, which defines four novel metrics: Prompt Attack Resilience Score, Prompt Attack Refusal Logic Score, Chain-Based Attack Resilience Score and Chain-Based Attack Rejection Time Score. Moreover, SecReEvalBench employs six questioning sequences for model assessment: one-off attack, successive attack, successive reverse attack, alternative attack, sequential ascending attack with escalating threat levels and sequential descending attack with diminishing threat levels. In addition, we introduce a dataset customized for the benchmark, which incorporates both neutral and malicious prompts, categorised across seven security domains and sixteen attack techniques. In applying this benchmark, we systematically evaluate five state-of-the-art open-weighted large language models, Llama 3.1, Gemma 2, Mistral v0.3, DeepSeek-R1 and Qwen 3. Our findings offer critical insights into the strengths and weaknesses of modern large language models in defending against evolving adversarial threats. The SecReEvalBench dataset is publicly available at https://kaggle.com/datasets/5a7ee22cf9dab6c93b55a73f630f6c9b42e936351b0ae98fbae6ddaca7fe248d, which provides a groundwork for advancing research in large language model security.

  • 2 authors
·
May 12

RadGenome-Chest CT: A Grounded Vision-Language Dataset for Chest CT Analysis

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

  • 7 authors
·
Apr 25, 2024

Reasoning with LLMs for Zero-Shot Vulnerability Detection

Automating software vulnerability detection (SVD) remains a critical challenge in an era of increasingly complex and interdependent software systems. Despite significant advances in Large Language Models (LLMs) for code analysis, prevailing evaluation methodologies often lack the context-aware robustness necessary to capture real-world intricacies and cross-component interactions. To address these limitations, we present VulnSage, a comprehensive evaluation framework and a dataset curated from diverse, large-scale open-source system software projects developed in C/C++. Unlike prior datasets, it leverages a heuristic noise pre-filtering approach combined with LLM-based reasoning to ensure a representative and minimally noisy spectrum of vulnerabilities. The framework supports multi-granular analysis across function, file, and inter-function levels and employs four diverse zero-shot prompt strategies: Baseline, Chain-of-Thought, Think, and Think & Verify. Through this evaluation, we uncover that structured reasoning prompts substantially improve LLM performance, with Think & Verify reducing ambiguous responses from 20.3% to 9.1% while increasing accuracy. We further demonstrate that code-specialized models consistently outperform general-purpose alternatives, with performance varying significantly across vulnerability types, revealing that no single approach universally excels across all security contexts. Link to dataset and codes: https://github.com/Erroristotle/VulnSage.git

  • 2 authors
·
Mar 22

Coverage-centric Coreset Selection for High Pruning Rates

One-shot coreset selection aims to select a representative subset of the training data, given a pruning rate, that can later be used to train future models while retaining high accuracy. State-of-the-art coreset selection methods pick the highest importance examples based on an importance metric and are found to perform well at low pruning rates. However, at high pruning rates, they suffer from a catastrophic accuracy drop, performing worse than even random sampling. This paper explores the reasons behind this accuracy drop both theoretically and empirically. We first propose a novel metric to measure the coverage of a dataset on a specific distribution by extending the classical geometric set cover problem to a distribution cover problem. This metric helps explain why coresets selected by SOTA methods at high pruning rates perform poorly compared to random sampling because of worse data coverage. We then propose a novel one-shot coreset selection method, Coverage-centric Coreset Selection (CCS), that jointly considers overall data coverage upon a distribution as well as the importance of each example. We evaluate CCS on five datasets and show that, at high pruning rates (e.g., 90%), it achieves significantly better accuracy than previous SOTA methods (e.g., at least 19.56% higher on CIFAR10) as well as random selection (e.g., 7.04% higher on CIFAR10) and comparable accuracy at low pruning rates. We make our code publicly available at https://github.com/haizhongzheng/Coverage-centric-coreset-selection.

  • 4 authors
·
Oct 27, 2022

Robust model benchmarking and bias-imbalance in data-driven materials science: a case study on MODNet

As the number of novel data-driven approaches to material science continues to grow, it is crucial to perform consistent quality, reliability and applicability assessments of model performance. In this paper, we benchmark the Materials Optimal Descriptor Network (MODNet) method and architecture against the recently released MatBench v0.1, a curated test suite of materials datasets. MODNet is shown to outperform current leaders on 6 of the 13 tasks, whilst closely matching the current leaders on a further 2 tasks; MODNet performs particularly well when the number of samples is below 10,000. Attention is paid to two topics of concern when benchmarking models. First, we encourage the reporting of a more diverse set of metrics as it leads to a more comprehensive and holistic comparison of model performance. Second, an equally important task is the uncertainty assessment of a model towards a target domain. Significant variations in validation errors can be observed, depending on the imbalance and bias in the training set (i.e., similarity between training and application space). By using an ensemble MODNet model, confidence intervals can be built and the uncertainty on individual predictions can be quantified. Imbalance and bias issues are often overlooked, and yet are important for successful real-world applications of machine learning in materials science and condensed matter.

  • 3 authors
·
Feb 3, 2021

CyberLLMInstruct: A New Dataset for Analysing Safety of Fine-Tuned LLMs Using Cyber Security Data

The integration of large language models (LLMs) into cyber security applications presents significant opportunities, such as enhancing threat analysis and malware detection, but can also introduce critical risks and safety concerns, including personal data leakage and automated generation of new malware. To address these challenges, we developed CyberLLMInstruct, a dataset of 54,928 instruction-response pairs spanning cyber security tasks such as malware analysis, phishing simulations, and zero-day vulnerabilities. The dataset was constructed through a multi-stage process. This involved sourcing data from multiple resources, filtering and structuring it into instruction-response pairs, and aligning it with real-world scenarios to enhance its applicability. Seven open-source LLMs were chosen to test the usefulness of CyberLLMInstruct: Phi 3 Mini 3.8B, Mistral 7B, Qwen 2.5 7B, Llama 3 8B, Llama 3.1 8B, Gemma 2 9B, and Llama 2 70B. In our primary example, we rigorously assess the safety of fine-tuned models using the OWASP top 10 framework, finding that fine-tuning reduces safety resilience across all tested LLMs and every adversarial attack (e.g., the security score of Llama 3.1 8B against prompt injection drops from 0.95 to 0.15). In our second example, we show that these same fine-tuned models can also achieve up to 92.50 percent accuracy on the CyberMetric benchmark. These findings highlight a trade-off between performance and safety, showing the importance of adversarial testing and further research into fine-tuning methodologies that can mitigate safety risks while still improving performance across diverse datasets and domains. The dataset creation pipeline, along with comprehensive documentation, examples, and resources for reproducing our results, is publicly available at https://github.com/Adelsamir01/CyberLLMInstruct.

  • 3 authors
·
Mar 12

A Vulnerability Code Intent Summary Dataset

In the era of Large Language Models (LLMs), the code summarization technique boosts a lot, along with the emergence of many new significant works. However, the potential of code summarization in the Computer Security Area still remains explored. Can we generate a code summary of a code snippet for its security intention? Thus, this work proposes an innovative large-scale multi-perspective Code Intent Summary Dataset named BADS , aiming to increase the understanding of a given code snippet and reduce the risk in the code developing process. The procedure of establishing a dataset can be divided into four steps: First, we collect samples of codes with known vulnerabilities as well as code generated by AI from multiple sources. Second, we do the data clean and format unification, then do the data combination. Third, we utilize the LLM to automatically Annotate the code snippet. Last, We do the human evaluation to double-check. The dataset contains X code examples which cover Y categories of vulnerability. Our data are from Z open-source projects and CVE entries, and compared to existing work, our dataset not only contains original code but also code function summary and security intent summary, providing context information for research in code security analysis. All information is in CSV format. The contributions of this paper are four-fold: the establishment of a high-quality, multi-perspective Code Intent Summary Dataset; an innovative method in data collection and processing; A new multi-perspective code analysis framework that promotes cross-disciplinary research in the fields of software engineering and cybersecurity; improving the practicality and scalability of the research outcomes by considering the code length limitations in real-world applications. Our dataset and related tools have been publicly released on GitHub.

  • 3 authors
·
Apr 10

Skywork-SWE: Unveiling Data Scaling Laws for Software Engineering in LLMs

Software engineering (SWE) has recently emerged as a crucial testbed for next-generation LLM agents, demanding inherent capabilities in two critical dimensions: sustained iterative problem-solving (e.g., >50 interaction rounds) and long-context dependency resolution (e.g., >32k tokens). However, the data curation process in SWE remains notoriously time-consuming, as it heavily relies on manual annotation for code file filtering and the setup of dedicated runtime environments to execute and validate unit tests. Consequently, most existing datasets are limited to only a few thousand GitHub-sourced instances. To this end, we propose an incremental, automated data-curation pipeline that systematically scales both the volume and diversity of SWE datasets. Our dataset comprises 10,169 real-world Python task instances from 2,531 distinct GitHub repositories, each accompanied by a task specified in natural language and a dedicated runtime-environment image for automated unit-test validation. We have carefully curated over 8,000 successfully runtime-validated training trajectories from our proposed SWE dataset. When fine-tuning the Skywork-SWE model on these trajectories, we uncover a striking data scaling phenomenon: the trained model's performance for software engineering capabilities in LLMs continues to improve as the data size increases, showing no signs of saturation. Notably, our Skywork-SWE model achieves 38.0% pass@1 accuracy on the SWE-bench Verified benchmark without using verifiers or multiple rollouts, establishing a new state-of-the-art (SOTA) among the Qwen2.5-Coder-32B-based LLMs built on the OpenHands agent framework. Furthermore, with the incorporation of test-time scaling techniques, the performance further improves to 47.0% accuracy, surpassing the previous SOTA results for sub-32B parameter models. We release the Skywork-SWE-32B model checkpoint to accelerate future research.

  • 11 authors
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Jun 23 3

CodeSense: a Real-World Benchmark and Dataset for Code Semantic Reasoning

Understanding and reasoning about code semantics is essential for enhancing code LLMs' abilities to solve real-world software engineering (SE) tasks. Although several code reasoning benchmarks exist, most rely on synthetic datasets or educational coding problems and focus on coarse-grained reasoning tasks such as input/output prediction, limiting their effectiveness in evaluating LLMs in practical SE contexts. To bridge this gap, we propose CodeSense, the first benchmark that makes available a spectrum of fine-grained code reasoning tasks concerned with the software engineering of real-world code. We collected Python, C and Java software projects from real-world repositories. We executed tests from these repositories, collected their execution traces, and constructed a ground truth dataset for fine-grained semantic reasoning tasks. We then performed comprehensive evaluations on state-of-the-art LLMs. Our results show a clear performance gap for the models to handle fine-grained reasoning tasks. Although prompting techniques such as chain-of-thought and in-context learning helped, the lack of code semantics in LLMs fundamentally limit models' capabilities of code reasoning. Besides dataset, benchmark and evaluation, our work produced an execution tracing framework and tool set that make it easy to collect ground truth for fine-grained SE reasoning tasks, offering a strong basis for future benchmark construction and model post training. Our code and data are located at https://codesense-bench.github.io/.

  • 7 authors
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May 31