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Jan 13

Agentic End-to-End De Novo Protein Design for Tailored Dynamics Using a Language Diffusion Model

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

  • 2 authors
·
Feb 14, 2025 2

Knowledge Graph Modeling-Driven Large Language Model Operating System (LLM OS) for Task Automation in Process Engineering Problem-Solving

We present the Process Engineering Operations Assistant (PEOA), an AI-driven framework designed to solve complex problems in the chemical and process industries. The framework employs a modular architecture orchestrated by a meta-agent, which serves as the central coordinator, managing an action generator and instruction-tuned small-scale language models (expert models). The action generator decomposes complex problems into sub-tasks and identifies suitable expert models to execute each, delivering precise solutions for multi-step problem-solving. Key techniques include advanced knowledge modeling using property graphs for improved information retrieval, facilitating more accurate and contextually relevant solutions. Additionally, the framework utilizes a teacher-student transfer-learning approach with GPT-4 (Omni) to fine-tune the action generator and expert models for domain adaptation, alongside an iterative problem-solving mechanism with sophisticated error handling. Custom datasets were developed to evaluate the framework against leading proprietary language models on various engineering tasks. The results demonstrate the framework effectiveness in automating calculations, accelerating prototyping, and providing AI-augmented decision support for industrial processes, marking a significant advancement in process engineering capabilities.

  • 3 authors
·
Aug 23, 2024

Fatigue-PINN: Physics-Informed Fatigue-Driven Motion Modulation and Synthesis

Fatigue modeling is essential for motion synthesis tasks to model human motions under fatigued conditions and biomechanical engineering applications, such as investigating the variations in movement patterns and posture due to fatigue, defining injury risk mitigation and prevention strategies, formulating fatigue minimization schemes and creating improved ergonomic designs. Nevertheless, employing data-driven methods for synthesizing the impact of fatigue on motion, receives little to no attention in the literature. In this work, we present Fatigue-PINN, a deep learning framework based on Physics-Informed Neural Networks, for modeling fatigued human movements, while providing joint-specific fatigue configurations for adaptation and mitigation of motion artifacts on a joint level, resulting in more realistic animations. To account for muscle fatigue, we simulate the fatigue-induced fluctuations in the maximum exerted joint torques by leveraging a PINN adaptation of the Three-Compartment Controller model to exploit physics-domain knowledge for improving accuracy. This model also introduces parametric motion alignment with respect to joint-specific fatigue, hence avoiding sharp frame transitions. Our results indicate that Fatigue-PINN accurately simulates the effects of externally perceived fatigue on open-type human movements being consistent with findings from real-world experimental fatigue studies. Since fatigue is incorporated in torque space, Fatigue-PINN provides an end-to-end encoder-decoder-like architecture, to ensure transforming joint angles to joint torques and vice-versa, thus, being compatible with motion synthesis frameworks operating on joint angles.

  • 2 authors
·
Feb 26, 2025

A Survey on the Optimization of Large Language Model-based Agents

With the rapid development of Large Language Models (LLMs), LLM-based agents have been widely adopted in various fields, becoming essential for autonomous decision-making and interactive tasks. However, current work typically relies on prompt design or fine-tuning strategies applied to vanilla LLMs, which often leads to limited effectiveness or suboptimal performance in complex agent-related environments. Although LLM optimization techniques can improve model performance across many general tasks, they lack specialized optimization towards critical agent functionalities such as long-term planning, dynamic environmental interaction, and complex decision-making. Although numerous recent studies have explored various strategies to optimize LLM-based agents for complex agent tasks, a systematic review summarizing and comparing these methods from a holistic perspective is still lacking. In this survey, we provide a comprehensive review of LLM-based agent optimization approaches, categorizing them into parameter-driven and parameter-free methods. We first focus on parameter-driven optimization, covering fine-tuning-based optimization, reinforcement learning-based optimization, and hybrid strategies, analyzing key aspects such as trajectory data construction, fine-tuning techniques, reward function design, and optimization algorithms. Additionally, we briefly discuss parameter-free strategies that optimize agent behavior through prompt engineering and external knowledge retrieval. Finally, we summarize the datasets and benchmarks used for evaluation and tuning, review key applications of LLM-based agents, and discuss major challenges and promising future directions. Our repository for related references is available at https://github.com/YoungDubbyDu/LLM-Agent-Optimization.

  • 7 authors
·
Mar 16, 2025

Automatic Stage Lighting Control: Is it a Rule-Driven Process or Generative Task?

Stage lighting plays an essential role in live music performances, influencing the engaging experience of both musicians and audiences. Given the high costs associated with hiring or training professional lighting engineers, Automatic Stage Lighting Control (ASLC) has gained increasing attention. However, most existing approaches only classify music into limited categories and map them to predefined light patterns, resulting in formulaic and monotonous outcomes that lack rationality. To address this issue, this paper presents an end-to-end solution that directly learns from experienced lighting engineers -- Skip-BART. To the best of our knowledge, this is the first work to conceptualize ASLC as a generative task rather than merely a classification problem. Our method modifies the BART model to take audio music as input and produce light hue and value (intensity) as output, incorporating a novel skip connection mechanism to enhance the relationship between music and light within the frame grid.We validate our method through both quantitative analysis and an human evaluation, demonstrating that Skip-BART outperforms conventional rule-based methods across all evaluation metrics and shows only a limited gap compared to real lighting engineers.Specifically, our method yields a p-value of 0.72 in a statistical comparison based on human evaluations with human lighting engineers, suggesting that the proposed approach closely matches human lighting engineering performance. To support further research, we have made our self-collected dataset, code, and trained model parameters available at https://github.com/RS2002/Skip-BART .

  • 4 authors
·
Jun 2, 2025

One Example Shown, Many Concepts Known! Counterexample-Driven Conceptual Reasoning in Mathematical LLMs

Leveraging mathematical Large Language Models (LLMs) for proof generation is a fundamental topic in LLMs research. We argue that the ability of current LLMs to prove statements largely depends on whether they have encountered the relevant proof process during training. This reliance limits their deeper understanding of mathematical theorems and related concepts. Inspired by the pedagogical method of "proof by counterexamples" commonly used in human mathematics education, our work aims to enhance LLMs' ability to conduct mathematical reasoning and proof through counterexamples. Specifically, we manually create a high-quality, university-level mathematical benchmark, CounterMATH, which requires LLMs to prove mathematical statements by providing counterexamples, thereby assessing their grasp of mathematical concepts. Additionally, we develop a data engineering framework to automatically obtain training data for further model improvement. Extensive experiments and detailed analyses demonstrate that CounterMATH is challenging, indicating that LLMs, such as OpenAI o1, have insufficient counterexample-driven proof capabilities. Moreover, our exploration into model training reveals that strengthening LLMs' counterexample-driven conceptual reasoning abilities is crucial for improving their overall mathematical capabilities. We believe that our work offers new perspectives on the community of mathematical LLMs.

  • 13 authors
·
Feb 11, 2025 2

Logics-STEM: Empowering LLM Reasoning via Failure-Driven Post-Training and Document Knowledge Enhancement

We present Logics-STEM, a state-of-the-art reasoning model fine-tuned on Logics-STEM-SFT-Dataset, a high-quality and diverse dataset at 10M scale that represents one of the largest-scale open-source long chain-of-thought corpora. Logics-STEM targets reasoning tasks in the domains of Science, Technology, Engineering, and Mathematics (STEM), and exhibits exceptional performance on STEM-related benchmarks with an average improvement of 4.68% over the next-best model at 8B scale. We attribute the gains to our data-algorithm co-design engine, where they are jointly optimized to fit a gold-standard distribution behind reasoning. Data-wise, the Logics-STEM-SFT-Dataset is constructed from a meticulously designed data curation engine with 5 stages to ensure the quality, diversity, and scalability, including annotation, deduplication, decontamination, distillation, and stratified sampling. Algorithm-wise, our failure-driven post-training framework leverages targeted knowledge retrieval and data synthesis around model failure regions in the Supervised Fine-tuning (SFT) stage to effectively guide the second-stage SFT or the reinforcement learning (RL) for better fitting the target distribution. The superior empirical performance of Logics-STEM reveals the vast potential of combining large-scale open-source data with carefully designed synthetic data, underscoring the critical role of data-algorithm co-design in enhancing reasoning capabilities through post-training. We make both the Logics-STEM models (8B and 32B) and the Logics-STEM-SFT-Dataset (10M and downsampled 2.2M versions) publicly available to support future research in the open-source community.

  • 19 authors
·
Jan 4

Enhancing Large Language Models for Secure Code Generation: A Dataset-driven Study on Vulnerability Mitigation

Large language models (LLMs) have brought significant advancements to code generation, benefiting both novice and experienced developers. However, their training using unsanitized data from open-source repositories, like GitHub, introduces the risk of inadvertently propagating security vulnerabilities. To effectively mitigate this concern, this paper presents a comprehensive study focused on evaluating and enhancing code LLMs from a software security perspective. We introduce SecuCoGenSecuCoGen has been uploaded as supplemental material and will be made publicly available after publication., a meticulously curated dataset targeting 21 critical vulnerability types. SecuCoGen comprises 180 samples and serves as the foundation for conducting experiments on three crucial code-related tasks: code generation, code repair and vulnerability classification, with a strong emphasis on security. Our experimental results reveal that existing models often overlook security concerns during code generation, leading to the generation of vulnerable code. To address this, we propose effective approaches to mitigate the security vulnerabilities and enhance the overall robustness of code generated by LLMs. Moreover, our study identifies weaknesses in existing models' ability to repair vulnerable code, even when provided with vulnerability information. Additionally, certain vulnerability types pose challenges for the models, hindering their performance in vulnerability classification. Based on these findings, we believe our study will have a positive impact on the software engineering community, inspiring the development of improved methods for training and utilizing LLMs, thereby leading to safer and more trustworthy model deployment.

  • 7 authors
·
Oct 24, 2023

SynLLM: A Comparative Analysis of Large Language Models for Medical Tabular Synthetic Data Generation via Prompt Engineering

Access to real-world medical data is often restricted due to privacy regulations, posing a significant barrier to the advancement of healthcare research. Synthetic data offers a promising alternative; however, generating realistic, clinically valid, and privacy-conscious records remains a major challenge. Recent advancements in Large Language Models (LLMs) offer new opportunities for structured data generation; however, existing approaches frequently lack systematic prompting strategies and comprehensive, multi-dimensional evaluation frameworks. In this paper, we present SynLLM, a modular framework for generating high-quality synthetic medical tabular data using 20 state-of-the-art open-source LLMs, including LLaMA, Mistral, and GPT variants, guided by structured prompts. We propose four distinct prompt types, ranging from example-driven to rule-based constraints, that encode schema, metadata, and domain knowledge to control generation without model fine-tuning. Our framework features a comprehensive evaluation pipeline that rigorously assesses generated data across statistical fidelity, clinical consistency, and privacy preservation. We evaluate SynLLM across three public medical datasets, including Diabetes, Cirrhosis, and Stroke, using 20 open-source LLMs. Our results show that prompt engineering significantly impacts data quality and privacy risk, with rule-based prompts achieving the best privacy-quality balance. SynLLM establishes that, when guided by well-designed prompts and evaluated with robust, multi-metric criteria, LLMs can generate synthetic medical data that is both clinically plausible and privacy-aware, paving the way for safer and more effective data sharing in healthcare research.

  • 3 authors
·
Aug 11, 2025

Fast and Accurate Zero-Training Classification for Tabular Engineering Data

In engineering design, navigating complex decision-making landscapes demands a thorough exploration of the design, performance, and constraint spaces, often impeded by resource-intensive simulations. Data-driven methods can mitigate this challenge by harnessing historical data to delineate feasible domains, accelerate optimization, or evaluate designs. However, the implementation of these methods usually demands machine-learning expertise and multiple trials to choose the right method and hyperparameters. This makes them less accessible for numerous engineering situations. Additionally, there is an inherent trade-off between training speed and accuracy, with faster methods sometimes compromising precision. In our paper, we demonstrate that a recently released general-purpose transformer-based classification model, TabPFN, is both fast and accurate. Notably, it requires no dataset-specific training to assess new tabular data. TabPFN is a Prior-Data Fitted Network, which undergoes a one-time offline training across a broad spectrum of synthetic datasets and performs in-context learning. We evaluated TabPFN's efficacy across eight engineering design classification problems, contrasting it with seven other algorithms, including a state-of-the-art AutoML method. For these classification challenges, TabPFN consistently outperforms in speed and accuracy. It is also the most data-efficient and provides the added advantage of being differentiable and giving uncertainty estimates. Our findings advocate for the potential of pre-trained models that learn from synthetic data and require no domain-specific tuning to make data-driven engineering design accessible to a broader community and open ways to efficient general-purpose models valid across applications. Furthermore, we share a benchmark problem set for evaluating new classification algorithms in engineering design.

  • 2 authors
·
Jan 12, 2024

Rethinking Autonomy: Preventing Failures in AI-Driven Software Engineering

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.

  • 2 authors
·
Aug 15, 2025

Assessing the Use of AutoML for Data-Driven Software Engineering

Background. Due to the widespread adoption of Artificial Intelligence (AI) and Machine Learning (ML) for building software applications, companies are struggling to recruit employees with a deep understanding of such technologies. In this scenario, AutoML is soaring as a promising solution to fill the AI/ML skills gap since it promises to automate the building of end-to-end AI/ML pipelines that would normally be engineered by specialized team members. Aims. Despite the growing interest and high expectations, there is a dearth of information about the extent to which AutoML is currently adopted by teams developing AI/ML-enabled systems and how it is perceived by practitioners and researchers. Method. To fill these gaps, in this paper, we present a mixed-method study comprising a benchmark of 12 end-to-end AutoML tools on two SE datasets and a user survey with follow-up interviews to further our understanding of AutoML adoption and perception. Results. We found that AutoML solutions can generate models that outperform those trained and optimized by researchers to perform classification tasks in the SE domain. Also, our findings show that the currently available AutoML solutions do not live up to their names as they do not equally support automation across the stages of the ML development workflow and for all the team members. Conclusions. We derive insights to inform the SE research community on how AutoML can facilitate their activities and tool builders on how to design the next generation of AutoML technologies.

  • 4 authors
·
Jul 20, 2023

CADmium: Fine-Tuning Code Language Models for Text-Driven Sequential CAD Design

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.

  • 5 authors
·
Jul 13, 2025

A Comprehensive Survey on Benchmarks and Solutions in Software Engineering of LLM-Empowered Agentic System

The integration of Large Language Models (LLMs) into software engineering has driven a transition from traditional rule-based systems to autonomous agentic systems capable of solving complex problems. However, systematic progress is hindered by a lack of comprehensive understanding of how benchmarks and solutions interconnect. This survey addresses this gap by providing the first holistic analysis of LLM-powered software engineering, offering insights into evaluation methodologies and solution paradigms. We review over 150 recent papers and propose a taxonomy along two key dimensions: (1) Solutions, categorized into prompt-based, fine-tuning-based, and agent-based paradigms, and (2) Benchmarks, including tasks such as code generation, translation, and repair. Our analysis highlights the evolution from simple prompt engineering to sophisticated agentic systems incorporating capabilities like planning, reasoning, memory mechanisms, and tool augmentation. To contextualize this progress, we present a unified pipeline illustrating the workflow from task specification to deliverables, detailing how different solution paradigms address various complexity levels. Unlike prior surveys that focus narrowly on specific aspects, this work connects 50+ benchmarks to their corresponding solution strategies, enabling researchers to identify optimal approaches for diverse evaluation criteria. We also identify critical research gaps and propose future directions, including multi-agent collaboration, self-evolving systems, and formal verification integration. This survey serves as a foundational guide for advancing LLM-driven software engineering. We maintain a GitHub repository that continuously updates the reviewed and related papers at https://github.com/lisaGuojl/LLM-Agent-SE-Survey.

  • 11 authors
·
Oct 10, 2025

ProphetFuzz: Fully Automated Prediction and Fuzzing of High-Risk Option Combinations with Only Documentation via Large Language Model

Vulnerabilities related to option combinations pose a significant challenge in software security testing due to their vast search space. Previous research primarily addressed this challenge through mutation or filtering techniques, which inefficiently treated all option combinations as having equal potential for vulnerabilities, thus wasting considerable time on non-vulnerable targets and resulting in low testing efficiency. In this paper, we utilize carefully designed prompt engineering to drive the large language model (LLM) to predict high-risk option combinations (i.e., more likely to contain vulnerabilities) and perform fuzz testing automatically without human intervention. We developed a tool called ProphetFuzz and evaluated it on a dataset comprising 52 programs collected from three related studies. The entire experiment consumed 10.44 CPU years. ProphetFuzz successfully predicted 1748 high-risk option combinations at an average cost of only \$8.69 per program. Results show that after 72 hours of fuzzing, ProphetFuzz discovered 364 unique vulnerabilities associated with 12.30\% of the predicted high-risk option combinations, which was 32.85\% higher than that found by state-of-the-art in the same timeframe. Additionally, using ProphetFuzz, we conducted persistent fuzzing on the latest versions of these programs, uncovering 140 vulnerabilities, with 93 confirmed by developers and 21 awarded CVE numbers.

  • 5 authors
·
Sep 1, 2024

Turbo: Informativity-Driven Acceleration Plug-In for Vision-Language Large Models

Vision-Language Large Models (VLMs) recently become primary backbone of AI, due to the impressive performance. However, their expensive computation costs, i.e., throughput and delay, impede potentials in the real-world scenarios. To achieve acceleration for VLMs, most existing methods focus on the model perspective: pruning, distillation, quantization, but completely overlook the data-perspective redundancy. To fill the overlook, this paper pioneers the severity of data redundancy, and designs one plug-and-play Turbo module guided by information degree to prune inefficient tokens from visual or textual data. In pursuit of efficiency-performance trade-offs, information degree takes two crucial factors into consideration: mutual redundancy and semantic value. Concretely, the former evaluates data duplication between sequential tokens; while the latter evaluates each token by its contribution to the overall semantics. As a result, tokens with high information degree carry less redundancy and stronger semantics. For VLMs' calculation, Turbo works as a user-friendly plug-in that sorts data referring to information degree, utilizing only top-level ones to save costs. Its advantages are multifaceted, e.g., being generally compatible to various VLMs across understanding and generation, simple use without re-training and trivial engineering efforts. On multiple VLMs benchmarks, we fully experiment to demonstrate the good acceleration of Turbo, under negligible performance drop.

  • 9 authors
·
Jul 16, 2024

LAPT: Label-driven Automated Prompt Tuning for OOD Detection with Vision-Language Models

Out-of-distribution (OOD) detection is crucial for model reliability, as it identifies samples from unknown classes and reduces errors due to unexpected inputs. Vision-Language Models (VLMs) such as CLIP are emerging as powerful tools for OOD detection by integrating multi-modal information. However, the practical application of such systems is challenged by manual prompt engineering, which demands domain expertise and is sensitive to linguistic nuances. In this paper, we introduce Label-driven Automated Prompt Tuning (LAPT), a novel approach to OOD detection that reduces the need for manual prompt engineering. We develop distribution-aware prompts with in-distribution (ID) class names and negative labels mined automatically. Training samples linked to these class labels are collected autonomously via image synthesis and retrieval methods, allowing for prompt learning without manual effort. We utilize a simple cross-entropy loss for prompt optimization, with cross-modal and cross-distribution mixing strategies to reduce image noise and explore the intermediate space between distributions, respectively. The LAPT framework operates autonomously, requiring only ID class names as input and eliminating the need for manual intervention. With extensive experiments, LAPT consistently outperforms manually crafted prompts, setting a new standard for OOD detection. Moreover, LAPT not only enhances the distinction between ID and OOD samples, but also improves the ID classification accuracy and strengthens the generalization robustness to covariate shifts, resulting in outstanding performance in challenging full-spectrum OOD detection tasks. Codes are available at https://github.com/YBZh/LAPT.

  • 4 authors
·
Jul 11, 2024

DiscoveryBench: Towards Data-Driven Discovery with Large Language Models

Can the rapid advances in code generation, function calling, and data analysis using large language models (LLMs) help automate the search and verification of hypotheses purely from a set of provided datasets? To evaluate this question, we present DiscoveryBench, the first comprehensive benchmark that formalizes the multi-step process of data-driven discovery. The benchmark is designed to systematically assess current model capabilities in discovery tasks and provide a useful resource for improving them. Our benchmark contains 264 tasks collected across 6 diverse domains, such as sociology and engineering, by manually deriving discovery workflows from published papers to approximate the real-world challenges faced by researchers, where each task is defined by a dataset, its metadata, and a discovery goal in natural language. We additionally provide 903 synthetic tasks to conduct controlled evaluations across task complexity. Furthermore, our structured formalism of data-driven discovery enables a facet-based evaluation that provides useful insights into different failure modes. We evaluate several popular LLM-based reasoning frameworks using both open and closed LLMs as baselines on DiscoveryBench and find that even the best system scores only 25%. Our benchmark, thus, illustrates the challenges in autonomous data-driven discovery and serves as a valuable resource for the community to make progress.

  • 10 authors
·
Jul 1, 2024

SWE-Dev: Evaluating and Training Autonomous Feature-Driven Software Development

Large Language Models (LLMs) have shown strong capability in diverse software engineering tasks, e.g. code completion, bug fixing, and document generation. However, feature-driven development (FDD), a highly prevalent real-world task that involves developing new functionalities for large, existing codebases, remains underexplored. We therefore introduce SWE-Dev, the first large-scale dataset (with 14,000 training and 500 test samples) designed to evaluate and train autonomous coding systems on real-world feature development tasks. To ensure verifiable and diverse training, SWE-Dev uniquely provides all instances with a runnable environment and its developer-authored executable unit tests. This collection not only provides high-quality data for Supervised Fine-Tuning (SFT), but also enables Reinforcement Learning (RL) by delivering accurate reward signals from executable unit tests. Our extensive evaluations on SWE-Dev, covering 17 chatbot LLMs, 10 reasoning models, and 10 Multi-Agent Systems (MAS), reveal that FDD is a profoundly challenging frontier for current AI (e.g., Claude-3.7-Sonnet achieves only 22.45\% Pass@3 on the hard test split). Crucially, we demonstrate that SWE-Dev serves as an effective platform for model improvement: fine-tuning on training set enabled a 7B model comparable to GPT-4o on hard split, underscoring the value of its high-quality training data. Code is available here https://github.com/justLittleWhite/SWE-Dev{https://github.com/justLittleWhite/SWE-Dev}.

  • 9 authors
·
May 22, 2025 1

SoulX-FlashTalk: Real-Time Infinite Streaming of Audio-Driven Avatars via Self-Correcting Bidirectional Distillation

Deploying massive diffusion models for real-time, infinite-duration, audio-driven avatar generation presents a significant engineering challenge, primarily due to the conflict between computational load and strict latency constraints. Existing approaches often compromise visual fidelity by enforcing strictly unidirectional attention mechanisms or reducing model capacity. To address this problem, we introduce SoulX-FlashTalk, a 14B-parameter framework optimized for high-fidelity real-time streaming. Diverging from conventional unidirectional paradigms, we use a Self-correcting Bidirectional Distillation strategy that retains bidirectional attention within video chunks. This design preserves critical spatiotemporal correlations, significantly enhancing motion coherence and visual detail. To ensure stability during infinite generation, we incorporate a Multi-step Retrospective Self-Correction Mechanism, enabling the model to autonomously recover from accumulated errors and preventing collapse. Furthermore, we engineered a full-stack inference acceleration suite incorporating hybrid sequence parallelism, Parallel VAE, and kernel-level optimizations. Extensive evaluations confirm that SoulX-FlashTalk is the first 14B-scale system to achieve a sub-second start-up latency (0.87s) while reaching a real-time throughput of 32 FPS, setting a new standard for high-fidelity interactive digital human synthesis.

  • 10 authors
·
Dec 29, 2025

Enhancing End Stage Renal Disease Outcome Prediction: A Multi-Sourced Data-Driven Approach

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

  • 2 authors
·
Oct 1, 2024

FailureSensorIQ: A Multi-Choice QA Dataset for Understanding Sensor Relationships and Failure Modes

We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.

  • 6 authors
·
Jun 3, 2025 1

DrivAerNet: A Parametric Car Dataset for Data-Driven Aerodynamic Design and Graph-Based Drag Prediction

This study introduces DrivAerNet, a large-scale high-fidelity CFD dataset of 3D industry-standard car shapes, and RegDGCNN, a dynamic graph convolutional neural network model, both aimed at aerodynamic car design through machine learning. DrivAerNet, with its 4000 detailed 3D car meshes using 0.5 million surface mesh faces and comprehensive aerodynamic performance data comprising of full 3D pressure, velocity fields, and wall-shear stresses, addresses the critical need for extensive datasets to train deep learning models in engineering applications. It is 60\% larger than the previously available largest public dataset of cars, and is the only open-source dataset that also models wheels and underbody. RegDGCNN leverages this large-scale dataset to provide high-precision drag estimates directly from 3D meshes, bypassing traditional limitations such as the need for 2D image rendering or Signed Distance Fields (SDF). By enabling fast drag estimation in seconds, RegDGCNN facilitates rapid aerodynamic assessments, offering a substantial leap towards integrating data-driven methods in automotive design. Together, DrivAerNet and RegDGCNN promise to accelerate the car design process and contribute to the development of more efficient vehicles. To lay the groundwork for future innovations in the field, the dataset and code used in our study are publicly accessible at https://github.com/Mohamedelrefaie/DrivAerNet

  • 3 authors
·
Mar 12, 2024

Large Language Models for Automated Data Science: Introducing CAAFE for Context-Aware Automated Feature Engineering

As the field of automated machine learning (AutoML) advances, it becomes increasingly important to incorporate domain knowledge into these systems. We present an approach for doing so by harnessing the power of large language models (LLMs). Specifically, we introduce Context-Aware Automated Feature Engineering (CAAFE), a feature engineering method for tabular datasets that utilizes an LLM to iteratively generate additional semantically meaningful features for tabular datasets based on the description of the dataset. The method produces both Python code for creating new features and explanations for the utility of the generated features. Despite being methodologically simple, CAAFE improves performance on 11 out of 14 datasets -- boosting mean ROC AUC performance from 0.798 to 0.822 across all dataset - similar to the improvement achieved by using a random forest instead of logistic regression on our datasets. Furthermore, CAAFE is interpretable by providing a textual explanation for each generated feature. CAAFE paves the way for more extensive semi-automation in data science tasks and emphasizes the significance of context-aware solutions that can extend the scope of AutoML systems to semantic AutoML. We release our https://github.com/automl/CAAFE{code}, a simple https://colab.research.google.com/drive/1mCA8xOAJZ4MaB_alZvyARTMjhl6RZf0a{demo} and a https://pypi.org/project/caafe/{python package}.

  • 3 authors
·
May 5, 2023

CoEvo: Continual Evolution of Symbolic Solutions Using Large Language Models

Large Language Models (LLMs) have emerged as transformative tools in artificial intelligence, capable of processing and understanding extensive human knowledge to enhance problem-solving across various domains. This paper explores the potential of LLMs to drive the discovery of symbolic solutions within scientific and engineering disciplines, where such solutions are crucial for advancing theoretical and practical applications. We propose a novel framework that utilizes LLMs in an evolutionary search methodology, augmented by a dynamic knowledge library that integrates and refines insights in an open-ended manner. This approach aims to tackle the dual challenges of efficiently navigating complex symbolic representation spaces and leveraging both existing and newly generated knowledge to foster open-ended innovation. By enabling LLMs to interact with and expand upon a knowledge library, we facilitate the continuous generation of novel solutions in diverse forms such as language, code, and mathematical expressions. Our experimental results demonstrate that this method not only enhances the efficiency of searching for symbolic solutions but also supports the ongoing discovery process, akin to human scientific endeavors. This study represents a first effort in conceptualizing the search for symbolic solutions as a lifelong, iterative process, marking a significant step towards harnessing AI in the perpetual pursuit of scientific and engineering breakthroughs. We have open-sourced our code and data, please visit https://github.com/pgg3/CoEvo for more information.

  • 3 authors
·
Dec 25, 2024