Explainable artificial intelligence (XAI) approaches have been increasingly applied in drug discovery to learn molecular representations and identify substructures driving property predictions. However, building end-to-end explainable models for structure-activity relationship (SAR) modeling for compound property prediction faces many challenges, such as the limited number of compound-protein interaction activity data for specific protein targets, and plenty of subtle changes in molecular configuration sites significantly affecting molecular properties. We exploit pairs of molecules with activity cliffs that share scaffolds but differ at substituent sites, characterized by large potency differences for specific protein targets. We propose a framework by implementing graph neural networks (GNNs) to leverage property and structure information from activity cliff pairs to predict compound-protein affinity (i.e., half maximal inhibitory concentration, IC50). To enhance model performance and explainability, we train GNNs with structure-aware loss functions using group lasso and sparse group lasso regularizations, which prune and highlight molecular subgraphs relevant to activity differences. We applied this framework to activity cliff data of molecules targeting three proto-oncogene tyrosine-protein kinase Src proteins (PDB IDs: 1O42, 2H8H, 4MXO). Our approach improved property prediction by integrating common and uncommon node information with sparse group lasso, as reflected in reduced root mean squared error (RMSE) and improved Pearson's correlation coefficient (PCC). Applying regularizations also enhances feature attribution for GNN by boosting graph-level global direction scores and improving atom-level coloring accuracy. These advances strengthen model interpretability in drug discovery pipelines, particularly for identifying critical molecular substructures in lead optimization.

This paper reviews the current progress in applying machine learning (ML) tools to solve NP-hard combinatorial optimization problems, with a focus on routing problems such as the traveling salesman problem (TSP) and the vehicle routing problem (VRP). Due to the inherent complexity of these problems, exact algorithms often require excessive computational time to find optimal solutions, while heuristics can only provide approximate solutions without guaranteeing optimality. With the recent success of machine learning models, there is a growing trend in proposing and implementing diverse ML techniques to enhance the resolution of these challenging routing problems. We propose a taxonomy categorizing ML-based routing methods into construction-based and improvement-based approaches, highlighting their applicability to various problem characteristics. This review aims to integrate traditional OR methods with state-of-the-art ML techniques, providing a structured framework to guide future research and address emerging VRP variants.

Recent advances in reasoning language models -- particularly those that use long, latent chains of thought -- have demonstrated remarkable capabilities in complex, agentic tasks. However, as these models operate over increasingly extended time horizons, their internal progress becomes opaque to users, complicating expectation management and real-time oversight. In this work, we investigate whether real-time progress prediction is feasible. We discretize progress and train a linear probe to classify reasoning states. We then introduce a two-stage fine-tuning approach that enables reasoning models to generate progress estimates (0$\rightarrow$100\%) during inference. Our best fine-tuned model achieves an average error of 10\% for sequences less than 16,000 tokens, offering a practical mechanism for monitoring and interpreting model reasoning in real time.

Deepfake (DF) attacks pose a growing threat as generative models become increasingly advanced. However, our study reveals that existing DF datasets fail to deceive human perception, unlike real DF attacks that influence public discourse. It highlights the need for more realistic DF attack vectors. We introduce PhonemeFake (PF), a DF attack that manipulates critical speech segments using language reasoning, significantly reducing human perception by up to 42% and benchmark accuracies by up to 94%. We release an easy-to-use PF dataset on HuggingFace and open-source bilevel DF segment detection model that adaptively prioritizes compute on manipulated regions. Our extensive experiments across three known DF datasets reveal that our detection model reduces EER by 91% while achieving up to 90% speed-up, with minimal compute overhead and precise localization beyond existing models as a scalable solution.

Large Language Models (LLMs), particularly slow-thinking models, often exhibit severe hallucination, outputting incorrect content due to an inability to accurately recognize knowledge boundaries during reasoning. While Reinforcement Learning (RL) can enhance complex reasoning abilities, its outcome-oriented reward mechanism often lacks factual supervision over the thinking process, further exacerbating the hallucination problem. To address the high hallucination in slow-thinking models, we propose Knowledge-enhanced RL, KnowRL. KnowRL guides models to perform fact-based slow thinking by integrating a factuality reward, based on knowledge verification, into the RL training process, helping them recognize their knowledge boundaries. KnowRL guides models to perform fact-based slow thinking by integrating a factuality reward, based on knowledge verification, into the RL training process, helping them recognize their knowledge boundaries. This targeted factual input during RL training enables the model to learn and internalize fact-based reasoning strategies. By directly rewarding adherence to facts within the reasoning steps, KnowRL fosters a more reliable thinking process. Experimental results on three hallucination evaluation datasets and two reasoning evaluation datasets demonstrate that KnowRL effectively mitigates hallucinations in slow-thinking models while maintaining their original strong reasoning capabilities. Our code is available at https://github.com/zjunlp/KnowRL.

Large Language Model (LLM)-based agents are increasingly employed to automate complex software engineering tasks, such as program repair and issue resolution. These agents operate by autonomously generating natural language thoughts, invoking external tools, and iteratively refining their solutions. Despite their widespread adoption, the internal decision-making processes of these agents remain largely unexplored, limiting our understanding of their operational dynamics and failure modes. In this paper, we present a large-scale empirical study of the thought-action-result trajectories of three state-of-the-art LLM-based agents: RepairAgent, AutoCodeRover, and OpenHands. We unify their interaction logs into a common format, capturing 120 trajectories and 2,822 LLM interactions focused on program repair and issue resolution. Our study combines quantitative analyses of structural properties, action patterns, and token usage with qualitative assessments of reasoning coherence and feedback integration. We identify key trajectory characteristics, such as iteration counts and token consumption, recurring action sequences, and the semantic coherence of thoughts, actions, and their results. Our findings reveal behavioral motifs and anti-patterns that distinguish successful from failed executions, providing actionable insights for improving agent design, including prompting strategies, failure diagnosis, and anti-pattern detection. We release our dataset and annotation framework to support further research on transparent and robust autonomous software engineering agents.

Large Language Models (LLMs) are widely used in real-time voice chat applications, typically in combination with text-to-speech (TTS) systems to generate audio responses. However, their large size often leads to noticeable latency between the end of user input and the start of audio output, resulting in suboptimal user experiences. This latency is particularly evident when LLMs are deployed as single-user voice assistants on consumer-grade hardware with limited computing capacity. We discovered that this latency is primarily dominated by the time it takes for the LLMs to generate the first sentence, which is required as input by the TTS systems that synthesize audio responses on a sentence-by-sentence basis. To address this bottleneck, we propose Predictive Generation (PredGen), a novel framework that mitigates-or even eliminates-this delay through speculative decoding at input time. PredGen generates candidate responses while the user is still speaking, enabling the system to begin TTS processing with minimal delay. Simulated experiments on the Lmsys and MT-Bench datasets show that the proposed method can effectively reduce the latency by around 2x across a wide range of use cases, while incurring only minimal additional computation cost at input time-computation that would otherwise go unused.

Large Language Model (LLM) agents have shown great potential in addressing real-world data science problems. LLM-driven data science agents promise to automate the entire machine learning pipeline, yet their real-world effectiveness remains limited. Existing frameworks depend on rigid, pre-defined workflows and inflexible coding strategies; consequently, they excel only on relatively simple, classical problems and fail to capture the empirical expertise that human practitioners bring to complex, innovative tasks. In this work, we introduce AutoMind, an adaptive, knowledgeable LLM-agent framework that overcomes these deficiencies through three key advances: (1) a curated expert knowledge base that grounds the agent in domain expert knowledge, (2) an agentic knowledgeable tree search algorithm that strategically explores possible solutions, and (3) a self-adaptive coding strategy that dynamically tailors code generation to task complexity. Evaluations on two automated data science benchmarks demonstrate that AutoMind delivers superior performance versus state-of-the-art baselines. Additional analyses confirm favorable effectiveness, efficiency, and qualitative solution quality, highlighting AutoMind as an efficient and robust step toward fully automated data science. Code is at https://github.com/innovatingAI/AutoMind.

Constructing real-world data-to-insight pipelines often involves data extraction from data lakes, data integration across heterogeneous data sources, and diverse operations from data cleaning to analysis. The design and implementation of data science pipelines require domain knowledge, technical expertise, and even project-specific insights. AI systems have shown remarkable reasoning, coding, and understanding capabilities. However, it remains unclear to what extent these capabilities translate into successful design and execution of such complex pipelines. We introduce KRAMABENCH: a benchmark composed of 104 manually-curated real-world data science pipelines spanning 1700 data files from 24 data sources in 6 different domains. We show that these pipelines test the end-to-end capabilities of AI systems on data processing, requiring data discovery, wrangling and cleaning, efficient processing, statistical reasoning, and orchestrating data processing steps given a high-level task. Our evaluation tests 5 general models and 3 code generation models using our reference framework, DS-GURU, which instructs the AI model to decompose a question into a sequence of subtasks, reason through each step, and synthesize Python code that implements the proposed design. Our results on KRAMABENCH show that, although the models are sufficiently capable of solving well-specified data science code generation tasks, when extensive data processing and domain knowledge are required to construct real-world data science pipelines, existing out-of-box models fall short. Progress on KramaBench represents crucial steps towards developing autonomous data science agents for real-world applications. Our code, reference framework, and data are available at https://github.com/mitdbg/KramaBench.

AI agents have significant potential to reshape cybersecurity, making a thorough assessment of their capabilities critical. However, existing evaluations fall short, because they are based on small-scale benchmarks and only measure static outcomes, failing to capture the full, dynamic range of real-world security challenges. To address these limitations, we introduce CyberGym, a large-scale benchmark featuring 1,507 real-world vulnerabilities across 188 software projects. Adjustable to different vulnerability analysis settings, CyberGym primarily tasks agents with generating a proof-of-concept test that reproduces a vulnerability, given only its text description and the corresponding codebase. Our extensive evaluation highlights that CyberGym effectively differentiates agents' and models' cybersecurity capabilities. Even the top-performing combinations only achieve a ~20% success rate, demonstrating the overall difficulty of CyberGym. Beyond static benchmarking, we show that CyberGym leads to the discovery of 35 zero-day vulnerabilities and 17 historically incomplete patches. These results underscore that CyberGym is not only a robust benchmark for measuring AI's progress in cybersecurity but also a platform for creating direct, real-world security impact.