Predicting interactions between biochemical entities is a core challenge in drug discovery and systems biology, often hindered by limited data and poor generalization to unseen entities. Traditional discriminative models frequently underperform in such settings. We propose BioCG (Biochemical Constrained Generation), a novel framework that reformulates interaction prediction as a constrained sequence generation task. BioCG encodes target entities as unique discrete sequences via Iterative Residual Vector Quantization (I-RVQ) and trains a generative model to produce the sequence of an interacting partner given a query entity. A trie-guided constrained decoding mechanism, built from a catalog of valid target sequences, concentrates the model's learning on the critical distinctions between valid biochemical options, ensuring all outputs correspond to an entity within the pre-defined target catalog. An information-weighted training objective further focuses learning on the most critical decision points. BioCG achieves state-of-the-art (SOTA) performance across diverse tasks, Drug-Target Interaction (DTI), Drug-Drug Interaction (DDI), and Enzyme-Reaction Prediction, especially in data-scarce and cold-start conditions.

We introduce MLE-Dojo, a Gym-style framework for systematically reinforcement learning, evaluating, and improving autonomous large language model (LLM) agents in iterative machine learning engineering (MLE) workflows. Unlike existing benchmarks that primarily rely on static datasets or single-attempt evaluations, MLE-Dojoprovides an interactive environment enabling agents to iteratively experiment, debug, and refine solutions through structured feedback loops. Built upon 200+ real-world Kaggle challenges, MLE-Dojocovers diverse, open-ended MLE tasks carefully curated to reflect realistic engineering scenarios such as data processing, architecture search, hyperparameter tuning, and code debugging. Its fully executable environment supports comprehensive agent training via both supervised fine-tuning and reinforcement learning, facilitating iterative experimentation, realistic data sampling, and real-time outcome verification. Extensive evaluations of eight frontier LLMs reveal that while current models achieve meaningful iterative improvements, they still exhibit significant limitations in autonomously generating long-horizon solutions and efficiently resolving complex errors.

Visual reasoning in multimodal large language models (MLLMs) has primarily been studied in static, fully observable settings, limiting their effectiveness in real-world environments where information is often incomplete due to occlusion or limited field of view. Humans, in contrast, actively explore and interact with their environment--moving, examining, and manipulating objects--to gather information through a closed-loop process integrating perception, reasoning, and action. Inspired by this human capability, we introduce the Active Visual Reasoning (AVR) task, extending visual reasoning to partially observable, interactive environments. AVR necessitates agents to: (1) actively acquire information via sequential physical actions, (2) integrate observations across multiple steps for coherent reasoning, and (3) dynamically adjust decisions based on evolving visual feedback. To rigorously evaluate AVR, we introduce CLEVR-AVR, a simulation benchmark featuring multi-round interactive environments designed to assess both reasoning correctness and information-gathering efficiency. We present AVR-152k, a large-scale dataset offers rich Chain-of-Thought (CoT) annotations detailing iterative reasoning for uncertainty identification, action-conditioned information gain prediction, and information-maximizing action selection, crucial for training agents in a higher-order Markov Decision Process. Building on this, we develop PhysVLM-AVR, an MLLM achieving state-of-the-art performance on CLEVR-AVR, embodied reasoning (OpenEQA, RoboVQA), and passive visual reasoning (GeoMath, Geometry30K). Our analysis also reveals that current embodied MLLMs, despite detecting information incompleteness, struggle to actively acquire and integrate new information through interaction, highlighting a fundamental gap in active reasoning capabilities.

Large Language Models (LLMs), such as OpenAI's o1 and DeepSeek's R1, excel at advanced reasoning tasks like math and coding via Reinforcement Learning with Verifiable Rewards (RLVR), but still struggle with puzzles solvable by humans without domain knowledge. We introduce ENIGMATA, the first comprehensive suite tailored for improving LLMs with puzzle reasoning skills. It includes 36 tasks across 7 categories, each with: 1) a generator that produces unlimited examples with controllable difficulty, and 2) a rule-based verifier for automatic evaluation. This generator-verifier design supports scalable, multi-task RL training, fine-grained analysis, and seamless RLVR integration. We further propose ENIGMATA-Eval, a rigorous benchmark, and develop optimized multi-task RLVR strategies.

Recent advances in large language models (LLMs) have enabled automated dataset labeling with minimal human supervision. While majority voting across multiple LLMs can improve label reliability by mitigating individual model biases, it incurs high computational costs due to repeated querying. In this work, we propose a novel online framework, Cost-aware Majority Voting (CaMVo), for efficient and accurate LLM-based dataset annotation. CaMVo adaptively selects a subset of LLMs for each data instance based on contextual embeddings, balancing confidence and cost without requiring pre-training or ground-truth labels. Leveraging a LinUCB-based selection mechanism and a Bayesian estimator over confidence scores, CaMVo estimates a lower bound on labeling accuracy for each LLM and aggregates responses through weighted majority voting. Our empirical evaluation on the MMLU and IMDBMovie Review datasets demonstrates that CaMVo achieves comparable or superior accuracy to full majority voting while significantly reducing labeling costs. This establishes CaMVo as a practical and robust solution for cost-efficient annotation in dynamic labeling environments.

Large Language Models (LLMs) are increasingly integrated into the software engineering ecosystem. Their test-time compute (TTC) reasoning capabilities show significant potential for understanding program logic and semantics beyond mere token recognition. However, current benchmarks for code reasoning lack a formal, program-centric deductive framework to ensure sound evaluation, and are incapable of assessing whether models genuinely reason about program semantics or merely exploit superficial associations between natural language and code tokens. To bridge this gap, we introduce TF-Bench, a benchmark designed to evaluate LLM reasoning based on type inference in System F, a task we refer to as program semantics reasoning. By employing verified transformations to remove semantically irrelevant natural language, we construct TF-Benchpure, a purely semanticsdriven variant of TF-Bench. Our analysis reveals substantial limitations in state-of-the-art LLMs, with the best-performing LLM (Claude-3.7-sonnet)

Object binding, the brain's ability to bind the many features that collectively represent an object into a coherent whole, is central to human cognition. It groups low-level perceptual features into high-level object representations, stores those objects efficiently and compositionally in memory, and supports human reasoning about individual object instances. While prior work often imposes object-centric attention (e.g., Slot Attention) explicitly to probe these benefits, it remains unclear whether this ability naturally emerges in pre-trained Vision Transformers (ViTs). Intuitively, they could: recognizing which patches belong to the same object should be useful for downstream prediction and thus guide attention. Motivated by the quadratic nature of self-attention, we hypothesize that ViTs represent whether two patches belong to the same object, a property we term IsSameObject.

Large language models (LLMs) have achieved unprecedented performance by leveraging vast pretraining corpora, yet their performance remains suboptimal in knowledge-intensive domains such as medicine and scientific research, where high factual precision is required. While synthetic data provides a promising avenue for augmenting domain knowledge, existing methods frequently generate redundant samples that do not align with the model's true knowledge gaps. To overcome this limitation, we propose a novel Structural Entropy-guided Knowledge Navigator (SENATOR) framework that addresses the intrinsic knowledge deficiencies of LLMs. Our approach employs the Structure Entropy (SE) metric to quantify uncertainty along knowledge graph paths and leverages Monte Carlo Tree Search (MCTS) to selectively explore regions where the model lacks domain-specific knowledge. Guided by these insights, the framework generates targeted synthetic data for supervised fine-tuning, enabling continuous self-improvement. Experimental results on LLaMA-3 and Qwen2 across multiple domain-specific benchmarks show that SENATOR effectively detects and repairs knowledge deficiencies, achieving notable performance improvements.

However, isolating these visual features is challenging due to the absence of annotated datasets.

Diffusion-based virtual staining methods of histopathology images have demonstrated outstanding potential for stain normalization and cross-dye staining (e.g., hematoxylin-eosin to immunohistochemistry). However, achieving pathology-correct cross-dye virtual staining with versatile tone controls poses significantchallenges due to the difficulty of decoupling the given pathology and tone con-ditions.