GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models consistently outperform random baselines and can exploit local sequence signals such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

Asymmetric Actor-Critic for Multi-turn LLM Agents

Large language models (LLMs) exhibit strong reasoning and conversational abilities, but ensuring reliable behavior in multi-turn interactions remains challenging. In many real-world applications, agents must succeed in one-shot settings where retries are impossible. Existing approaches either rely on reflection or post-hoc evaluation, which require additional attempts, or assume fully trainable models that cannot leverage proprietary LLMs. We propose an asymmetric actor-critic framework for reliable conversational agents. A powerful proprietary LLM acts as the actor, while a smaller open-source critic provides runtime supervision, monitoring the actor's actions and intervening within the same interaction trajectory. Unlike training-based actor-critic methods, our framework supervises a fixed actor operating in open-ended conversational environments. The design leverages a generation-verification asymmetry: while high-quality generation requires large models, effective oversight can often be achieved by smaller ones. We further introduce a data generation pipeline that produces supervision signals for critic fine-tuning without modifying the actor. Experiments on $τ$-bench and UserBench show that our approach significantly improves reliability and task success over strong single-agent baselines. Moreover, lightweight open-source critics rival or surpass larger proprietary models in the critic role, and critic fine-tuning yields additional gains over several state-of-the-art methods.

Beyond Where to Look: Trajectory-Guided Reinforcement Learning for Multimodal RLVR

Recent advances in Reinforcement Learning with Verifiable Rewards (RLVR) for multimodal large language models (MLLMs) have mainly focused on improving final answer correctness and strengthening visual grounding. However, a critical bottleneck remains: although models can attend to relevant visual regions, they often fail to effectively incorporate visual evidence into subsequent reasoning, leading to reasoning chains that are weakly grounded in visual facts. To address this issue, we propose Trajectory-Guided Reinforcement Learning (TGRL), which guides the policy model to integrate visual evidence into fine-grained reasoning processes using expert reasoning trajectories from stronger models. We further introduce token-level reweighting and trajectory filtering to ensure stable and effective policy optimization. Extensive experiments on multiple multimodal reasoning benchmarks demonstrate that TGRL consistently improves reasoning performance and effectively bridges the gap between visual perception and logical reasoning.

Bridging Perception and Reasoning: Token Reweighting for RLVR in Multimodal LLMs

Extending Reinforcement Learning with Verifiable Rewards (RLVR) to multimodal large language models (MLLMs) faces a fundamental challenge: their responses inherently interleave perception-related tokens, which ground visual content, with reasoning-related tokens, which construct reasoning chains. These token types instantiate distinct yet interdependent capacities -- visual grounding and symbolic reasoning -- making isolated optimization insufficient. Through token-level empirical analysis, we demonstrate that optimizing either perception- or reasoning-only tokens consistently underperforms full optimization, underscoring their inherent coupling. To address this, we propose a plug-and-play Token-Reweighting (ToR) strategy that explicitly models this interdependence by identifying critical tokens of both types and dynamically reweighting them during RLVR training. Applied on top of existing methods (e.g., GRPO and DAPO), ToR delivers consistent performance gains across multiple multi-modal reasoning benchmarks, achieving state-of-the-art performance with both accurate visual grounding and coherent reasoning.

Sparse but Critical: A Token-Level Analysis of Distributional Shifts in RLVR Fine-Tuning of LLMs

Reinforcement learning with verifiable rewards (RLVR) has significantly improved reasoning in large language models (LLMs), yet the token-level mechanisms underlying these improvements remain unclear. We present a systematic empirical study of RLVR's distributional effects organized around three main analyses: (1) token-level characterization of distributional shifts between base and RL models, (2) the impact of token-level distributional shifts on sequence-level reasoning performance through cross-sampling interventions, and (3) fine-grained mechanics of these shifts at the token level. We find that RL fine-tuning induces highly sparse and targeted changes, with only a small fraction of token distributions exhibiting meaningful divergence between the base and RL policies. We further characterize the structure and evolution of these shifts through analyses of token entropy, positional concentration, and reallocation of probability mass. To assess the functional importance of these sparse changes, we conduct cross-sampling experiments that selectively swap token choices between the base and RL models with varying intervention budgets. We show that inserting only a small fraction of RL-sampled tokens into base generations progressively recovers RL performance gains, while injecting a similarly small number of base token choices into otherwise RL-generated sequences collapses performance to base levels, isolating a small set of token-level decisions directly responsible for RLVR's performance gains. Finally, we explore divergence-weighted variants of the advantage signal as a diagnostic intervention, finding that they can yield improvements over baselines. Together, our results shed light on the distributional changes induced by RLVR and provide a fine-grained, token-level lens for understanding RLVR fine-tuning as a targeted refinement process.

Attention in Space: Functional Roles of VLM Heads for Spatial Reasoning

Despite remarkable advances in large Vision-Language Models (VLMs), spatial reasoning remains a persistent challenge. In this work, we investigate how attention heads within VLMs contribute to spatial reasoning by analyzing their functional roles through a mechanistic interpretability lens. We introduce CogVSR, a dataset that decomposes complex spatial reasoning questions into step-by-step subquestions designed to simulate human-like reasoning via a chain-of-thought paradigm, with each subquestion linked to specific cognitive functions such as spatial perception or relational reasoning. Building on CogVSR, we develop a probing framework to identify and characterize attention heads specialized for these functions. Our analysis across diverse VLM families reveals that these functional heads are universally sparse, vary in number and distribution across functions. Notably, spatially specialized heads are fewer than those for other cognitive functions, highlighting their scarcity. We propose methods to activate latent spatial heads, improving spatial understanding. Intervention experiments further demonstrate their critical role in spatial reasoning: removing functional heads leads to performance degradation, while emphasizing them enhances accuracy. This study provides new interpretability driven insights into how VLMs attend to space and paves the way for enhancing complex spatial reasoning in multimodal models.

FIPO: Eliciting Deep Reasoning with Future-KL Influenced Policy Optimization

We present Future-KL Influenced Policy Optimization (FIPO), a reinforcement learning algorithm designed to overcome reasoning bottlenecks in large language models. While GRPO style training scales effectively, it typically relies on outcome-based rewards (ORM) that distribute a global advantage uniformly across every token in a trajectory. We argue that this coarse-grained credit assignment imposes a performance ceiling by failing to distinguish critical logical pivots from trivial tokens. FIPO addresses this by incorporating discounted future-KL divergence into the policy update, creating a dense advantage formulation that re-weights tokens based on their influence on subsequent trajectory behavior. Empirically, FIPO enables models to break through the length stagnation seen in standard baselines. Evaluated on Qwen2.5-32B, FIPO extends the average chain-of-thought length from roughly 4,000 to over 10,000 tokens and increases AIME 2024 Pass@1 accuracy from 50.0% to a peak of 58.0% (converging at approximately 56.0\%). This outperforms both DeepSeek-R1-Zero-Math-32B (around 47.0%) and o1-mini (approximately 56.0%). Our results suggest that establishing dense advantage formulations is a vital path for evolving ORM-based algorithms to unlock the full reasoning potential of base models. We open-source our training system, built on the verl framework.

CRAFT: Aligning Diffusion Models with Fine-Tuning Is Easier Than You Think

Aligning Diffusion models has achieved remarkable breakthroughs in generating high-quality, human preference-aligned images. Existing techniques, such as supervised fine-tuning (SFT) and DPO-style preference optimization, have become principled tools for fine-tuning diffusion models. However, SFT relies on high-quality images that are costly to obtain, while DPO-style methods depend on large-scale preference datasets, which are often inconsistent in quality. Beyond data dependency, these methods are further constrained by computational inefficiency. To address these two challenges, we propose Composite Reward Assisted Fine-Tuning (CRAFT), a lightweight yet powerful fine-tuning paradigm that requires significantly reduced training data while maintaining computational efficiency. It first leverages a Composite Reward Filtering (CRF) technique to construct a high-quality and consistent training dataset and then perform an enhanced variant of SFT. We also theoretically prove that CRAFT actually optimizes the lower bound of group-based reinforcement learning, establishing a principled connection between SFT with selected data and reinforcement learning. Our extensive empirical results demonstrate that CRAFT with only 100 samples can easily outperform recent SOTA preference optimization methods with thousands of preference-paired samples. Moreover, CRAFT can even achieve 11-220$\times$ faster convergences than the baseline preference optimization methods, highlighting its extremely high efficiency.

GroupGuard: A Framework for Modeling and Defending Collusive Attacks in Multi-Agent Systems

While large language model-based agents demonstrate great potential in collaborative tasks, their interactivity also introduces security vulnerabilities. In this paper, we propose and model group collusive attacks, a highly destructive threat in which multiple agents coordinate via sociological strategies to mislead the system. To address this challenge, we introduce GroupGuard, a training-free defense framework that employs a multi-layered defense strategy, including continuous graph-based monitoring, active honeypot inducement, and structural pruning, to identify and isolate collusive agents. Experimental results across five datasets and four topologies demonstrate that group collusive attacks increase the attack success rate by up to 15\% compared to individual attacks. GroupGuard consistently achieves high detection accuracy (up to 88\%) and effectively restores collaborative performance, providing a robust solution for securing multi-agent systems.

ToolTree: Efficient LLM Agent Tool Planning via Dual-Feedback Monte Carlo Tree Search and Bidirectional Pruning

Large Language Model (LLM) agents are increasingly applied to complex, multi-step tasks that require interaction with diverse external tools across various domains. However, current LLM agent tool planning methods typically rely on greedy, reactive tool selection strategies that lack foresight and fail to account for inter-tool dependencies. In this paper, we present ToolTree, a novel Monte Carlo tree search-inspired planning paradigm for tool planning. ToolTree explores possible tool usage trajectories using a dual-stage LLM evaluation and bidirectional pruning mechanism that enables the agent to make informed, adaptive decisions over extended tool-use sequences while pruning less promising branches before and after the tool execution. Empirical evaluations across both open-set and closed-set tool planning tasks on 4 benchmarks demonstrate that ToolTree consistently improves performance while keeping the highest efficiency, achieving an average gain of around 10\% compared to the state-of-the-art planning paradigm.