A Versatile AI Agent for Rare Disease Diagnosis and Risk Gene Prioritization

Accurate and timely diagnosis is essential for effective treatment, particularly in the context of rare diseases. However, current diagnostic workflows often lead to prolonged assessment times and low accuracy. To address these limitations, we introduce Hygieia, a multi-modal AI agent system designed to support precision disease diagnosis by integrating diverse data sources, including phenotypic features, genetic profiles, and clinical records. Hygieia features a router-based and knowledge-enhanced framework that mitigates hallucination and tailors diagnostic strategies to different disease categories. Notably, it prioritizes risk-related genomic factors for rare diseases and provides confidence scores to assist clinical decision-making. We conducted a comprehensive evaluation demonstrating that Hygieia achieves state-of-the-art performance across multiple diagnostic benchmarks. In collaboration with clinical experts from Yale School of Medicine and Duke-NUS Medical School, we further validated its practical utility by showing (1) Hygieia's superior diagnostic performance compared to physicians with an improvement from 12%-60% and (2) its effectiveness in assisting clinicians with medical records for handling real-world cases. Our findings indicate that Hygieia not only enhances diagnostic accuracy and interpretability but also significantly reduces clinician workload, highlighting its potential as a valuable tool in clinical decision support systems.

BenchGuard: Who Guards the Benchmarks? Automated Auditing of LLM Agent Benchmarks

As benchmarks grow in complexity, many apparent agent failures are not failures of the agent at all - they are failures of the benchmark itself: broken specifications, implicit assumptions, and rigid evaluation scripts that penalize valid alternative approaches. We propose employing frontier LLMs as systematic auditors of evaluation infrastructure, and realize this vision through BenchGuard, the first automated auditing framework for task-oriented, execution-based agent benchmarks. BenchGuard cross-verifies all benchmark artifacts via structured LLM protocols, optionally incorporating agent solutions or execution traces as additional diagnostic evidence. Deployed on two prominent scientific benchmarks, BenchGuard identified 12 author-confirmed issues in ScienceAgentBench - including fatal errors rendering tasks unsolvable - and exactly matched 83.3% of expert-identified issues on the BIXBench Verified-50 subset, catching defects that prior human review missed entirely. A full audit of 50 complex bioinformatics tasks costs under USD 15, making automated benchmark auditing a practical and valuable complement to human review. These findings point toward AI-assisted benchmark development, where frontier models serve not only as subjects of evaluation but as active participants in validating the evaluation infrastructure itself.

MOSS-VoiceGenerator: Create Realistic Voices with Natural Language Descriptions

Voice design from natural language aims to generate speaker timbres directly from free-form textual descriptions, allowing users to create voices tailored to specific roles, personalities, and emotions. Such controllable voice creation benefits a wide range of downstream applications-including storytelling, game dubbing, role-play agents, and conversational assistants, making it a significant task for modern Text-to-Speech models. However, existing models are largely trained on carefully recorded studio data, which produces speech that is clean and well-articulated, yet lacks the lived-in qualities of real human voices. To address these limitations, we present MOSS-VoiceGenerator, an open-source instruction-driven voice generation model that creates new timbres directly from natural language prompts. Motivated by the hypothesis that exposure to real-world acoustic variation produces more perceptually natural voices, we train on large-scale expressive speech data sourced from cinematic content. Subjective preference studies demonstrate its superiority in overall performance, instruction-following, and naturalness compared to other voice design models.

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.

Incorporating contextual information into KGWAS for interpretable GWAS discovery

Genome-Wide Association Studies (GWAS) identify associations between genetic variants and disease; however, moving beyond associations to causal mechanisms is critical for therapeutic target prioritization. The recently proposed Knowledge Graph GWAS (KGWAS) framework addresses this challenge by linking genetic variants to downstream gene-gene interactions via a knowledge graph (KG), thereby improving detection power and providing mechanistic insights. However, the original KGWAS implementation relies on a large general-purpose KG, which can introduce spurious correlations. We hypothesize that cell-type specific KGs from disease-relevant cell types will better support disease mechanism discovery. Here, we show that the general-purpose KG in KGWAS can be substantially pruned with no loss of statistical power on downstream tasks, and that performance further improves by incorporating gene-gene relationships derived from perturb-seq data. Importantly, using a sparse, context-specific KG from direct perturb-seq evidence yields more consistent and biologically robust disease-critical networks.

On the Direction of RLVR Updates for LLM Reasoning: Identification and Exploitation

Reinforcement learning with verifiable rewards (RLVR) has substantially improved the reasoning capabilities of large language models. While existing analyses identify that RLVR-induced changes are sparse, they primarily focus on the \textbf{magnitude} of these updates, largely overlooking their \textbf{direction}. In this work, we argue that the direction of updates is a more critical lens for understanding RLVR's effects, which can be captured by the signed, token-level log probability difference $Δ\log p$ between the base and final RLVR models. Through statistical analysis and token-replacement interventions, we demonstrate that $Δ\log p$ more effectively identifies sparse, yet reasoning-critical updates than magnitude-based metrics (\eg divergence or entropy). Building on this insight, we propose two practical applications: (1) a \textit{test-time extrapolation} method that amplifies the policy along the learned $Δ\log p$ direction to improve reasoning accuracy without further training; (2) a \textit{training-time reweighting} method that focuses learning on low-probability (corresponding to higher $Δ\log p$) tokens, which improves reasoning performance across models and benchmarks. Our work establishes the direction of change as a key principle for analyzing and improving RLVR.

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.

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.

MOSS-TTSD: Text to Spoken Dialogue Generation

Spoken dialogue generation is crucial for applications like podcasts, dynamic commentary, and entertainment content, but poses significant challenges compared to single-utterance text-to-speech (TTS). Key requirements include accurate turn-taking, cross-turn acoustic consistency, and long-form stability, which current models often fail to address due to a lack of dialogue context modeling. To bridge this gap, we present MOSS-TTSD, a spoken dialogue synthesis model designed for expressive, multi-party conversational speech across multiple languages. With enhanced long-context modeling, MOSS-TTSD generates long-form spoken conversations from dialogue scripts with explicit speaker tags, supporting up to 60 minutes of single-pass synthesis, multi-party dialogue with up to 5 speakers, and zero-shot voice cloning from a short reference audio clip. The model supports various mainstream languages, including English and Chinese, and is adapted to several long-form scenarios. Additionally, to address limitations of existing evaluation methods, we propose TTSD-eval, an objective evaluation framework based on forced alignment that measures speaker attribution accuracy and speaker similarity without relying on speaker diarization tools. Both objective and subjective evaluation results show that MOSS-TTSD surpasses strong open-source and proprietary baselines in dialogue synthesis.