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Pengfei Liu

Publications and source records attributed to Pengfei Liu.

At least 55 records · Page 3Linked to original sources
arXiv2026

RareCollab: an LLM-powered framework for multimodal reasoning in Mendelian disease diagnosis

Rare disease diagnosis increasingly relies on integrating genomic, phenotypic and transcriptomic evidence, yet these signals remain difficult to reconcile within a common interpretive framework. Here we present RareCollab, an LLM-powered framework for multimodal reasoning in Mendelian disease diagnosis that integrates more than 100 diagnostic evidence signals across DNA, RNA, phenotype, curated variant-level knowledge, and in-silico pathogenicity evidence. This design enables large language models to operate as calibrated, interpretable reasoning modules rather than as a single end-to-end ranker. We applied RareCollab to 890 patients from three cohorts, including 119 Undiagnosed Diseases Network probands with paired DNA and RNA data, constituting a large systematic benchmark for multimodal rare disease diagnosis under paired genomic and transcriptomic evaluation. In this real-world multimodal benchmark, RareCollab prioritized 94% of diagnostic genes within the top 10. Across recall thresholds from top 1 to top 10, it consistently outperformed proprietary phenotype-driven LLM baselines including Claude Sonnet 4.6 and GPT-5-mini by more than 25% on average and surpassed established state-of-the-art variant prioritization methods by 11%-24%. RareCollab also reshapes the diagnostic contribution of RNA evidence, which contributes to prioritization of the diagnostic gene in 35% of cases (42/119). Together, these results establish RareCollab as a scalable and interpretable framework for multimodal rare disease diagnosis.

q-bio.GN↗
arXiv2026

V-STC: A Time-Efficient Multi-Vehicle Coordinated Trajectory Planning Approach

Coordinating the motions of multiple autonomous vehicles (AVs) requires planning frameworks that ensure safety while making efficient use of space and time. This paper presents a new approach, termed variable-time-step spatio-temporal corridor (V-STC), that enhances the temporal efficiency of multi-vehicle coordination. An optimization model is formulated to construct a V-STC for each AV, in which both the spatial configuration of the corridor cubes and their time durations are treated as decision variables. By allowing the corridor's spatial position and time step to vary, the constructed V-STC reduces the overall temporal occupancy of each AV while maintaining collision-free separation in the spatio-temporal domain. Based on the generated V-STC, a dynamically feasible trajectory is then planned independently for each AV. Simulation studies demonstrate that the proposed method achieves safe multi-vehicle coordination and yields more time-efficient motion compared with existing STC approaches.

cs.RO↗
arXiv2026

AgencyBench: Benchmarking the Frontiers of Autonomous Agents in 1M-Token Real-World Contexts

Large Language Models (LLMs) based autonomous agents demonstrate multifaceted capabilities to contribute substantially to economic production. However, existing benchmarks remain focused on single agentic capability, failing to capture long-horizon real-world scenarios. Moreover, the reliance on human-in-the-loop feedback for realistic tasks creates a scalability bottleneck, hindering automated rollout collection and evaluation. To bridge this gap, we introduce AgencyBench, a comprehensive benchmark derived from daily AI usage, evaluating 6 core agentic capabilities across 32 real-world scenarios, comprising 138 tasks with specific queries, deliverables, and rubrics. These scenarios require an average of 90 tool calls, 1 million tokens, and hours of execution time to resolve. To enable automated evaluation, we employ a user simulation agent to provide iterative feedback, and a Docker sandbox to conduct visual and functional rubric-based assessment. Experiments reveal that closed-source models significantly outperform open-source models (48.4% vs 32.1%). Further analysis reveals significant disparities across models in resource efficiency, feedback-driven self-correction, and specific tool-use preferences. Finally, we investigate the impact of agentic scaffolds, observing that proprietary models demonstrate superior performance within their native ecosystems (e.g., Claude-4.5-Opus via Claude-Agent-SDK), while open-source models exhibit distinct performance peaks, suggesting potential optimization for specific execution frameworks. AgencyBench serves as a critical testbed for next-generation agents, highlighting the necessity of co-optimizing model architecture with agentic frameworks. We believe this work sheds light on the future direction of autonomous agents, and we release the full benchmark and evaluation toolkit at https://github.com/GAIR-NLP/AgencyBench.

cs.AI↗
arXiv2026

One RL to See Them All: Visual Triple Unified Reinforcement Learning

Reinforcement learning (RL) is becoming an important direction for post-training vision-language models (VLMs), but public training methodologies for unified multimodal RL remain much less mature, especially for heterogeneous reasoning and perception-heavy tasks. We propose V-Triune, a Visual Triple Unified Reinforcement Learning methodology for unified multimodal RL. It organizes training around three coordinated abstractions: Sample-Level Reward Routing, Verifier-Level Outcome Verification, and Source-Level Diagnostics. Within this methodology, Dynamic IoU provides localization-specific reward shaping that avoids reward ambiguity under loose thresholds and reward sparsity under strict ones. Built on V-Triune, we develop Orsta (7B, 32B), a family of models jointly trained on eight reasoning and perception tasks. Under matched budgets, unified training matches or outperforms specialist mixtures. The final Orsta models improve over their backbones on MEGA-Bench, compare favorably with strong multi-task RL-VLM baselines, and transfer these gains to a broad set of downstream benchmarks. These results show that unified RL can improve both reasoning and perception within a single VLM RL pipeline.The V-Triune system, along with the Orsta models, is publicly available at https://github.com/MiniMax-AI/One-RL-to-See-Them-All.

cs.CV↗
arXiv2026

AlphaEval: Evaluating Agents in Production

The rapid deployment of AI agents in commercial settings has outpaced the development of evaluation methodologies that reflect production realities. Existing benchmarks measure agent capabilities through retrospectively curated tasks with well-specified requirements and deterministic metrics -- conditions that diverge fundamentally from production environments where requirements contain implicit constraints, inputs are heterogeneous multi-modal documents with information fragmented across sources, tasks demand undeclared domain expertise, outputs are long-horizon professional deliverables, and success is judged by domain experts whose standards evolve over time. We present AlphaEval, a production-grounded benchmark of 94 tasks sourced from seven companies deploying AI agents in their core business, spanning six O*NET (Occupational Information Network) domains. Unlike model-centric benchmarks, AlphaEval evaluates complete agent products -- Claude Code, Codex, etc. -- as commercial systems, capturing performance variations invisible to model-level evaluation. Our evaluation framework covers multiple paradigms (LLM-as-a-Judge, reference-driven metrics, formal verification, rubric-based assessment, automated UI testing, etc.), with individual domains composing multiple paradigms. Beyond the benchmark itself, we contribute a requirement-to-benchmark construction framework -- a systematic methodology that transforms authentic production requirements into executable evaluation tasks in minimal time. This framework standardizes the entire pipeline from requirement to evaluation, providing a reproducible, modular process that any organization can adopt to construct production-grounded benchmarks for their own domains.

cs.CL↗
arXiv2026

Proximal Supervised Fine-Tuning

Supervised fine-tuning (SFT) of foundation models often leads to poor generalization, where prior capabilities deteriorate after tuning on new tasks or domains. Inspired by trust-region policy optimization (TRPO) and proximal policy optimization (PPO) in reinforcement learning (RL), we propose Proximal SFT (PSFT). This fine-tuning objective incorporates the benefits of trust-region, effectively constraining policy drift during SFT while maintaining competitive tuning. By viewing SFT as a special case of policy gradient methods with constant positive advantages, we derive PSFT that stabilizes optimization and leads to generalization, while leaving room for further optimization in subsequent post-training stages. Experiments across mathematical and human-value domains show that PSFT matches SFT in-domain, outperforms it in out-of-domain generalization, remains stable under prolonged training without causing entropy collapse, and provides a stronger foundation for the subsequent optimization.

cs.LG↗
arXiv2026

SepSeq: A Training-Free Framework for Long Numerical Sequence Processing in LLMs

While transformer-based Large Language Models (LLMs) theoretically support massive context windows, they suffer from severe performance degradation when processing long numerical sequences. We attribute this failure to the attention dispersion in the Softmax mechanism, which prevents the model from concentrating attention. To overcome this, we propose Separate Sequence (SepSeq), a training-free, plug-and-play framework to mitigate dispersion by strategically inserting separator tokens. Mechanistically, we demonstrate that separator tokens act as an attention sink, recalibrating attention to focus on local segments while preserving global context. Extensive evaluations on 9 widely-adopted LLMs confirm the effectiveness of our approach: SepSeq yields an average relative accuracy improvement of 35.6% across diverse domains while reducing total inference token consumption by 16.4% on average.

cs.CL↗
arXiv2026

Formulation and verification of multiscale gyrokinetic simulation of kinetic-MHD processes in toroidal plasmas

A comprehensive gyrokinetic simulation model has been implemented in the global toroidal gyrokinetic code (GTC) and verified for studying low-frequency waves and turbulence in magnetic fusion plasmas by treating all kinetic-MHD processes on an equal footing. A theoretical framework has been formulated to unify various methods for efficiently solving the electron drift kinetic equation in multiscale simulations by separating electron responses into analytic and non-analytic parts based on the smallness parameter of electron-to-ion mass ratio. The model can be reduced to the ideal MHD model with both the linear dispersion relation and the nonlinear ponderomotive force in theory and simulation. The model is used for the verification and validation of simulating internal kink modes in the DIII-D tokamak with accurate calculations of equilibrium parallel current and compressible magnetic perturbation. A large simulation database has been generated to train a surrogate model to predict the kink instability. Statistical analysis shows that the radial location of safety factor q=1 flux-surface and the plasma beta inside the q=1 surface are the most important parameters for predicting the kink instability.

physics.plasm-ph↗
arXiv2026

Rubrics to Tokens: Bridging Response-level Rubrics and Token-level Rewards in Instruction Following Tasks

Rubric-based Reinforcement Learning (RL) has emerged as a promising approach for aligning Large Language Models (LLMs) with complex, open-domain instruction following tasks. However, existing methods predominantly rely on response-level rewards, introducing severe reward sparsity and reward ambiguity problems. To address these issues, we propose Rubrics to Tokens (RTT), a novel rubric-based RL framework that bridges coarse response-level scores and fine-grained token-level credit assignment. RTT introduces a Token-Level Relevance Discriminator to predict which tokens in the response are responsible for a specific constraint, and optimizes the policy model via RTT-GRPO, which integrates response-level and token-level advantages within a unified framework. Furthermore, when transitioning from one-dimensional, outcome-level reward to three-dimensional reward space in the token-level rubric-based RL, we propose a novel group normalization method, called Intra-sample Token Group Normalization, to accommodate this shift. Extensive experiments and benchmarks demonstrate that RTT consistently outperforms other baselines in both instruction- and rubric-level accuracy across different models.

cs.CL↗
arXiv2026

One Sample to Rule Them All: Extreme Data Efficiency in Multidiscipline Reasoning with Reinforcement Learning

The reasoning ability of large language models (LLMs) can be unleashed with reinforcement learning (RL) (OpenAI, 2024; DeepSeek-AI et al., 2025a; Zeng et al., 2025). The success of existing RL attempts in LLMs usually rely on high-quality samples of large volumes. In this paper, we challenge conventional assumptions about data requirements in RL for LLMs by demonstrating the effectiveness of one-shot reinforcement learning. Specifically, we introduce polymath learning, a framework for designing one training sample that elicits multidisciplinary reasoning improvement. We present three key findings: (1) A single, strategically selected math reasoning sample can produce significant performance improvements across multiple domains, including physics, chemistry, and biology; (2) Analysis of salient mathematical skills provides insight into the characteristics associated with effective polymath samples; and (3) An engineered synthetic sample that integrates multidisciplinary elements and broader skill coverage achieves stronger performance than naturally occurring individual samples. Across various reasoning benchmarks, polymath learning achieves stronger performance than larger datasets, demonstrating that reasoning structure and skills in samples, rather than quantity, may be the key to unlock enhanced reasoning capabilities in language models. Our results suggest a shift, dubbed as sample engineering, toward precision engineering of samples that complements simply increasing data volume.

cs.LG↗
arXiv2026

LatentUM: Unleashing the Potential of Interleaved Cross-Modal Reasoning via a Latent-Space Unified Model

Unified models (UMs) hold promise for their ability to understand and generate content across heterogeneous modalities. Compared to merely generating visual content, the use of UMs for interleaved cross-modal reasoning is more promising and valuable, e.g., for solving understanding problems that require dense visual thinking, improving visual generation through self-reflection, or modeling visual dynamics of the physical world guided by stepwise action interventions. However, existing UMs necessitate pixel decoding as a bridge due to their disjoint visual representations for understanding and generation, which is both ineffective and inefficient. In this paper, we introduce LatentUM, a novel unified model that represents all modalities within a shared semantic latent space, eliminating the need for pixel-space mediation between visual understanding and generation. This design naturally enables flexible interleaved cross-modal reasoning and generation. Beyond improved computational efficiency, the shared representation substantially alleviates codec bias and strengthens cross-modal alignment, allowing LatentUM to achieve state-of-the-art performance on the Visual Spatial Planning benchmark, push the limits of visual generation through self-reflection, and support world modeling by predicting future visual states within the shared semantic latent space.

cs.CV↗
arXiv2026

ASI-Evolve: AI Accelerates AI

Can AI accelerate the development of AI itself? While recent agentic systems have shown strong performance on well-scoped tasks with rapid feedback, it remains unclear whether they can tackle the costly, long-horizon, and weakly supervised research loops that drive real AI progress. We present ASI-Evolve, an agentic framework for AI-for-AI research that closes this loop through a learn-design-experiment-analyze cycle. ASI-Evolve augments standard evolutionary agents with two key components: a cognition base that injects accumulated human priors into each round of exploration, and a dedicated analyzer that distills complex experimental outcomes into reusable insights for future iterations. To our knowledge, ASI-Evolve is the first unified framework to demonstrate AI-driven discovery across three central components of AI development: data, architectures, and learning algorithms. In neural architecture design, it discovered 105 SOTA linear attention architectures, with the best discovered model surpassing DeltaNet by +0.97 points, nearly 3x the gain of recent human-designed improvements. In pretraining data curation, the evolved pipeline improves average benchmark performance by +3.96 points, with gains exceeding 18 points on MMLU. In reinforcement learning algorithm design, discovered algorithms outperform GRPO by up to +12.5 points on AMC32, +11.67 points on AIME24, and +5.04 points on OlympiadBench. We further provide initial evidence that this AI-for-AI paradigm can transfer beyond the AI stack through experiments in mathematics and biomedicine. Together, these results suggest that ASI-Evolve represents a promising step toward enabling AI to accelerate AI across the foundational stages of development, offering early evidence for the feasibility of closed-loop AI research.

cs.AI↗
arXiv2026

CiQi-Agent: Aligning Vision, Tools and Aesthetics in Multimodal Agent for Cultural Reasoning on Chinese Porcelains

The connoisseurship of antique Chinese porcelain demands extensive historical expertise, material understanding, and aesthetic sensitivity, making it difficult for non-specialists to engage. To democratize cultural-heritage understanding and assist expert connoisseurship, we introduce CiQi-Agent -- a domain-specific Porcelain Connoisseurship Agent for intelligent analysis of antique Chinese porcelain. CiQi-Agent supports multi-image porcelain inputs and enables vision tool invocation and multimodal retrieval-augmented generation, performing fine-grained connoisseurship analysis across six attributes: dynasty, reign period, kiln site, glaze color, decorative motif, and vessel shape. Beyond attribute classification, it captures subtle visual details, retrieves relevant domain knowledge, and integrates visual and textual evidence to produce coherent, explainable connoisseurship descriptions. To achieve this capability, we construct a large-scale, expert-annotated dataset CiQi-VQA, comprising 29,596 porcelain specimens, 51,553 images, and 557,940 visual question--answering pairs, and further establish a comprehensive benchmark CiQi-Bench aligned with the previously mentioned six attributes. CiQi-Agent is trained through supervised fine-tuning, reinforcement learning, and a tool-augmented reasoning framework that integrates two categories of tools: a vision tool and multimodal retrieval tools. Experimental results show that CiQi-Agent (7B) outperforms all competitive open- and closed-source models across all six attributes on CiQi-Bench, achieving on average 12.2\% higher accuracy than GPT-5. The model and dataset have been released and are publicly available at https://huggingface.co/datasets/SII-Monument-Valley/CiQi-VQA.

cs.CV↗
arXiv2026

PRBench: End-to-end Paper Reproduction in Physics Research

AI agents powered by large language models exhibit strong reasoning and problem-solving capabilities, enabling them to assist scientific research tasks such as formula derivation and code generation. However, whether these agents can reliably perform end-to-end reproduction from real scientific papers remains an open question. We introduce PRBench, a benchmark of 30 expert-curated tasks spanning 11 subfields of physics. Each task requires an agent to comprehend the methodology of a published paper, implement the corresponding algorithms from scratch, and produce quantitative results matching the original publication. Agents are provided only with the task instruction and paper content, and operate in a sandboxed execution environment. All tasks are contributed by domain experts from over 20 research groups at the School of Physics, Peking University, each grounded in a real published paper and validated through end-to-end reproduction with verified ground-truth results and detailed scoring rubrics. Using an agentified assessment pipeline, we evaluate a set of coding agents on PRBench and analyze their capabilities across key dimensions of scientific reasoning and execution. The best-performing agent, OpenAI Codex powered by GPT-5.3-Codex, achieves a mean overall score of 34%. All agents exhibit a zero end-to-end callback success rate, with particularly poor performance in data accuracy and code correctness. We further identify systematic failure modes, including errors in formula implementation, inability to debug numerical simulations, and fabrication of output data. Overall, PRBench provides a rigorous benchmark for evaluating progress toward autonomous scientific research.

cs.CL↗
arXiv2026

daVinci-LLM:Towards the Science of Pretraining

The foundational pretraining phase determines a model's capability ceiling, as post-training struggles to overcome capability foundations established during pretraining, yet it remains critically under-explored. This stems from a structural paradox: organizations with computational resources operate under commercial pressures that inhibit transparent disclosure, while academic institutions possess research freedom but lack pretraining-scale computational resources. daVinci-LLM occupies this unexplored intersection, combining industrial-scale resources with full research freedom to advance the science of pretraining. We adopt a fully-open paradigm that treats openness as scientific methodology, releasing complete data processing pipelines, full training processes, and systematic exploration results. Recognizing that the field lacks systematic methodology for data processing, we employ the Data Darwinism framework, a principled L0-L9 taxonomy from filtering to synthesis. We train a 3B-parameter model from random initialization across 8T tokens using a two-stage adaptive curriculum that progressively shifts from foundational capabilities to reasoning-intensive enhancement. Through 200+ controlled ablations, we establish that: processing depth systematically enhances capabilities, establishing it as a critical dimension alongside volume scaling; different domains exhibit distinct saturation dynamics, necessitating adaptive strategies from proportion adjustments to format shifts; compositional balance enables targeted intensification while preventing performance collapse; how evaluation protocol choices shape our understanding of pretraining progress. By releasing the complete exploration process, we enable the community to build upon our findings and systematic methodologies to form accumulative scientific knowledge in pretraining.

cs.AI↗
arXiv2026

Caption Generation for Dongba Paintings via Prompt Learning and Semantic Fusion

Dongba paintings, the treasured pictorial legacy of the Naxi people in southwestern China, feature richly layered visual elements, vivid color palettes, and pronounced ethnic and regional cultural symbolism, yet their automatic textual description remains largely unexplored owing to severe domain shift when mainstream captioning models are applied directly. This paper proposes \textbf{PVGF-DPC} (\textit{Prompt and Visual Semantic-Generation Fusion-based Dongba Painting Captioning}), an encoder-decoder framework that integrates a content prompt module with a novel visual semantic-generation fusion loss to bridge the gap between generic natural-image captioning and the culturally specific imagery found in Dongba art. A MobileNetV2 encoder extracts discriminative visual features, which are injected into the layer normalization of a 10-layer Transformer decoder initialized with pretrained BERT weights; meanwhile, the content prompt module maps the image feature vector to culture-aware labels -- such as \emph{deity}, \emph{ritual pattern}, or \emph{hell ghost} -- and constructs a post-prompt that steers the decoder toward thematically accurate descriptions. The visual semantic-generation fusion loss jointly optimizes the cross-entropy objectives of both the prompt predictor and the caption generator, encouraging the model to extract key cultural and visual cues and to produce captions that are semantically aligned with the input image. We construct a dedicated Dongba painting captioning dataset comprising 9{}408 augmented images with culturally grounded annotations spanning seven thematic categories.

cs.CV↗
arXiv2026

Speed by Simplicity: A Single-Stream Architecture for Fast Audio-Video Generative Foundation Model

We present daVinci-MagiHuman, an open-source audio-video generative foundation model for human-centric generation. daVinci-MagiHuman jointly generates synchronized video and audio using a single-stream Transformer that processes text, video, and audio within a unified token sequence via self-attention only. This single-stream design avoids the complexity of multi-stream or cross-attention architectures while remaining easy to optimize with standard training and inference infrastructure. The model is particularly strong in human-centric scenarios, producing expressive facial performance, natural speech-expression coordination, realistic body motion, and precise audio-video synchronization. It supports multilingual spoken generation across Chinese (Mandarin and Cantonese), English, Japanese, Korean, German, and French. For efficient inference, we combine the single-stream backbone with model distillation, latent-space super-resolution, and a Turbo VAE decoder, enabling generation of a 5-second 256p video in 2 seconds on a single H100 GPU. In automatic evaluation, daVinci-MagiHuman achieves the highest visual quality and text alignment among leading open models, along with the lowest word error rate (14.60%) for speech intelligibility. In pairwise human evaluation, it achieves win rates of 80.0% against Ovi 1.1 and 60.9% against LTX 2.3 over 2000 comparisons. We open-source the complete model stack, including the base model, the distilled model, the super-resolution model, and the inference codebase.

cs.CV↗
arXiv2026

TransText: Alpha-as-RGB Representation for Transparent Text Animation

We introduce the first method, to the best of our knowledge, for adapting image-to-video models to layer-aware text (glyph) animation, a capability critical for practical dynamic visual design. Existing approaches predominantly handle the transparency-encoding (alpha channel) as an extra latent dimension appended to the RGB space, necessitating the reconstruction of the underlying RGB-centric variational autoencoder (VAE). However, given the scarcity of high-quality transparent glyph data, retraining the VAE is computationally expensive and may erode the robust semantic priors learned from massive RGB corpora, potentially leading to latent pattern mixing. To mitigate these limitations, we propose TransText, a framework based on a novel Alpha-as-RGB paradigm to jointly model appearance and transparency without modifying the pre-trained generative manifold. TransText embeds the alpha channel as an RGB-compatible visual signal through latent spatial concatenation, explicitly ensuring strict cross-modal (RGB-and-Alpha) consistency while preventing feature entanglement. Our experiments demonstrate that TransText significantly outperforms baselines, generating coherent, high-fidelity transparent animations with diverse, fine-grained effects.

cs.CV↗