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Mengdi Liu

Publications and source records attributed to Mengdi Liu.

At least 19 recordsLinked to original sources
arXiv2026

E$^2$-OPSD: Taming Entropy Overshoot in On-Policy Self-Distillation

On-policy self-distillation (OPSD) provides dense token-level supervision without a second model: one network acts as teacher with the reference solution and as student with only the problem. We identify a specific failure mode of this recipe. During training, student token entropy rises past the teacher's and remains elevated, a pattern we call entropy overshoot. We trace it to both sides of distillation. The reference-conditioned teacher is confident along its answer-directed reasoning path, but this confidence transfers poorly to student-generated prefixes, making its supervision overly tied to answer-specific cues rather than reusable reasoning patterns; meanwhile, the forward KL used by OPSD continually diffuses the student's predictive distribution without pulling it back. We introduce E$^2$-OPSD to address both causes. Exemplar-guided teaching replaces the current answer with a retrieved solved neighboring problem, providing transferable reasoning guidance without revealing the destination and better matching student-reachable states. Entropy-aware distillation uses the student-teacher entropy gap to determine the direction and strength of each token's correction. E$^2$-OPSD improves math reasoning by up to 4.3 points in mean@16 over OPSD, while out-of-domain evaluations show gains over the corresponding base models of up to 4.9 points in mean@16 and 5.5 points in pass@8. Despite these gains, E$^2$-OPSD remains simple, requiring no additional forward passes or networks. Code repo: https://github.com/orionfei/E2-OPSD.

cs.LG↗
arXiv2026

JANUS: Enhancing Long-Horizon Autonomous Research with Co-Evolving World Models

Long-horizon autonomous research has shown promise in accelerating scientific progress through sustained cycles of hypothesis generation, implementation, and validation. However, this Generate-Execute-Feedback paradigm relies on reactive trial-and-error, where costly and time-consuming executions introduce severe feedback delays, throttling evolutionary progress under explosively expanding search space. To address this challenge, we propose JANUS, a framework that unifies future outcomes forecasting and past experience reflection through a Predict-Verify-Evolve loop driven by a co-evolving world model. Within an evolving graph, the research agent proposes candidates while world model scores them by forecasting value improvement, information gain, and exploration utility, then accordingly selects, refines, or prunes branches prior to execution. After receiving ground-truth feedback, JANUS distills experience into evolving skills: hierarchical skills for research agent, exploration-strategy skills for world model, and their coordination protocols. This mechanism enables continual co-evolution: the research agent sharpens candidate generation while the world model refines its predictive judgment over extended horizons. Extensive evaluations on MLS-Bench-Lite and real research tasks demonstrate that JANUS significantly outperforms state-of-the-art baselines, achieving both higher evolving efficiency and ceiling.

cs.AI↗
arXiv2026

Masked Diffusion Language Agents for Tool-Integrated Chemical Reasoning

Designing tool-integrated reasoning agent systems for complex chemical tasks remains a fundamental challenge. Although recent chemical agents have demonstrated promising performance through the integration of external tools, they are still built on the autoregressive paradigm, which is inherently constrained by causal attention and left-to-right generation. As a result, they often struggle with bidirectional molecular understanding, global coordinated tool planning and multi-source evidence integration. To address this challenge, we introduce ChemDiffAgent, the first masked diffusion language agent for tool-integrated chemical reasoning. It reformulates chemical reasoning as iterative denoising over interleaved reasoning and tool-use trajectories, enabling tool-use decisions to be jointly determined under full-trajectory context and thereby better aligning the agent's decision boundary with its knowledge boundary. We further analyze how this paradigm benefits agentic reasoning through harder infilling subproblems during training and flexible arbitrary-order decoding during inference. Then we develop a two-stage post-training framework, comprising agentic supervised fine-tuning and variance-reduced preference optimization, to enhance tool-use and reasoning capabilities. We also construct a comprehensive benchmark covering six chemistry tasks across both single-turn and multi-turn tool-use scenarios. Under matched budgets and evaluation, ChemDiffAgent consistently outperforms autoregressive agents, achieving an overall improvement of approximately 20%. Notably, our 8B model achieves performance comparable to, in some cases surpassing, significantly larger frontier models, such as GPT 5.5 and Claude Opus 4.7. Code is available at https://github.com/bilemond/ChemDiffAgent.

cs.AI↗
arXiv2026

MindFlow: Mind Supernet Powered Thinking Flows for Research Idea Innovation

Research idea innovation is a fundamental engine of scientific progress, yet it remains difficult to generate and evaluate in a scalable and controllable way. This challenge lies in its inherently open-ended and multi-objective nature, where ideas should balance novelty, plausibility and feasibility. While recent LLM-based approaches have made progress through carefully designed prompts or agent pipelines, they are constrained by predefined, static ideation workflows. To address this limitation, we propose MindFlow, a framework that explicitly formulates ideation as a graph-structured Flow in Mind, which is composed of modular thinking operators and modeled by a probabilistic mind supernet. Given a research topic, a controller dynamically samples thinking flows to generate candidate ideas. This open-ended problem is optimized using a tournament-based relative ranking, enabling the controller to progressively favor higher-quality thinking flows. We further introduce an evaluation protocol that jointly assesses problem finding and problem solving, going beyond title- or abstractonly judgments. Across diverse topics, MindFlow shows its superiority as an explicit, controllable and optimizable research idea innovator.

cs.AI↗
arXiv2026

MAST: Motif-Augmented Diffusion with Search Tree for Spectroscopic Molecular Structure Elucidation

Elucidating molecular structures from spectra is a foundational problem in chemical and materials characterization, yet remains challenging due to spectral ambiguity and the vast molecular space. Although recent diffusion-based generators show strong promise for spectra-conditioned elucidation, existing methods struggle to learn robust spectra-structure relationships from limited paired data when relying solely on global spectral representation. Moreover, the repeated full sampling inference strategy incurs substantial computation overhead. To address these limitations, we propose \textbf{MAST}, a \textbf{M}otif-\textbf{A}ugmented diffusion framework with \textbf{S}earch \textbf{T}ree, for joint 2D-3D spectroscopic molecular structure elucidation. MAST introduces explicit, interpretable \emph{motif priors} as intermediate evidences throughout denoising, reducing conditional ambiguity and facilitating spectra-conditioned optimization. We further cast diffusion sampling as \emph{reward-guided tree search} to prioritize high-reward denoising trajectories, yielding a compact set of spectra-consistent candidates under limited budgets. On the QM9S multi-spectra benchmark, MAST achieves \textbf{94.89\%} exact recovery and improves 3D fidelity, while preserving high chemical validity and stability. Code is available at https://github.com/Jia040223/MAST.

physics.chem-ph↗
arXiv2026

ViCoR: Reliable Molecular Structure Extraction via Spatially Aligned Verification and Executable Revision

Reliable optical chemical structure recognition (OCSR) is essential for building high-quality chemical data from scientific literature, yet even small recognition errors can propagate into chemical databases and downstream models. In practice, recognized structures often require manual inspection and correction before use, making large-scale data curation costly and difficult to scale. We therefore study Selective Structure Recognition (SSR), a post-recognition setting that automatically produces reliable structured outputs while rejecting unresolved cases. Selection-only approaches can improve reliability by rejection, but cannot create additional correct outputs beyond those produced by the base recognizer. We propose ViCoR, a repair-before-rejection framework for iterative VerIfiCatiOn and Revision. Its key idea is to make observation-prediction correspondence explicit: coordinate-preserving rendering establishes spatial correspondence between the source image and predicted structure, while index anchoring maps localized visual discrepancies to executable graph edits without full-structure regeneration. A shared VLM is progressively trained from verification to revision. On two real-world OCSR benchmarks, ViCoR improves overall accuracy from 73.53\% to 88.26\% and from 61.83\% to 84.32\%, while achieving over 97\% accepted accuracy at 85--89\% coverage. The resulting molecular data further improve reaction-extraction F1 by 15.5 points and literature-sourced reaction prediction accuracy by 7.7 and 5.8 points, demonstrating the value of automated reliability control for scientific data curation and downstream chemical learning.

cs.CV↗
arXiv2026

SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery

Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state. We present SciForge, a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services. SciForge is built around five pillars: (i) \emph{goal-scoped scientific decision governance} for \textbf{goal-oriented} research, with review gates and shared review surfaces; (ii) \emph{translate-then-reason} for \textbf{multimodal} input, routing scientific objects through domain translators before the agent reasons; (iii) \emph{evidence governance} for \textbf{auditable} traceability, linking claims to provenance chains and audit findings; (iv) \emph{collaborative team science} for \textbf{collaborative} research, enabling multi-role decision governance, with shared team workspaces planned for future releases; and (v) \emph{real-world application scenarios} for \textbf{practical} impact, demonstrated through eight end-to-end user cases, with flagship demonstrations including multi-day agentic research sprints for gene discovery, AI-guided de novo protein design, molecular optimization, and genome-to-BGC discovery. The system combines a thin interaction layer, contextual research capability patterns, an Agent Runtime and Workflow Engine, an Evidence-DAG audit sidecar and a Scientific Model Router. SciForge currently runs as a desktop application, with mobile supervision support; future releases will deepen team collaboration. The system is open-source and available at https://github.com/AGI4Sci/SciForge

cs.AI↗
arXiv2026

AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories

Systematic ablations are essential to attribute performance gains in AI Virtual Cells, yet they are rarely performed because biological repositories are under-standardized and tightly coupled to domain-specific data and formats. While recent coding agents can translate ideas into implementations, they typically stop at producing code and lack a verifier that can reproduce strong baselines and rigorously test which components truly matter. We introduce AblateCell, a reproduce-then-ablate agent for virtual cell repositories that closes this verification gap. AblateCell first reproduces reported baselines end-to-end by auto-configuring environments, resolving dependency and data issues, and rerunning official evaluations while emitting verifiable artifacts. It then conducts closed-loop ablation by generating a graph of isolated repository mutations and adaptively selecting experiments under a reward that trades off performance impact and execution cost. Evaluated on three single-cell perturbation prediction repositories (CPA, GEARS, BioLORD), AblateCell achieves 88.9% (+29.9% to human expert) end-to-end workflow success and 93.3% (+53.3% to heuristic) accuracy in recovering ground-truth critical components. These results enable scalable, repository-grounded verification and attribution directly on biological codebases.

cs.AI↗
arXiv2026

Unlabeled Cross-Center Automatic Analysis for TAAD: An Integrated Framework from Segmentation to Clinical Features

Type A Aortic Dissection (TAAD) is a life-threatening cardiovascular emergency that demands rapid and precise preoperative evaluation. While key anatomical and pathological features are decisive for surgical planning, current research focuses predominantly on improving segmentation accuracy, leaving the reliable, quantitative extraction of clinically actionable features largely under-explored. Furthermore, constructing comprehensive TAAD datasets requires labor-intensive, expert level pixel-wise annotations, which is impractical for most clinical institutions. Due to significant domain shift, models trained on a single center dataset also suffer from severe performance degradation during cross-institutional deployment. This study addresses a clinically critical challenge: the accurate extraction of key TAAD clinical features during cross-institutional deployment in the total absence of target-domain annotations. To this end, we propose an unsupervised domain adaptation (UDA)-driven framework for the automated extraction of TAAD clinical features. The framework leverages limited source-domain labels while effectively adapting to unlabeled data from target domains. Tailored for real-world emergency workflows, our framework aims to achieve stable cross-institutional multi-class segmentation, reliable and quantifiable clinical feature extraction, and practical deployability independent of high-cost annotations. Extensive experiments demonstrate that our method significantly improves cross-domain segmentation performance compared to existing state-of-the-art approaches. More importantly, a reader study involving multiple cardiovascular surgeons confirms that the automatically extracted clinical features provide meaningful assistance for preoperative assessment, highlighting the practical utility of the proposed end-to-end segmentation-to-feature pipeline.

cs.CV↗
arXiv2026

LensWalk: Agentic Video Understanding by Planning How You See in Videos

The dense, temporal nature of video presents a profound challenge for automated analysis. Despite the use of powerful Vision-Language Models, prevailing methods for video understanding are limited by the inherent disconnect between reasoning and perception: they rely on static, pre-processed information and cannot actively seek raw evidence from video as their understanding evolves. To address this, we introduce LensWalk, a flexible agentic framework that empowers a Large Language Model reasoner to control its own visual observation actively. LensWalk establishes a tight reason-plan-observe loop where the agent dynamically specifies, at each step, the temporal scope and sampling density of the video it observes. Using a suite of versatile, Vision-Language Model based tools parameterized by these specifications, the agent can perform broad scans for cues, focus on specific segments for fact extraction, and stitch evidence from multiple moments for holistic verification. This design allows for progressive, on-demand evidence gathering that directly serves the agent's evolving chain of thought. Without requiring any model fine-tuning, LensWalk delivers substantial, plug-and-play performance gains on multiple model recipes, boosting their accuracy by over 5\% on challenging long-video benchmarks like LVBench and Video-MME. Our analysis reveals that enabling an agent to control how it sees is key to unlocking more accurate, robust, and interpretable video reasoning.

cs.CV↗
arXiv2025

Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

cs.AI↗
arXiv2025

ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search

Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering native sequences, they often overlook the one-to-many nature of the problem: multiple diverse sequences can fold into the same structure. This motivates the need for a generative model capable of designing diverse sequences while preserving structural consistency. To address this trade-off, we introduce ProtInvTree, the first reward-guided tree-search framework for protein inverse folding. ProtInvTree reformulates sequence generation as a deliberate, step-wise decision-making process, enabling the exploration of multiple design paths and exploitation of promising candidates through self-evaluation, lookahead, and backtracking. We propose a two-stage focus-and-grounding action mechanism that decouples position selection and residue generation. To efficiently evaluate intermediate states, we introduce a jumpy denoising strategy that avoids full rollouts. Built upon pretrained protein language models, ProtInvTree supports flexible test-time scaling by expanding the search depth and breadth without retraining. Empirically, ProtInvTree outperforms state-of-the-art baselines across multiple benchmarks, generating structurally consistent yet diverse sequences, including those far from the native ground truth.

q-bio.BM↗
arXiv2025

PFMBench: Protein Foundation Model Benchmark

This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair evaluation and in-depth understanding. Since ESM-1B, numerous protein foundation models have emerged, each with unique datasets and methodologies. However, evaluations often focus on limited tasks tailored to specific models, hindering insights into broader generalization and limitations. Specifically, researchers struggle to understand the relationships between tasks, assess how well current models perform across them, and determine the criteria in developing new foundation models. To fill this gap, we present PFMBench, a comprehensive benchmark evaluating protein foundation models across 38 tasks spanning 8 key areas of protein science. Through hundreds of experiments on 17 state-of-the-art models across 38 tasks, PFMBench reveals the inherent correlations between tasks, identifies top-performing models, and provides a streamlined evaluation protocol. Code is available at \href{https://github.com/biomap-research/PFMBench}{\textcolor{blue}{GitHub}}.

q-bio.BM↗
arXiv2025

G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion

Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However, current phenotype prediction models are limited to individual species and expensive phenotype labeling process, making the genotype-to-phenotype prediction a highly domain-dependent and data-scarce problem. To this end, we suggest taking images as morphological proxies, facilitating cross-species generalization through large-scale multimodal pretraining. We propose the first genotype-to-phenotype diffusion model (G2PDiffusion) that generates morphological images from DNA considering two critical evolutionary signals, i.e., multiple sequence alignments (MSA) and environmental contexts. The model contains three novel components: 1) a MSA retrieval engine that identifies conserved and co-evolutionary patterns; 2) an environment-aware MSA conditional encoder that effectively models complex genotype-environment interactions; and 3) an adaptive phenomic alignment module to improve genotype-phenotype consistency. Extensive experiments show that integrating evolutionary signals with environmental context enriches the model's understanding of phenotype variability across species, thereby offering a valuable and promising exploration into advanced AI-assisted genomic analysis.

cs.LG↗
arXiv2024

CP-DETR: Concept Prompt Guide DETR Toward Stronger Universal Object Detection

Recent research on universal object detection aims to introduce language in a SoTA closed-set detector and then generalize the open-set concepts by constructing large-scale (text-region) datasets for training. However, these methods face two main challenges: (i) how to efficiently use the prior information in the prompts to genericise objects and (ii) how to reduce alignment bias in the downstream tasks, both leading to sub-optimal performance in some scenarios beyond pre-training. To address these challenges, we propose a strong universal detection foundation model called CP-DETR, which is competitive in almost all scenarios, with only one pre-training weight. Specifically, we design an efficient prompt visual hybrid encoder that enhances the information interaction between prompt and visual through scale-by-scale and multi-scale fusion modules. Then, the hybrid encoder is facilitated to fully utilize the prompted information by prompt multi-label loss and auxiliary detection head. In addition to text prompts, we have designed two practical concept prompt generation methods, visual prompt and optimized prompt, to extract abstract concepts through concrete visual examples and stably reduce alignment bias in downstream tasks. With these effective designs, CP-DETR demonstrates superior universal detection performance in a broad spectrum of scenarios. For example, our Swin-T backbone model achieves 47.6 zero-shot AP on LVIS, and the Swin-L backbone model achieves 32.2 zero-shot AP on ODinW35. Furthermore, our visual prompt generation method achieves 68.4 AP on COCO val by interactive detection, and the optimized prompt achieves 73.1 fully-shot AP on ODinW13.

cs.CV↗
arXiv2023

Exploration of visual prompt in Grounded pre-trained open-set detection

Text prompts are crucial for generalizing pre-trained open-set object detection models to new categories. However, current methods for text prompts are limited as they require manual feedback when generalizing to new categories, which restricts their ability to model complex scenes, often leading to incorrect detection results. To address this limitation, we propose a novel visual prompt method that learns new category knowledge from a few labeled images, which generalizes the pre-trained detection model to the new category. To allow visual prompts to represent new categories adequately, we propose a statistical-based prompt construction module that is not limited by predefined vocabulary lengths, thus allowing more vectors to be used when representing categories. We further utilize the category dictionaries in the pre-training dataset to design task-specific similarity dictionaries, which make visual prompts more discriminative. We evaluate the method on the ODinW dataset and show that it outperforms existing prompt learning methods and performs more consistently in combinatorial inference.

cs.CV↗
arXiv2023

Private Data Valuation and Fair Payment in Data Marketplaces

Data valuation is an essential task in a data marketplace. It aims at fairly compensating data owners for their contribution. There is increasing recognition in the machine learning community that the Shapley value -- a foundational profit-sharing scheme in cooperative game theory -- has major potential to value data, because it uniquely satisfies basic properties for fair credit allocation and has been shown to be able to identify data sources that are useful or harmful to model performance. However, calculating the Shapley value requires accessing original data sources. It still remains an open question how to design a real-world data marketplace that takes advantage of the Shapley value-based data pricing while protecting privacy and allowing fair payments. In this paper, we propose the {\em first} prototype of a data marketplace that values data sources based on the Shapley value in a privacy-preserving manner and at the same time ensures fair payments. Our approach is enabled by a suite of innovations on both algorithm and system design. We firstly propose a Shapley value calculation algorithm that can be efficiently implemented via multiparty computation (MPC) circuits. The key idea is to learn a performance predictor that can directly predict model performance corresponding to an input dataset without performing actual training. We further optimize the MPC circuit design based on the structure of the performance predictor. We further incorporate fair payment into the MPC circuit to guarantee that the data that the buyer pays for is exactly the same as the one that has been valuated. Our experimental results show that the proposed new data valuation algorithm is as effective as the original expensive one. Furthermore, the customized MPC protocol is efficient and scalable.

cs.CR↗
arXiv2020

A Survey on Universal Design for Fitness Wearable Devices

Driven by the visions of Internet of Things and 5G communications, recent years have seen a paradigm shift in personal mobile devices, from smartphones towards wearable devices. Wearable devices come in many different forms targeting different application scenarios. Among these, the fitness wearable devices (FWDs) are proven to be one of the forms that intrigue the market and occupy an increasing trend in terms of the market share. Nevertheless, although the fitness wearable devices nowadays are functionally self-contained based on the advanced sensor, computation, and communicative technologies, there is still a large gap to truly satisfy the target customer group, i.e., accessible to and usable by a larger quantity of users. This fuels the research area on applying the universal design principles to fitness wearable devices. In this survey, we first present the background of FWDs and show the acceptance and adaption challenges of the corresponding user groups. We then review the universal design principle and how it and its relative approaches could be used in FWDs. Further, we collect the available FWDs that bear the universal design principles in their development circles. Last, we open up the discussion based on the surveyed literature and provide the insight of potential future work.

cs.HC↗