arXiv subjects

Liuzhenghao Lv

Publications and source records attributed to Liuzhenghao Lv.

12 recordsLinked to original sources

arXiv2026

RipplePLM: Structural and Property Decoupling for Protein Mutation Effect Generation

Protein mutation effect generation asks a model to describe the functional consequence of a point mutation in natural language. Existing protein-to-text systems typically encode mutation information into undifferentiated representations, overlooking the organization of mutation-induced evidence across structural and biochemical factors. We propose RipplePLM, a mutation-aware generation framework centered on Direct-Distal Cross-Attention (DDCA). By constructing a residue-level Mutation Perturbation Field from pre-trained protein language models, DDCA leverages predicted contact maps to organize mutation representations into two pathways: the mutation site's immediate contact neighborhood and its multi-hop distal context. To complement this structural decomposition, we further introduce the Property Latent Chain (PLChain), which injects expert-guided supervision of biochemical property changes (e.g., thermostability and optimal pH) into the LLM hidden-state pathway through latent property tokens. On MutaDescribe, RipplePLM improves over mutation-specific baselines on temporal and structural splits; under a matched-backbone comparison, average structural-split ROUGE-L increases from {22.23} to {35.65}. Expert evaluation further shows a higher proportion of biologically accurate or relevant descriptions than the mutation-specific baseline. Additional ablations, representation diagnostics, and low-$N$ fitness regression experiments further support the effectiveness of the learned mutation-aware representations. Code: https://github.com/Lyu6PosHao/RipplePLM.

cs.CE↗

arXiv2026

OpenAI4S: Code as Action, Science as Sessions

AI co-scientists could accelerate computational research, but over a long-running study the workflow also has to stay inspectable, resumable and reproducible, which requires persistent computational state and provenance. Here we present OpenAI4S, an open-source scientific research agent built around the principle of \emph{Code as Action, Science as Sessions}. OpenAI4S combines a persistent computing runtime with research-session management: orchestration is handled through structured tool calls, while scientific actions are represented as complete code cells executed in persistent Python and R kernels. An append-only Action Ledger, per-cell execution records, versioned artifacts, environment records, and workspace checkpoints preserve how results were produced and support session recovery, branching, and extension. Configurable sandboxing, permission controls, and code and trajectory screening provide complementary safeguards. We evaluate OpenAI4S on 36 research scenarios spanning retrosynthesis, molecular dynamics, protein binder design, protein mutation, catalyst screening, and mineral spectroscopy, measuring scientific task accuracy, workflow completeness, and reproducibility of the resulting repositories. OpenAI4S achieves an overall score of 7.83, compared with 5.7--6.4 for a general-purpose coding harness evaluated with three frontier models, with the largest gains on long-horizon and computation-intensive workflows. These results suggest that integrating persistent execution with session-level provenance can improve the reliability of AI-assisted scientific workflows. Environment specification and full rerunnability remain weak for every evaluated system, ours included, so reproducibility is still an open problem for scientific agents. The system is available under the MIT license at \href{https://github.com/PKU-YuanGroup/OpenAI4S}{github.com/PKU-YuanGroup/OpenAI4S}.

cs.AI↗

arXiv2026

LabEvolver: Training-Free Experience Evolution for Safe and Grounded Wet-Lab Agents

We introduce LabEvolver, a training-free framework that equips safe and grounded wet-lab agents with episodic memory from execution experience. LabEvolver couples a state-grounded inner trial loop for adaptive perception, online planning, and safety validation with an outer evolution loop that distills completed trajectories into reusable skill, strategy, and safety experience. On robotic solution-preparation tasks, LabEvolver demonstrates real-world feasibility, reducing pH-regulation completion time and safety-gate intercepts by 48.2% and 60.0%, respectively. On ALFWorld, it further improves cumulative success rate within 20 steps from 76.2% with ReAct to 91.4% over 500 continual tasks, showing generality beyond wet-lab settings. These results support learn-by-doing experience evolution as a feasible path toward closed-loop automated scientific discovery. The project page is available at https://andygao6186.github.io/LabEvolver/.

cs.RO↗

arXiv2026

BioProBench: A Corpus and Benchmark for Biological Protocol Reasoning in Autonomous Science

The realization of autonomous scientific experimentation is currently limited by LLMs' struggle to grasp the strict procedural logic and accuracy required by biological protocols. To address this fundamental challenge, we present \textbf{BioProBench}, a comprehensive resource for procedural reasoning in biology. BioProBench is grounded in \textbf{BioProCorpus}, a foundational collection of 22,413 human-written protocols. From this corpus, we systematically constructed a dataset of 523,784 task instances, offering both a large-scale training resource and a rigorous benchmark with novel metrics. Evaluating 10 mainstream LLMs, we find that while general comprehension is high, performance drops significantly on tasks demanding deep reasoning, quantitative precision, and safety awareness. To demonstrate the value of BioProCorpus in mitigating these issues, we developed \textbf{ProAgent}, grounded in our corpus, ProAgent substantially advances the state-of-the-art. https://github.com/YuyangSunshine/bioprobench and https://huggingface.co/BioProBench.

cs.CL↗

arXiv2026

BioProAgent: Neuro-Symbolic Grounding for Constrained Scientific Planning

Large language models (LLMs) have demonstrated significant reasoning capabilities in scientific discovery but struggle to bridge the gap to physical execution in wet-labs. In these irreversible environments, probabilistic hallucinations are not merely incorrect; they can cause equipment damage or experimental failure. We propose BioProAgent, a neuro-symbolic framework that anchors probabilistic planning in a deterministic Finite State Machine (FSM). We introduce a State-Augmented Planning mechanism that enforces a rigorous Design-Verify-Rectify workflow, ensuring hardware compliance before execution. Furthermore, we address the context bottleneck inherent in complex device schemas by Semantic Symbol Grounding, reducing token consumption by ~6* through symbolic abstraction. In the extended BioProBench benchmark, BioProAgent achieves 95.6% physical compliance (compared to 21.0% for ReAct), demonstrating that neuro-symbolic constraints are essential for reliable autonomy in irreversible physical environments. Code: https://github.com/YuyangSunshine/bioproagent | Website: https://yuyangsunshine.github.io/BioPro-Project.

cs.AI↗

arXiv2026

MoleCode unlocks structural intelligence in large language models

Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in which topology is implicit, forcing LLMs to reconstruct molecular structure before performing the requested chemical operation. Here we introduce MoleCode, an LLM-native, training-free, graph-explicit molecular language in which all molecular components are represented as typed entities with persistent identifiers and explicit relations. MoleCode makes molecular topology directly readable, editable and auditable within the language context, allowing an LLM to operate on structure rather than recover it from syntax. Across molecular reasoning, editing, generation and analysis tasks, this representational shift improves frontier LLMs most strongly when structural access is limiting: unfamiliar molecules, topology-sensitive operations, larger structures and repetitive polymers. It also changes how inference is allocated, replacing long reasoning traces devoted to implicit structural reconstruction with shorter, more chemically directed reasoning over explicit atoms and bonds. In molecular optimization, this enables localized, property-aligned edits that preserve structural similarity to the starting compounds. The same Subgraph--Node--Edge grammar extends beyond small molecules to polymers, Markush structures, mechanism-style transformations and interleaved scientific documents, including research articles and patent disclosures in which chemical information is distributed across text and images. These results suggest that the interface between scientific objects and LLMs should not treat structure as something to be decoded from text. When the object of reasoning is relational, the structure itself should be part of the language.

q-bio.BM↗

arXiv2025

ProLLaMA: A Protein Large Language Model for Multi-Task Protein Language Processing

Recent advances in Protein Language Models (PLMs) have transformed protein engineering, yet unlike their counterparts in Natural Language Processing (NLP), current PLMs exhibit a fundamental limitation: they excel in either Protein Language Understanding (PLU) or Protein Language Generation (PLG), but rarely both. This fragmentation hinders progress in protein engineering. To bridge this gap, we introduce ProLLaMA, a multitask protein language model enhanced by the Evolutionary Protein Generation Framework (EPGF). We construct a comprehensive instruction dataset containing approximately 13 million samples with over 11,000 superfamily annotations to facilitate better modeling of sequence-function landscapes. We leverage a two-stage training approach to develop ProLLaMA, a multitask LLM with protein domain expertise. Our EPGF addresses the mismatch between statistic language modeling and biological constraints through three innovations: a multi-dimensional interpretable scorer, hierarchical efficient decoding, and a probabilistic-biophysical joint selection mechanism. Extensive experiments demonstrate that ProLLaMA excels in both unconditional and controllable protein generation tasks, achieving superior structural quality metrics compared to existing PLMs. Additionally, ProLLaMA demonstrates strong understanding capabilities with a 67.1% exact match rate in superfamily prediction. EPGF significantly enhances the biological viability of generated sequences, as evidenced by improved biophysical scores (+4.3%) and structural metrics (+14.5%). The project is available at https://github.com/PKU-YuanGroup/ProLLaMA.

cs.CE↗

arXiv2025

How to Detect and Defeat Molecular Mirage: A Metric-Driven Benchmark for Hallucination in LLM-based Molecular Comprehension

Large language models are increasingly used in scientific domains, especially for molecular understanding and analysis. However, existing models are affected by hallucination issues, resulting in errors in drug design and utilization. In this paper, we first analyze the sources of hallucination in LLMs for molecular comprehension tasks, specifically the knowledge shortcut phenomenon observed in the PubChem dataset. To evaluate hallucination in molecular comprehension tasks with computational efficiency, we introduce \textbf{Mol-Hallu}, a novel free-form evaluation metric that quantifies the degree of hallucination based on the scientific entailment relationship between generated text and actual molecular properties. Utilizing the Mol-Hallu metric, we reassess and analyze the extent of hallucination in various LLMs performing molecular comprehension tasks. Furthermore, the Hallucination Reduction Post-processing stage~(HRPP) is proposed to alleviate molecular hallucinations, Experiments show the effectiveness of HRPP on decoder-only and encoder-decoder molecular LLMs. Our findings provide critical insights into mitigating hallucination and improving the reliability of LLMs in scientific applications.

cs.CL↗

arXiv2025

Navigating Chemical-Linguistic Sharing Space with Heterogeneous Molecular Encoding

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+8.9\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

cs.CE↗

arXiv2024

Multi-granularity Score-based Generative Framework Enables Efficient Inverse Design of Complex Organics

Efficiently retrieving an enormous chemical library to design targeted molecules is crucial for accelerating drug discovery, organic chemistry, and optoelectronic materials. Despite the emergence of generative models to produce novel drug-like molecules, in a more realistic scenario, the complexity of functional groups (e.g., pyrene, acenaphthylene, and bridged-ring systems) and extensive molecular scaffolds remain challenging obstacles for the generation of complex organics. Traditionally, the former demands an extra learning process, e.g., molecular pre-training, and the latter requires expensive computational resources. To address these challenges, we propose OrgMol-Design, a multi-granularity framework for efficiently designing complex organics. Our OrgMol-Design is composed of a score-based generative model via fragment prior for diverse coarse-grained scaffold generation and a chemical-rule-aware scoring model for fine-grained molecular structure design, circumventing the difficulty of intricate substructure learning without losing connection details among fragments. Our approach achieves state-of-the-art performance in four real-world and more challenging benchmarks covering broader scientific domains, outperforming advanced molecule generative models. Additionally, it delivers a substantial speedup and graphics memory reduction compared to diffusion-based graph models. Our results also demonstrate the importance of leveraging fragment prior for a generalized molecule inverse design model.

cs.CE↗

arXiv2024

Machine Mindset: An MBTI Exploration of Large Language Models

We present a novel approach for integrating Myers-Briggs Type Indicator (MBTI) personality traits into large language models (LLMs), addressing the challenges of personality consistency in personalized AI. Our method, "Machine Mindset," involves a two-phase fine-tuning and Direct Preference Optimization (DPO) to embed MBTI traits into LLMs. This approach ensures that models internalize these traits, offering a stable and consistent personality profile. We demonstrate the effectiveness of our models across various domains, showing alignment between model performance and their respective MBTI traits. The paper highlights significant contributions in the development of personality datasets and a new training methodology for personality integration in LLMs, enhancing the potential for personalized AI applications. We also open-sourced our model and part of the data at \url{https://github.com/PKU-YuanGroup/Machine-Mindset}.

cs.CL↗

arXiv2024

Optimal ANN-SNN Conversion with Group Neurons

Spiking Neural Networks (SNNs) have emerged as a promising third generation of neural networks, offering unique characteristics such as binary outputs, high sparsity, and biological plausibility. However, the lack of effective learning algorithms remains a challenge for SNNs. For instance, while converting artificial neural networks (ANNs) to SNNs circumvents the need for direct training of SNNs, it encounters issues related to conversion errors and high inference time delays. In order to reduce or even eliminate conversion errors while decreasing inference time-steps, we have introduced a novel type of neuron called Group Neurons (GNs). One GN is composed of multiple Integrate-and-Fire (IF) neurons as members, and its neural dynamics are meticulously designed. Based on GNs, we have optimized the traditional ANN-SNN conversion framework. Specifically, we replace the IF neurons in the SNNs obtained by the traditional conversion framework with GNs. The resulting SNNs, which utilize GNs, are capable of achieving accuracy levels comparable to ANNs even within extremely short inference time-steps. The experiments on CIFAR10, CIFAR100, and ImageNet datasets demonstrate the superiority of the proposed methods in terms of both inference accuracy and latency. Code is available at https://github.com/Lyu6PosHao/ANN2SNN_GN.

cs.NE↗