Haibin Wen
Publications
Autogenesis: A Self-Evolving Agent Protocol
Recent advances in LLM based agent systems have shown promise in tackling complex, long horizon tasks. However, existing agent protocols (e.g., A2A and MCP) under specify cross entity lifecycle and context management, version tracking, and evolution safe update interfaces, which encourages monolithic compositions and brittle glue code. We introduce Autogenesis Protocol (AGP), a self evolution protocol that decouples what evolves from how evolution occurs. Its Resource Substrate Protocol Layer (RSPL) models prompts, agents, tools, environments, and memory as protocol registered resources with explicit state, lifecycle, and versioned interfaces. Its Self Evolution Protocol Layer (SEPL) specifies a closed loop operator interface for proposing, assessing, and committing improvements with auditable lineage and rollback. Building on AGP, we present Autogenesis System (AGS), a self-evolving multi-agent system that dynamically instantiates, retrieves, and refines protocol-registered resources during execution. We evaluate AGS on multiple challenging benchmarks that require long horizon planning and tool use across heterogeneous resources. The results demonstrate consistent improvements over strong baselines, supporting the effectiveness of agent resource management and closed loop self evolution. The code is available at https://github.com/DVampire/Autogenesis.
ResearchEVO: An End-to-End Framework for Automated Scientific Discovery and Documentation
An important recurring pattern in scientific breakthroughs is a two-stage process: an initial phase of undirected experimentation that yields an unexpected finding, followed by a retrospective phase that explains why the finding works and situates it within existing theory. We present ResearchEVO, an end-to-end framework that computationally instantiates this discover-then-explain paradigm. The Evolution Phase employs LLM-guided bi-dimensional co-evolution -- simultaneously optimizing both algorithmic logic and overall architecture -- to search the space of code implementations purely by fitness, without requiring any understanding of the solutions it produces. The Writing Phase then takes the best-performing algorithm and autonomously generates a complete, publication-ready research paper through sentence-level retrieval-augmented generation with explicit anti-hallucination verification and automated experiment design. To our knowledge, ResearchEVO is the first system to cover this full pipeline end to end: no prior work jointly performs principled algorithm evolution and literature-grounded scientific documentation. We validate the framework on two cross-disciplinary scientific problems -- Quantum Error Correction using real Google quantum hardware data, and Physics-Informed Neural Networks -- where the Evolution Phase discovered human-interpretable algorithmic mechanisms that had not been previously proposed in the respective domain literatures. In both cases, the Writing Phase autonomously produced compilable LaTeX manuscripts that correctly grounded these blind discoveries in existing theory via RAG, with zero fabricated citations.
Logos: An evolvable reasoning engine for rational molecular design
The discovery and design of functional molecules remain central challenges across chemistry,biology, and materials science. While recent advances in machine learning have accelerated molecular property prediction and candidate generation, existing models tend to excel either in physical fidelity without transparent reasoning, or in flexible reasoning without guarantees of chemical validity. This imbalance limits the reliability of artificial intelligence systems in real scientific design workflows.Here we present Logos, a compact molecular reasoning model that integrates multi-step logical reasoning with strict chemical consistency. Logos is trained using a staged strategy that first exposes the model to explicit reasoning examples linking molecular descriptions to structural decisions, and then progressively aligns these reasoning patterns with molecular representations. In a final training phase, chemical rules and invariants are incorporated directly into the optimization objective, guiding the model toward chemically valid outputs. Across multiple benchmark datasets, Logos achieves strong performance in both structural accuracy and chemical validity, matching or surpassing substantially larger general-purpose language models while operating with a fraction of their parameters. Beyond benchmark evaluation, the model exhibits stable behaviour in molecular optimization tasks involving multiple, potentially conflicting constraints. By explicitly exposing intermediate reasoning steps, Logos enables human inspection and assessment of the design logic underlying each generated structure. These results indicate that jointly optimizing for reasoning structure and physical consistency offers a practical pathway toward reliable and interpretable AI systems for molecular science, supporting closer integration of artificial intelligence into scientific discovery processes.
EvoCodeBench: A Human-Performance Benchmark for Self-Evolving LLM-Driven Coding Systems
As large language models (LLMs) continue to advance in programming tasks, LLM-driven coding systems have evolved from one-shot code generation into complex systems capable of iterative improvement during inference. However, existing code benchmarks primarily emphasize static correctness and implicitly assume fixed model capability during inference. As a result, they do not capture inference-time self-evolution, such as whether accuracy and efficiency improve as an agent iteratively refines its solutions. They also provide limited accounting of resource costs and rarely calibrate model performance against that of human programmers. Moreover, many benchmarks are dominated by high-resource languages, leaving cross-language robustness and long-tail language stability underexplored. Therefore, we present EvoCodeBench, a benchmark for evaluating self-evolving LLM-driven coding systems across programming languages with direct comparison to human performance. EvoCodeBench tracks performance dynamics, measuring solution correctness alongside efficiency metrics such as solving time, memory consumption, and improvement algorithmic design over repeated problem-solving attempts. To ground evaluation in a human-centered reference frame, we directly compare model performance with that of human programmers on the same tasks, enabling relative performance assessment within the human ability distribution. Furthermore, EvoCodeBench supports multiple programming languages, enabling systematic cross-language and long-tail stability analyses under a unified protocol. Our results demonstrate that self-evolving systems exhibit measurable gains in efficiency over time, and that human-relative and multi-language analyses provide insights unavailable through accuracy alone. EvoCodeBench establishes a foundation for evaluating coding intelligence in evolving LLM-driven systems.