Haibin Wen

Zhe Zhao, Haibin Wen, Yingcheng Wu et al.

Scientific discovery demands intelligence, perseverance, and serendipity across vast search spaces. Today, top scientific capabilities remain siloed--one AI system for biological analysis, another for clinical reasoning, mathematical derivation, or materials simulation--and no pre-designed team can anticipate every skill a question will need. Science Earth is a planet-scale scientific runtime in which any capability--a simulation cluster, a wet-lab robot, a proof engine, a single-cell pipeline--can connect to any other, with collaboration structure emerging from the question itself. Its underlying EACN protocol lets capabilities discover one another, negotiate task ownership, and adjudicate across incompatible evidentiary standards without prior knowledge of who will meet whom. This shifts the organizing challenge from workflow design to open-ended connectivity. Two runs validate this under structurally distinct conditions. In a trans-Pacific higher-order Kuramoto synchronization study, agents identified and corrected a closure-ratio assumption in Ott-Antonsen analytic theory that fails outside the Lorentzian limit, within thirty minutes. In an eight-agent single-cell run on the 4.88M-cell Kang 2024 pan-cancer atlas, heterogeneous capabilities coupled over a 64.9-hour window with one structural external instruction, producing three new result layers and anchoring findings against an independent wet-lab study on an adjacent CCR8- TIGIT+ Treg subset. These cases are a first empirical reading, not a benchmark sweep. They show that when AI capabilities are truly connectable and coordination emerges from the problem, scientific reasoning becomes a distributed, self-correcting process--a step towards scaling AI-native discovery to the planet.

Wentao Zhang, Zhe Zhao, Haibin Wen et al.

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.

Haibin Wen, Zhe Zhao, Fanfu Wang et al.

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.

Zhe Zhao, Haibin Wen, Jiaming Ma et al.

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.

Zhe Zhao, Haibin Wen, Pengkun Wang et al.

Large language models (LLMs) have greatly accelerated the automation of algorithm generation and optimization. However, current methods such as EoH and FunSearch mainly rely on predefined templates and expert-specified functions that focus solely on the local evolution of key functionalities. Consequently, they fail to fully leverage the synergistic benefits of the overall architecture and the potential of global optimization. In this paper, we introduce an end-to-end algorithm generation and optimization framework based on LLMs. Our approach utilizes the deep semantic understanding of LLMs to convert natural language requirements or human-authored papers into code solutions, and employs a two-dimensional co-evolution strategy to optimize both functional and structural aspects. This closed-loop process spans problem analysis, code generation, and global optimization, automatically identifying key algorithm modules for multi-level joint optimization and continually enhancing performance and design innovation. Extensive experiments demonstrate that our method outperforms traditional local optimization approaches in both performance and innovation, while also exhibiting strong adaptability to unknown environments and breakthrough potential in structural design. By building on human research, our framework generates and optimizes novel algorithms that surpass those designed by human experts, broadening the applicability of LLMs for algorithm design and providing a novel solution pathway for automated algorithm development.

Wentao Zhang, Jianfeng Wang, Liheng Liang et al.

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.

Zhe Zhao, Yuheng Yang, Haibin Wen et al.

The integration of Large Language Models (LLMs) with Evolutionary Computation (EC) has unlocked new frontiers in scientific discovery but remains shackled by a fundamental constraint: the reliance on an Oracle--an objective, machine-computable fitness function. This paper breaks this barrier by asking: Can evolution thrive in a purely subjective landscape governed solely by LLM judges? We introduce MADE (Multi-Agent Decomposed Evolution), a framework that tames the inherent noise of subjective evaluation through "Problem Specification." By decomposing vague instructions into specific, verifiable sub-requirements, MADE transforms high-variance LLM feedback into stable, precise selection pressure. The results are transformative: across complex benchmarks like DevAI and InfoBench, MADE outperforms strong baselines by over 50% in software requirement satisfaction (39.9% to 61.9%) and achieves a 95% perfect pass rate on complex instruction following. This work validates a fundamental paradigm shift: moving from optimizing "computable metrics" to "describable qualities," thereby unlocking evolutionary optimization for the vast open-ended domains where no ground truth exists.

Zhe Zhao, Pengkun Wang, Xu Wang et al.

Pre-training GNNs to extract transferable knowledge and apply it to downstream tasks has become the de facto standard of graph representation learning. Recent works focused on designing self-supervised pre-training tasks to extract useful and universal transferable knowledge from large-scale unlabeled data. However, they have to face an inevitable question: traditional pre-training strategies that aim at extracting useful information about pre-training tasks, may not extract all useful information about the downstream task. In this paper, we reexamine the pre-training process within traditional pre-training and fine-tuning frameworks from the perspective of Information Bottleneck (IB) and confirm that the forgetting phenomenon in pre-training phase may cause detrimental effects on downstream tasks. Therefore, we propose a novel \underline{D}elayed \underline{B}ottlenecking \underline{P}re-training (DBP) framework which maintains as much as possible mutual information between latent representations and training data during pre-training phase by suppressing the compression operation and delays the compression operation to fine-tuning phase to make sure the compression can be guided with labeled fine-tuning data and downstream tasks. To achieve this, we design two information control objectives that can be directly optimized and further integrate them into the actual model design. Extensive experiments on both chemistry and biology domains demonstrate the effectiveness of DBP.