Yihan Zhu

Gang Liu, Jie Chen, Yihan Zhu et al.

In-context learning allows large models to adapt to new tasks from a few demonstrations, but it has shown limited success in molecular design. Existing databases such as ChEMBL contain molecular properties spanning millions of biological assays, yet labeled data for each property remain scarce. To address this limitation, we introduce demonstration-conditioned diffusion models (DemoDiff), which define task contexts using a small set of molecule-score examples instead of text descriptions. These demonstrations guide a denoising Transformer to generate molecules aligned with target properties. For scalable pretraining, we develop a new molecular tokenizer with Node Pair Encoding that represents molecules at the motif level, requiring 5.5$\times$ fewer nodes. We curate a dataset containing millions of context tasks from multiple sources covering both drugs and materials, and pretrain a 0.7-billion-parameter model on it. Across 33 design tasks in six categories, DemoDiff matches or surpasses language models 100-1000$\times$ larger and achieves an average rank of 3.63 compared to 5.25-10.20 for domain-specific approaches. These results position DemoDiff as a molecular foundation model for in-context molecular design. Our code is available at https://github.com/liugangcode/DemoDiff.

Gang Liu, Yihan Zhu, Jie Chen et al.

Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in complex domains, while pure deep research proposes ideas without validation, resulting in unrealistic or unimplementable solutions. We present DeepEvolve, an agent that integrates deep research with algorithm evolution, uniting external knowledge retrieval, cross-file code editing, and systematic debugging under a feedback-driven iterative loop. Each iteration not only proposes new hypotheses but also refines, implements, and tests them, avoiding both shallow improvements and unproductive over-refinements. Across nine benchmarks in chemistry, mathematics, biology, materials, and patents, DeepEvolve consistently improves the initial algorithm, producing executable new algorithms with sustained gains. By bridging the gap between unguided evolution and research without grounding, DeepEvolve provides a reliable framework for advancing scientific algorithm discovery. Our code is available at https://github.com/liugangcode/deepevolve.

Yihan Zhu, Gang Liu, Eric Inae et al.

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

Ling Wang, Songnan Liu, Jianan Wang et al.

Applying Large Language Models (LLMs) to heterogeneous enterprise systems is hindered by hallucinations and failures in multi-hop, n-ary reasoning. Existing paradigms (e.g., GraphRAG, NL2SQL) lack the semantic grounding and auditable execution required for these complex environments. We introduce HEAR, an enterprise agentic reasoner built on a Stratified Hypergraph Ontology. Its base Graph Layer virtualizes provenance-aware data interfaces, while the Hyperedge Layer encodes n-ary business rules and procedural protocols. Operating an evidence-driven reasoning loop, HEAR dynamically orchestrates ontology tools for structured multi-hop analysis without requiring LLM retraining. Evaluations on supply-chain tasks, including order fulfillment blockage root cause analysis (RCA), show HEAR achieves up to 94.7% accuracy. Crucially, HEAR demonstrates adaptive efficiency: utilizing procedural hyperedges to minimize token costs, while leveraging topological exploration for rigorous correctness on complex queries. By matching proprietary model performance with open-weight backbones and automating manual diagnostics, HEAR establishes a scalable, auditable foundation for enterprise intelligence.