arXiv subjects

Botian Wang

Publications and source records attributed to Botian Wang.

4 recordsLinked to original sources

arXiv2026

Solvent: Long-Horizon Reasoning for Multi-Step Retrosynthesis

Multi-step retrosynthesis requires recursively transforming a target molecule through successive reaction steps into purchasable building blocks, and recent work has begun to draw on large language model (LLM) reasoning to tackle the task. In its latest evolution, LLM reasoning has entered the long-horizon regime: models pursue objectives across interdependent steps, interact with environments, and adapt to feedback. This shift has markedly advanced LLM capabilities, as illustrated by breakthroughs in AI-driven mathematical research. At this frontier, we introduce Solvent, an 8B LLM that successfully extends long-horizon reasoning to multi-step retrosynthesis. Through a two-round post-training curriculum, Solvent learns to interleave iterative synthesis planning, external availability verification, and adaptive route revision. Experiments show that, following a $2.1\times$ performance boost from RL, Solvent scores 61.86% across four benchmarks, surpassing mid-scale language models and prior search-based retrosynthesis systems, and rivaling frontier trillion-parameter LLMs.

cs.AI↗

arXiv2026

QProtFuse: Query-Guided Layer Fusion for Retrieval-Augmented Protein Function Prediction

Predicting protein functions from amino acid sequences is essential to understanding biological processes. Large language models (LLMs) offer flexible function descriptions to natural-language queries, yet their limited protein understanding motivates retrieval-augmented generation (RAG). Existing protein RAG methods primarily expand external retrieval signals while overlooking the rich knowledge encoded within a single protein language model (PLM). We show that retrieval performance varies across PLM layers and biological tasks, making conventional final-layer selection suboptimal. To this end, we propose QProtFuse, which uses queries to adaptively fuse multi-layer protein features and jointly learns protein and annotation retrieval through intra-modal and cross-modal contrastive objectives. On Prot-Inst-OOD, QProtFuse achieves the best protein and annotation retrieval scores, reaching 16.4\% Recall@1 with annotation reranking. These gains improve downstream RAG-based function descriptions, yielding the highest LLM-as-a-judge scores for both Qwen3-8B (6.22/10) and DeepSeek-V4-Pro (6.68/10). Ablations and weight analyses demonstrate the value of query-guided fusion and complementary training objectives for exploiting a PLM's internal knowledge.

cs.IR↗

arXiv2026

Enhancing Spatial Reasoning in Large Language Models for Metal-Organic Frameworks Structure Prediction

Metal-organic frameworks (MOFs) are porous crystalline materials with broad applications such as carbon capture and drug delivery, yet accurately predicting their 3D structures remains a significant challenge. While Large Language Models (LLMs) have shown promise in generating crystal structures, their application to MOFs is hindered by MOFs' high structural complexity arising from the large number of atoms in unit cell. Inspired by the success of block-wise paradigms in deep generative models for MOFs, we pioneer the application of LLMs in this domain by introducing MOF-LLM, the first LLM framework specifically adapted for block-level MOF structure prediction. To effectively harness LLMs for this 3D modular assembly task, our training paradigm integrates spatial-aware continual pre-training (CPT), structural supervised fine-tuning (SFT), and matching-driven reinforcement learning (RL). By incorporating explicit spatial priors and optimizing structural stability via Soft Adaptive Policy Optimization (SAPO), our approach substantially enhances the spatial reasoning in a Qwen-3 8B model for MOF structure prediction. Comprehensive experiments demonstrate that MOF-LLM achieves state-of-the-art performance with a match rate of 35.78% while exhibiting superior sampling efficiency of 0.04 seconds per structure.

cs.LG↗

arXiv2026

MoMa: A Modular Deep Learning Framework for Material Property Prediction

Deep learning methods for material property prediction have been widely explored to advance materials discovery. However, the prevailing pre-train then fine-tune paradigm often fails to address the inherent diversity and disparity of material tasks. To overcome these challenges, we introduce MoMa, a Modular framework for Materials that first trains specialized modules across a wide range of tasks and then adaptively composes synergistic modules tailored to each downstream scenario. Evaluation across 17 datasets demonstrates the superiority of MoMa, with a substantial 14% average improvement over the strongest baseline. Few-shot and continual learning experiments further highlight MoMa's potential for real-world applications. Pioneering a new paradigm of modular material learning, MoMa will be open-sourced to foster broader community collaboration.

cs.LG↗