Innovator-VL: A Multimodal Large Language Model for Scientific Discovery

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.

Bohrium + SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scale

AI agents are emerging as a practical way to run multi-step scientific workflows that interleave reasoning with tool use and verification, pointing to a shift from isolated AI-assisted steps toward \emph{agentic science at scale}. This shift is increasingly feasible, as scientific tools and models can be invoked through stable interfaces and verified with recorded execution traces, and increasingly necessary, as AI accelerates scientific output and stresses the peer-review and publication pipeline, raising the bar for traceability and credible evaluation. However, scaling agentic science remains difficult: workflows are hard to observe and reproduce; many tools and laboratory systems are not agent-ready; execution is hard to trace and govern; and prototype AI Scientist systems are often bespoke, limiting reuse and systematic improvement from real workflow signals. We argue that scaling agentic science requires an infrastructure-and-ecosystem approach, instantiated in Bohrium+SciMaster. Bohrium acts as a managed, traceable hub for AI4S assets -- akin to a HuggingFace of AI for Science -- that turns diverse scientific data, software, compute, and laboratory systems into agent-ready capabilities. SciMaster orchestrates these capabilities into long-horizon scientific workflows, on which scientific agents can be composed and executed. Between infrastructure and orchestration, a \emph{scientific intelligence substrate} organizes reusable models, knowledge, and components into executable building blocks for workflow reasoning and action, enabling composition, auditability, and improvement through use. We demonstrate this stack with eleven representative master agents in real workflows, achieving orders-of-magnitude reductions in end-to-end scientific cycle time and generating execution-grounded signals from real workloads at multi-million scale.

Fused Gromov-Wasserstein Contrastive Learning for Effective Enzyme-Reaction Screening

Enzymes are crucial catalysts that enable a wide range of biochemical reactions. Efficiently identifying specific enzymes from vast protein libraries is essential for advancing biocatalysis. Traditional computational methods for enzyme screening and retrieval are time-consuming and resource-intensive. Recently, deep learning approaches have shown promise. However, these methods focus solely on the interaction between enzymes and reactions, overlooking the inherent hierarchical relationships within each domain. To address these limitations, we introduce FGW-CLIP, a novel contrastive learning framework based on optimizing the fused Gromov-Wasserstein distance. FGW-CLIP incorporates multiple alignments, including inter-domain alignment between reactions and enzymes and intra-domain alignment within enzymes and reactions. By introducing a tailored regularization term, our method minimizes the Gromov-Wasserstein distance between enzyme and reaction spaces, which enhances information integration across these domains. Extensive evaluations demonstrate the superiority of FGW-CLIP in challenging enzyme-reaction tasks. On the widely-used EnzymeMap benchmark, FGW-CLIP achieves state-of-the-art performance in enzyme virtual screening, as measured by BEDROC and EF metrics. Moreover, FGW-CLIP consistently outperforms across all three splits of ReactZyme, the largest enzyme-reaction benchmark, demonstrating robust generalization to novel enzymes and reactions. These results position FGW-CLIP as a promising framework for enzyme discovery in complex biochemical settings, with strong adaptability across diverse screening scenarios.

MM-R5: MultiModal Reasoning-Enhanced ReRanker via Reinforcement Learning for Document Retrieval

Multimodal document retrieval systems enable information access across text, images, and layouts, benefiting various domains like document-based question answering, report analysis, and interactive content summarization. Rerankers improve retrieval precision by reordering retrieved candidates. However, current multimodal reranking methods remain underexplored, with significant room for improvement in both training strategies and overall effectiveness. Moreover, the lack of explicit reasoning makes it difficult to analyze and optimize these methods further. In this paper, We propose MM-R5, a MultiModal Reasoning-Enhanced ReRanker via Reinforcement Learning for Document Retrieval, aiming to provide a more effective and reliable solution for multimodal reranking tasks. MM-R5 is trained in two stages: supervised fine-tuning (SFT) and reinforcement learning (RL). In the SFT stage, we focus on improving instruction-following and guiding the model to generate complete and high-quality reasoning chains. To support this, we introduce a novel data construction strategy that produces rich, high-quality reasoning data. In the RL stage, we design a task-specific reward framework, including a reranking reward tailored for multimodal candidates and a composite template-based reward to further refine reasoning quality. We conduct extensive experiments on MMDocIR, a challenging public benchmark spanning multiple domains. MM-R5 achieves state-of-the-art performance on most metrics and delivers comparable results to much larger models on the remaining ones. Moreover, compared to the best retrieval-only method, MM-R5 improves recall@1 by over 4%. These results validate the effectiveness of our reasoning-enhanced training pipeline.

Tokenizing Electron Cloud in Protein-Ligand Interaction Learning

The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Most deep-learning-based prediction approaches focus on structures of atoms or fragments. However, quantum chemical properties, such as electronic structures, are the key to unveiling interaction patterns but remain largely underexplored. To bridge this gap, we propose ECBind, a method for tokenizing electron cloud signals into quantized embeddings, enabling their integration into downstream tasks such as binding affinity prediction. By incorporating electron densities, ECBind helps uncover binding modes that cannot be fully represented by atom-level models. Specifically, to remove the redundancy inherent in electron cloud signals, a structure-aware transformer and hierarchical codebooks encode 3D binding sites enriched with electron structures into tokens. These tokenized codes are then used for specific tasks with labels. To extend its applicability to a wider range of scenarios, we utilize knowledge distillation to develop an electron-cloud-agnostic prediction model. Experimentally, ECBind demonstrates state-of-the-art performance across multiple tasks, achieving improvements of 6.42\% and 15.58\% in per-structure Pearson and Spearman correlation coefficients, respectively.

FlightGPT: Towards Generalizable and Interpretable UAV Vision-and-Language Navigation with Vision-Language Models

Unmanned Aerial Vehicle (UAV) Vision-and-Language Navigation (VLN) is vital for applications such as disaster response, logistics delivery, and urban inspection. However, existing methods often struggle with insufficient multimodal fusion, weak generalization, and poor interpretability. To address these challenges, we propose FlightGPT, a novel UAV VLN framework built upon Vision-Language Models (VLMs) with powerful multimodal perception capabilities. We design a two-stage training pipeline: first, Supervised Fine-Tuning (SFT) using high-quality demonstrations to improve initialization and structured reasoning; then, Group Relative Policy Optimization (GRPO) algorithm, guided by a composite reward that considers goal accuracy, reasoning quality, and format compliance, to enhance generalization and adaptability. Furthermore, FlightGPT introduces a Chain-of-Thought (CoT)-based reasoning mechanism to improve decision interpretability. Extensive experiments on the city-scale dataset CityNav demonstrate that FlightGPT achieves state-of-the-art performance across all scenarios, with a 9.22\% higher success rate than the strongest baseline in unseen environments. Our implementation is publicly available.

PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models

Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing various conformation generation methods for small molecules and proteins, these methods struggle to generate polymer conformations due to polymers' unique structural characteristics. The scarcity of polymer conformation datasets further limits progress, making this promising area largely unexplored. In this work, we propose PolyConf, a pioneering tailored polymer conformation generation method that leverages hierarchical generative models to unlock new possibilities for this task. Specifically, we decompose the polymer conformation into a series of local conformations (i.e., the conformations of its repeating units), generating these local conformations through an autoregressive model. We then generate corresponding orientation transformations via a diffusion model to assemble these local conformations into the complete polymer conformation. Moreover, we develop the first benchmark with a high-quality polymer conformation dataset derived from molecular dynamics simulations to boost related research in this area. The comprehensive evaluation demonstrates that PolyConf consistently generates high-quality polymer conformations, facilitating advancements in polymer modeling and simulation.

Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding (3D GU) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates 3D GU tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse 3D GU tasks within a single autoregressive framework. Extensive experiments across multiple microscopic 3D GU tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

Representation Learning, Large-Scale 3D Molecular Pretraining, Molecular Property

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Inverse Materials Design by Large Language Model-Assisted Generative Framework

Deep generative models hold great promise for inverse materials design, yet their efficiency and accuracy remain constrained by data scarcity and model architecture. Here, we introduce AlloyGAN, a closed-loop framework that integrates Large Language Model (LLM)-assisted text mining with Conditional Generative Adversarial Networks (CGANs) to enhance data diversity and improve inverse design. Taking alloy discovery as a case study, AlloyGAN systematically refines material candidates through iterative screening and experimental validation. For metallic glasses, the framework predicts thermodynamic properties with discrepancies of less than 8% from experiments, demonstrating its robustness. By bridging generative AI with domain knowledge and validation workflows, AlloyGAN offers a scalable approach to accelerate the discovery of materials with tailored properties, paving the way for broader applications in materials science.