arXiv subjects

Fenglei Cao

Publications and source records attributed to Fenglei Cao.

13 recordsLinked to original sources

arXiv2026

Monkey King Bang: A Unified Scientific Multimodal Foundation Model

Scientific discovery is increasingly shifting from isolated disciplines to multi-domain reasoning, and AI for science faces a similar transition. Existing systems are either specialised for individual domains or unify scientific data mainly through text tokenisation and prompt-based interfaces, limiting their ability to handle diverse scientific inputs, produce modality-native outputs, and support joint understanding, reasoning, and generation across scientific domains. We introduce MKB, a unified scientific multimodal model for both understanding and generation, built around a shared Transformer backbone and modality-tailored encoders, adapters, and decoders. MKB covers six scientific branches, including DNA, RNA, proteins, small molecules, earth science, and medical images, and supports native outputs such as biological sequences, molecular strings, meteorological fields, and segmentation masks. Training follows a two-stage modality-then-language curriculum: Stage 1 aligns modality-specific components with the frozen backbone, and Stage 2 consolidates them with the language backbone using mixed scientific and general corpora. Experiments show that MKB achieves competitive scientific understanding across biological and molecular benchmarks, produces high-fidelity native outputs for weather forecasting, biological generation, and medical-image segmentation, and largely retains the general capabilities of its Qwen3-VL backbone. These results demonstrate the feasibility of the proposed paradigm, suggesting that shared-backbone models with modality-tailored components can provide a promising foundation for future cross-domain scientific multimodal exploration. The model and code are publicly available at https://github.com/Shanghai-Academy-of-AI-For-Science/MKB and https://huggingface.co/sais-org/MKB.

cs.LG↗

arXiv2026

Nested Spatio-Temporal Time Series Forecasting

Spatiotemporal forecasting is critical for real-world applications like traffic management, yet capturing reliable interactions remains challenging under noisy and non-stationary conditions. Existing methods primarily rely on historical spatial priors, often failing to account for evolving temporal correlations and suffering from systematic errors. In this work, we propose a nested forecasting framework that couples future macro-level regional trends with micro-level historical observations, enabling top-down guidance from abstract future representations for fine-grained forecasting. Specifically, we employ a spectral clustering-based approach to construct semantically coherent regions, providing both theoretical and empirical evidence that this representation effectively filters systematic noise while preserving essential trends. Building on this, we develop a progressive coarse-to-fine predictor to integrate these representative features into the inference process. This enables the model to leverage trend predictions to anticipate dynamic anomalies, such as periodic offsets, in advance. Furthermore, extensive experiments on multiple high-dimensional datasets demonstrate that our method consistently outperforms state-of-the-art baselines, validating the effectiveness of future macro-guided nested forecasting.

cs.LG↗

arXiv2026

Suiren-1.0 Technical Report: A Family of Molecular Foundation Models

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

physics.chem-ph↗

arXiv2026

Equivariant Asynchronous Diffusion: An Adaptive Denoising Schedule for Accelerated Molecular Conformation Generation

Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between training and inference. Conversely, synchronous diffusion models denoise all atoms at once, offering a molecule-level horizon but failing to capture the causal relationships inherent in hierarchical molecular structures. We introduce Equivariant Asynchronous Diffusion (EAD) to overcome these limitations. EAD is a novel diffusion model that combines the strengths of both approaches: it uses an asynchronous denoising schedule to better capture molecular hierarchy while maintaining a molecule-level horizon. Since these relationships are often complex, we propose a dynamic scheduling mechanism to adaptively determine the denoising timestep. Experimental results show that EAD achieves state-of-the-art performance in 3D molecular generation.

cs.LG↗

arXiv2026

A Pre-trained Reaction Embedding Descriptor Capturing Bond Transformation Patterns

With the rise of data-driven reaction prediction models, effective reaction descriptors are crucial for bridging the gap between real-world chemistry and digital representations. However, general-purpose, reaction-wise descriptors remain scarce. This study introduces RXNEmb, a novel reaction-level descriptor derived from RXNGraphormer, a model pre-trained to distinguish real reactions from fictitious ones with erroneous bond changes, thereby learning intrinsic bond formation and cleavage patterns. We demonstrate its utility by data-driven re-clustering of the USPTO-50k dataset, yielding a classification that more directly reflects bond-change similarities than rule-based categories. Combined with dimensionality reduction, RXNEmb enables visualization of reaction space diversity. Furthermore, attention weight analysis reveals the model's focus on chemically critical sites, providing mechanistic insight. RXNEmb serves as a powerful, interpretable tool for reaction fingerprinting and analysis, paving the way for more data-centric approaches in reaction analysis and discovery.

cs.LG↗

arXiv2025

Equivariant Spherical Transformer for Efficient Molecular Modeling

Equivariant Graph Neural Networks (GNNs) have significantly advanced the modeling of 3D molecular structure by leveraging group representations. However, their message passing, heavily relying on Clebsch-Gordan tensor product convolutions, suffers from restricted expressiveness due to the limited non-linearity and low degree of group representations. To overcome this, we introduce the Equivariant Spherical Transformer (EST), a novel plug-and-play framework that applies a Transformer-like architecture to the Fourier spatial domain of group representations. EST achieves higher expressiveness than conventional models while preserving the crucial equivariant inductive bias through a uniform sampling strategy of spherical Fourier transforms. As demonstrated by our experiments on challenging benchmarks like OC20 and QM9, EST-based models achieve state-of-the-art performance. For the complex molecular systems within OC20, small models empowered by EST can outperform some larger models and those using additional data. In addition to demonstrating such strong expressiveness,we provide both theoretical and experimental validation of EST's equivariance as well, paving the way for new research in this area.

cs.LG↗

arXiv2025

Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generation

Generating physically realistic 3D molecular structures remains a core challenge in molecular generative modeling. While diffusion models equipped with equivariant neural networks have made progress in capturing molecular geometries, they often struggle to produce equilibrium structures that adhere to physical principles such as force field consistency. To bridge this gap, we propose Reinforcement Learning with Physical Feedback (RLPF), a novel framework that extends Denoising Diffusion Policy Optimization to 3D molecular generation. RLPF formulates the task as a Markov decision process and applies proximal policy optimization to fine-tune equivariant diffusion models. Crucially, RLPF introduces reward functions derived from force-field evaluations, providing direct physical feedback to guide the generation toward energetically stable and physically meaningful structures. Experiments on the QM9 and GEOM-drug datasets demonstrate that RLPF significantly improves molecular stability compared to existing methods. These results highlight the value of incorporating physics-based feedback into generative modeling. The code is available at: https://github.com/ZhijianZhou/RLPF/tree/verl_diffusion.

cs.LG↗

arXiv2025

ChemAmp: Amplified Chemistry Tools via Composable Agents

Although LLM-based agents are proven to master tool orchestration in scientific fields, particularly chemistry, their single-task performance remains limited by underlying tool constraints. To this end, we propose tool amplification, a novel paradigm that enhances the collective capabilities of specialized tools through optimized, dynamic coordination within individual tasks. Instantiating this paradigm, we introduce ChemAmp, a computationally lightweight framework that dynamically treats chemistry tools (e.g., UniMol2, Chemformer) as composable building-block agents. It constructs task-specialized super-agents that transcend atomic tool constraints with limited data ($\leq$10 samples). Our evaluations across four core chemistry tasks molecular design, molecule captioning, reaction prediction, and property prediction demonstrate that ChemAmp outperforms chemistry-specialized models, generalist LLMs, and agent systems with tool orchestration. Critically, this bottom-up construction strategy enables 94\% inference token cost reductions versus vanilla multi-agent systems.

cs.LG↗

arXiv2025

Equivariant Masked Position Prediction for Efficient Molecular Representation

Graph neural networks (GNNs) have shown considerable promise in computational chemistry. However, the limited availability of molecular data raises concerns regarding GNNs' ability to effectively capture the fundamental principles of physics and chemistry, which constrains their generalization capabilities. To address this challenge, we introduce a novel self-supervised approach termed Equivariant Masked Position Prediction (EMPP), grounded in intramolecular potential and force theory. Unlike conventional attribute masking techniques, EMPP formulates a nuanced position prediction task that is more well-defined and enhances the learning of quantum mechanical features. EMPP also bypasses the approximation of the Gaussian mixture distribution commonly used in denoising methods, allowing for more accurate acquisition of physical properties. Experimental results indicate that EMPP significantly enhances performance of advanced molecular architectures, surpassing state-of-the-art self-supervised approaches. Our code is released in https://github.com/ajy112/EMPP

cs.LG↗

arXiv2025

ChemHTS: Hierarchical Tool Stacking for Enhancing Chemical Agents

Large Language Models (LLMs) have demonstrated remarkable potential in scientific research, particularly in chemistry-related tasks such as molecular design, reaction prediction, and property estimation. While tool-augmented LLMs have been introduced to enhance reasoning and computation in these domains, existing approaches suffer from tool invocation errors and lack effective collaboration among diverse tools, limiting their overall performance. To address these challenges, we propose ChemHTS (Chemical Hierarchical Tool Stacking), a novel method that optimizes tool invocation pathways through a hierarchical stacking strategy. ChemHTS consists of two key stages: tool self-stacking warmup and multi-layer decision optimization, enabling LLMs to refine tool usage dynamically. We evaluate ChemHTS across four classical chemistry tasks and demonstrate its superiority over strong baselines, including GPT-4o, DeepSeek-R1, and chemistry-specific models, including ChemDFM. Furthermore, we define four distinct tool-stacking behaviors to enhance interpretability, providing insights into the effectiveness of tool collaboration. Our dataset and code are publicly available at \url{https://github.com/Chang-pw/ChemHTS}.

cs.CE↗

arXiv2024

An Open Quantum Chemistry Property Database of 120 Kilo Molecules with 20 Million Conformers

Artificial intelligence is revolutionizing computational chemistry, bringing unprecedented innovation and efficiency to the field. To further advance research and expedite progress, we introduce the Quantum Open Organic Molecular (QO2Mol) database -- a large-scale quantum chemistry dataset designed for professional and transformative research in organic molecular sciences under an open-source license. The database comprises 120,000 organic molecules and approximately 20 million conformers, encompassing 10 different elements (C, H, O, N, S, P, F, Cl, Br, I), with heavy atom counts exceeding 40. Utilizing the high-precision B3LYP/def2-SVP quantum mechanical level, each conformation was meticulously computed for quantum mechanical properties, including potential energy and forces. These molecules are derived from fragments of compounds in ChEMBL, ensuring their structural relevance to real-world compounds. Its extensive coverage of molecular structures and diverse elemental composition enables comprehensive studies of structure-property relationships, enhancing the accuracy and applicability of machine learning models in predicting molecular behaviors. The QO2Mol database and benchmark codes are available at https://github.com/saiscn/QO2Mol/ .

physics.chem-ph↗

arXiv2024

Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures

Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed to the limited availability, diversity, and heterogeneity of dynamic protein datasets. To address this gap, we propose to enhance existing prestigious static 3D protein structural databases, such as the Protein Data Bank (PDB), by integrating dynamic data and additional physical properties. Specifically, we introduce a large-scale dataset, Dynamic PDB, encompassing approximately 12.6K proteins, each subjected to all-atom molecular dynamics (MD) simulations lasting 1 microsecond to capture conformational changes. Furthermore, we provide a comprehensive suite of physical properties, including atomic velocities and forces, potential and kinetic energies of proteins, and the temperature of the simulation environment, recorded at 1 picosecond intervals throughout the simulations. For benchmarking purposes, we evaluate state-of-the-art methods on the proposed dataset for the task of trajectory prediction. To demonstrate the value of integrating richer physical properties in the study of protein dynamics and related model design, we base our approach on the SE(3) diffusion model and incorporate these physical properties into the trajectory prediction process. Preliminary results indicate that this straightforward extension of the SE(3) model yields improved accuracy, as measured by MAE and RMSD, when the proposed physical properties are taken into consideration. https://fudan-generative-vision.github.io/dynamicPDB/ .

q-bio.BM↗

arXiv2011

The Structural, Energetic and Electronic Properties of Doped Carbon Nanotubes by Encapsulation of MCp2 (M=Fe, Co, Ni): a Theoretical Investigation

Metallocenes can be encapsulated inside the carbon nanotubes. The structural, energetic and electronic properties of organometallic MCp2@SWCNT are obtained from DFT method. We verify that such encapsulation is noncovalent functionalization, and examined binding energies and charge transfers of MCp2@(16,0)SWCNT systems. Consistent with recent experimental findings, the optimal distance between FeCp2 center and near tube-wall is 4.7 (5.1) Å for the configuration where MCp2's five-fold axis is parallel (vertical) to nanotube axis, while the minimal diameter is 9.4 (10.2) Å to exothermically encapsulate FeCp2 molecules. Finally we clarify the doping effects near the bandgap by encapsulations of CoCp2 and NiCp2.

cond-mat.mtrl-sci↗