He Cao

Tianhe Ren, Shilong Liu, Feng Li et al.

The DEtection TRansformer (DETR) algorithm has received considerable attention in the research community and is gradually emerging as a mainstream approach for object detection and other perception tasks. However, the current field lacks a unified and comprehensive benchmark specifically tailored for DETR-based models. To address this issue, we develop a unified, highly modular, and lightweight codebase called detrex, which supports a majority of the mainstream DETR-based instance recognition algorithms, covering various fundamental tasks, including object detection, segmentation, and pose estimation. We conduct extensive experiments under detrex and perform a comprehensive benchmark for DETR-based models. Moreover, we enhance the performance of detection transformers through the refinement of training hyper-parameters, providing strong baselines for supported algorithms.We hope that detrex could offer research communities a standardized and unified platform to evaluate and compare different DETR-based models while fostering a deeper understanding and driving advancements in DETR-based instance recognition. Our code is available at https://github.com/IDEA-Research/detrex. The project is currently being actively developed. We encourage the community to use detrex codebase for further development and contributions.

Xuantong Liu, Jianfeng Zhang, Tianyang Hu et al.

Although deep neural networks achieve tremendous success on various classification tasks, the generalization ability drops sheer when training datasets exhibit long-tailed distributions. One of the reasons is that the learned representations (i.e. features) from the imbalanced datasets are less effective than those from balanced datasets. Specifically, the learned representation under class-balanced distribution will present the Neural Collapse (NC) phenomena. NC indicates the features from the same category are close to each other and from different categories are maximally distant, showing an optimal linear separable state of classification. However, the pattern differs on imbalanced datasets and is partially responsible for the reduced performance of the model. In this work, we propose two explicit feature regularization terms to learn high-quality representation for class-imbalanced data. With the proposed regularization, NC phenomena will appear under the class-imbalanced distribution, and the generalization ability can be significantly improved. Our method is easily implemented, highly effective, and can be plugged into most existing methods. The extensive experimental results on widely-used benchmarks show the effectiveness of our method

He Cao, Jianan Wang, Tianhe Ren et al.

Score-based diffusion models have captured widespread attention and funded fast progress of recent vision generative tasks. In this paper, we focus on diffusion model backbone which has been much neglected before. We systematically explore vision Transformers as diffusion learners for various generative tasks. With our improvements the performance of vanilla ViT-based backbone (IU-ViT) is boosted to be on par with traditional U-Net-based methods. We further provide a hypothesis on the implication of disentangling the generative backbone as an encoder-decoder structure and show proof-of-concept experiments verifying the effectiveness of a stronger encoder for generative tasks with ASymmetriC ENcoder Decoder (ASCEND). Our improvements achieve competitive results on CIFAR-10, CelebA, LSUN, CUB Bird and large-resolution text-to-image tasks. To the best of our knowledge, we are the first to successfully train a single diffusion model on text-to-image task beyond 64x64 resolution. We hope this will motivate people to rethink the modeling choices and the training pipelines for diffusion-based generative models.

He Cao, Zijing Liu, Xingyu Lu et al.

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

Jiamin Wu, He Cao, Yuan Yao

Ligand molecule conformation generation is a critical challenge in drug discovery. Deep learning models have been developed to tackle this problem, particularly through the use of generative models in recent years. However, these models often generate conformations that lack meaningful structure and randomness due to the absence of essential side information. Examples of such side information include the chemical and geometric features of the target protein, ligand-target compound interactions, and ligand chemical properties. Without these constraints, the generated conformations may not be suitable for further selection and design of new drugs. To address this limitation, we propose a novel method for generating ligand conformations that leverage side information and incorporate flexible constraints into standard diffusion models. Drawing inspiration from the concept of message passing, we introduce ligand-target massage passing block, a mechanism that facilitates the exchange of information between target nodes and ligand nodes, thereby incorporating target node features. To capture non-covalent interactions, we introduce ligand-target compound inter and intra edges. To further improve the biological relevance of the generated conformations, we train energy models using scalar chemical features. These models guide the progress of the standard Denoising Diffusion Probabilistic Models, resulting in more biologically meaningful conformations. We evaluate the performance of SIDEGEN using the PDBBind-2020 dataset, comparing it against other methods. The results demonstrate improvements in both Aligned RMSD and Ligand RMSD evaluations. Specifically, our model outperforms GeoDiff (trained on PDBBind-2020) by 20% in terms of the median aligned RMSD metric.

Zijing Liu, Bin Feng, He Cao et al.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

Juntong Wu, Zijing Liu, He Cao et al.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

He Cao, Yanjun Shao, Zhiyuan Liu et al.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

Xingyu Lu, He Cao, Zijing Liu et al.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

Hao Li, He Cao, Bin Feng et al.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Tianshuo Zhang, Wenzhe Zhai, Rui Yann et al.

Fluid-structure interaction is common in engineering and natural systems, where floating-body motion is governed by added mass, drag, and background flows. Modeling these dissipative dynamics is difficult: black-box neural models regress state derivatives with limited interpretability and unstable long-horizon predictions. We propose Floating-Body Hydrodynamic Neural Networks (FHNN), a physics-structured framework that predicts interpretable hydrodynamic parameters such as directional added masses, drag coefficients, and a streamfunction-based flow, and couples them with analytic equations of motion. This design constrains the hypothesis space, enhances interpretability, and stabilizes integration. On synthetic vortex datasets, FHNN achieves up to an order-of-magnitude lower error than Neural ODEs, recovers physically consistent flow fields. Compared with Hamiltonian and Lagrangian neural networks, FHNN more effectively handles dissipative dynamics while preserving interpretability, which bridges the gap between black-box learning and transparent system identification.

June M. Liu, He Cao, Renliang Sun et al.

Generating emotionally appropriate responses in conversations with large language models presents a significant challenge due to the complexities of human emotions and cognitive processes, which remain largely underexplored in their critical role in social interactions. In this study, we introduce a two-stage automatic data generation framework to create CAPE, a Chinese dataset named Cognitive Appraisal theory-based Emotional corpus. This corpus facilitates the generation of dialogues with contextually appropriate emotional responses by accounting for diverse personal and situational factors. We propose two tasks utilizing this dataset: emotion prediction and next utterance prediction. Both automated and human evaluations demonstrate that agents trained on our dataset can deliver responses that are more aligned with human emotional expressions. Our study shows the potential for advancing emotional expression in conversational agents, paving the way for more nuanced and meaningful human-computer interactions.

Tianhe Ren, Shilong Liu, Ailing Zeng et al.

We introduce Grounded SAM, which uses Grounding DINO as an open-set object detector to combine with the segment anything model (SAM). This integration enables the detection and segmentation of any regions based on arbitrary text inputs and opens a door to connecting various vision models. As shown in Fig.1, a wide range of vision tasks can be achieved by using the versatile Grounded SAM pipeline. For example, an automatic annotation pipeline based solely on input images can be realized by incorporating models such as BLIP and Recognize Anything. Additionally, incorporating Stable-Diffusion allows for controllable image editing, while the integration of OSX facilitates promptable 3D human motion analysis. Grounded SAM also shows superior performance on open-vocabulary benchmarks, achieving 48.7 mean AP on SegInW (Segmentation in the wild) zero-shot benchmark with the combination of Grounding DINO-Base and SAM-Huge models.

Yukun Huang, Jianan Wang, Ailing Zeng et al.

We present DreamWaltz, a novel framework for generating and animating complex 3D avatars given text guidance and parametric human body prior. While recent methods have shown encouraging results for text-to-3D generation of common objects, creating high-quality and animatable 3D avatars remains challenging. To create high-quality 3D avatars, DreamWaltz proposes 3D-consistent occlusion-aware Score Distillation Sampling (SDS) to optimize implicit neural representations with canonical poses. It provides view-aligned supervision via 3D-aware skeleton conditioning which enables complex avatar generation without artifacts and multiple faces. For animation, our method learns an animatable 3D avatar representation from abundant image priors of diffusion model conditioned on various poses, which could animate complex non-rigged avatars given arbitrary poses without retraining. Extensive evaluations demonstrate that DreamWaltz is an effective and robust approach for creating 3D avatars that can take on complex shapes and appearances as well as novel poses for animation. The proposed framework further enables the creation of complex scenes with diverse compositions, including avatar-avatar, avatar-object and avatar-scene interactions. See https://dreamwaltz3d.github.io/ for more vivid 3D avatar and animation results.