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Cong Fu

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8 papers

1 author row

TMLR Journal 2026 Journal Article

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials

Cong Fu
Yuchao Lin
Zachary Krueger
Haiyang Yu
Maho Nakata
Jianwen Xie
Emine Kucukbenli
Xiaofeng Qian

Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP pre-trained models are trained with supervised learning to predict energy and forces given 3D molecular structures. Once trained, we show that the pre-trained models can be used in different ways to obtain geometries either explicitly or implicitly. First, it can be used to obtain approximate low-energy 3D geometries via geometry optimization. While these geometries do not consistently reach DFT-level chemical accuracy or convergence, they can still improve downstream performance compared to non-relaxed structures. To mitigate potential biases and enhance downstream predictions, we introduce geometry fine-tuning based on the relaxed 3D geometries. Second, the pre-trained models can be directly fine-tuned for property prediction when ground truth 3D geometries are available. Our results demonstrate that MLIP pre-trained models trained on relaxation data can learn transferable molecular representations to improve downstream molecular property prediction and can provide practically valuable but approximate molecular geometries that benefit property predictions. Our code is publicly available at: https://github.com/divelab/AIRS/.

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NeurIPS Conference 2025 Conference Paper

Tensor Decomposition Networks for Fast Machine Learning Interatomic Potential Computations

Yuchao Lin
Cong Fu
Zachary Krueger
Haiyang Yu
Maho Nakata
Jianwen Xie
Emine Kucukbenli
Xiaofeng Qian

SO(3)-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks whose CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of SO(3)-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the O(L^3) CG paths into a single shared parameter set without compromising equivariance, where L is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from O(L^6) to O(L^4). We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations. Our code is publicly available as part of the AIRS library (https: //github. com/divelab/AIRS).

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JBHI Journal 2024 Journal Article

PSEENet: A Pseudo-Siamese Neural Network Incorporating Electroencephalography and Electrooculography Characteristics for Heterogeneous Sleep Staging

Wei Zhou
Ning Shen
Ligang Zhou
Minghui Liu
Yiyuan Zhang
Cong Fu
Huan Yu
Feng Shu

Sleep staging plays a critical role in evaluating the quality of sleep. Currently, most studies are either suffering from dramatic performance drops when coping with varying input modalities or unable to handle heterogeneous signals. To handle heterogeneous signals and guarantee favorable sleep staging performance when a single modality is available, a pseudo-siamese neural network (PSN) to incorporate electroencephalography (EEG), electrooculography (EOG) characteristics is proposed (PSEENet). PSEENet consists of two parts, spatial mapping modules (SMMs) and a weight-shared classifier. SMMs are used to extract high-dimensional features. Meanwhile, joint linkages among multi-modalities are provided by quantifying the similarity of features. Finally, with the cooperation of heterogeneous characteristics, associations within various sleep stages can be established by the classifier. The evaluation of the model is validated on two public datasets, namely, Montreal Archive of Sleep Studies (MASS) and SleepEDFX, and one clinical dataset from Huashan Hospital of Fudan University (HSFU). Experimental results show that the model can handle heterogeneous signals, provide superior results under multimodal signals and show good performance with single modality. PSEENet obtains accuracy of 79. 1%, 82. 1% with EEG, EEG and EOG on Sleep-EDFX, and significantly improves the accuracy with EOG from 73. 7% to 76% by introducing similarity information.

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JBHI Journal 2024 Journal Article

Towards Real-Time Sleep Stage Prediction and Online Calibration Based on Architecturally Switchable Deep Learning Models

Hangyu Zhu
Yonglin Wu
Yao Guo
Cong Fu
Feng Shu
Huan Yu
Wei Chen
Chen Chen

Despite the recent advances in automatic sleep staging, few studies have focused on real-time sleep staging to promote the regulation of sleep or the intervention of sleep disorders. In this paper, a novel network named SwSleepNet, that can handle both precisely offline sleep staging, and online sleep stages prediction and calibration is proposed. For offline analysis, the proposed network coordinates sequence broadening module (SBM), sequential CNN (SCNN), squeeze and excitation (SE) block, and sequence consolidation module (SCM) to balance the operational efficiency of the network and the comprehensive feature extraction. For online analysis, only SCNN and SE are involved in predicting the sleep stage within a short-time segment of the recordings. Once more than two successive segments have disparate predictions, the calibration mechanism will be triggered, and contextual information will be involved. In addition, to investigate the appropriate time of the segment that is suitable to predict a sleep stage, segments with five-second, three-second, and two-second data are analyzed. The performance of SwSleepNet is validated on two publicly available datasets Sleep-EDF Expanded and Montreal Archive of Sleep Studies (MASS), and one clinical dataset Huashan Hospital Fudan University (HSFU), with the offline accuracy of 84. 5%, 86. 7%, and 81. 8%, respectively, which outperforms the state-of-the-art methods. Additionally, for the online sleep staging, the dedicated calibration mechanism allows SwSleepNet to achieve high accuracy over 80% on three datasets with the short-time segments, demonstrating the robustness and stability of SwSleepNet. This study presents a real-time sleep staging architecture, which is expected to pave the way for accurate sleep regulation and intervention.

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JBHI Journal 2023 Journal Article

MaskSleepNet: A Cross-Modality Adaptation Neural Network for Heterogeneous Signals Processing in Sleep Staging

Hangyu Zhu
Wei Zhou
Cong Fu
Yonglin Wu
Ning Shen
Feng Shu
Huan Yu
Wei Chen

Deep learning methods have become an important tool for automatic sleep staging in recent years. However, most of the existing deep learning-based approaches are sharply constrained by the input modalities, where any insertion, substitution, and deletion of input modalities would directly lead to the unusable of the model or a deterioration in the performance. To solve the modality heterogeneity problems, a novel network architecture named MaskSleepNet is proposed. It consists of a masking module, a multi-scale convolutional neural network (MSCNN), a squeezing and excitation (SE) block, and a multi-headed attention (MHA) module. The masking module consists of a modality adaptation paradigm that can cooperate with modality discrepancy. The MSCNN extracts features from multiple scales and specially designs the size of the feature concatenation layer to prevent invalid or redundant features from zero-setting channels. The SE block further optimizes the weights of the features to optimize the network learning efficiency. The MHA module outputs the prediction results by learning the temporal information between the sleeping features. The performance of the proposed model was validated on two publicly available datasets, Sleep-EDF Expanded (Sleep-EDFX) and Montreal Archive of Sleep Studies (MASS), and a clinical dataset, Huashan Hospital Fudan University (HSFU). The proposed MaskSleepNet can achieve favorable performance with input modality discrepancy, e. g. for single-channel EEG signal, it can reach 83. 8%, 83. 4%, 80. 5%, for two-channel EEG+EOG signals it can reach 85. 0%, 84. 9%, 81. 9% and for three-channel EEG+EOG+EMG signals, it can reach 85. 7%, 87. 5%, 81. 1% on Sleep-EDFX, MASS, and HSFU, respectively. In contrast the accuracy of the state-of-the-art approach which fluctuated widely between 69. 0% and 89. 4%. The experimental results exhibit that the proposed model can maintain superior performance and robustness in handling input modality discrepancy issues.

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JMLR Journal 2021 Journal Article

DIG: A Turnkey Library for Diving into Graph Deep Learning Research

Meng Liu
Youzhi Luo
Limei Wang
Yaochen Xie
Hao Yuan
Shurui Gui
Haiyang Yu
Zhao Xu

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2021. ( edit, beta )

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IJCAI Conference 2019 Conference Paper

COP: Customized Deep Model Compression via Regularized Correlation-Based Filter-Level Pruning

Wenxiao Wang
Cong Fu
Jishun Guo
Deng Cai
Xiaofei He

Neural network compression empowers the effective yet unwieldy deep convolutional neural networks (CNN) to be deployed in resource-constrained scenarios. Most state-of-the-art approaches prune the model in filter-level according to the "importance" of filters. Despite their success, we notice they suffer from at least two of the following problems: 1) The redundancy among filters is not considered because the importance is evaluated independently. 2) Cross-layer filter comparison is unachievable since the importance is defined locally within each layer. Consequently, we must manually specify layer-wise pruning ratios. 3) They are prone to generate sub-optimal solutions because they neglect the inequality between reducing parameters and reducing computational cost. Reducing the same number of parameters in different positions in the network may reduce different computational cost. To address the above problems, we develop a novel algorithm named as COP (correlation-based pruning), which can detect the redundant filters efficiently. We enable the cross-layer filter comparison through global normalization. We add parameter-quantity and computational-cost regularization terms to the importance, which enables the users to customize the compression according to their preference (smaller or faster). Extensive experiments have shown COP outperforms the others significantly. The code is released at https: //github. com/ZJULearning/COP.

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IJCAI Conference 2018 Conference Paper

Translating Embeddings for Knowledge Graph Completion with Relation Attention Mechanism

Wei Qian
Cong Fu
Yu Zhu
Deng Cai
Xiaofei He

Knowledge graph embedding is an essential problem in knowledge extraction. Recently, translation based embedding models (e. g. , TransE) have received increasingly attentions. These methods try to interpret the relations among entities as translations from head entity to tail entity and achieve promising performance on knowledge graph completion. Previous researchers attempt to transform the entity embedding concerning the given relation for distinguishability. Also, they naturally think the relation-related transforming should reflect attention mechanism, which means it should focus on only a part of the attributes. However, we found previous methods are failed with creating attention mechanism, and the reason is that they ignore the hierarchical routine of human cognition. When predicting whether a relation holds between two entities, people first check the category of entities, then they focus on fined-grained relation-related attributes to make the decision. In other words, the attention should take effect on entities filtered by the right category. In this paper, we propose a novel knowledge graph embedding method named TransAt to learn the translation based embedding, relation-related categories of entities and relation-related attention simultaneously. Extensive experiments show that our approach outperforms state-of-the-art methods significantly on public datasets, and our method can learn the true attention varying among relations.

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