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Researcher profile

Bing Su

Bing Su contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceComputer VisionCryptography and SecurityData Structures and Algorithmsecon.EMMethodology

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Published work

8 published item(s)

preprint2026arXiv

From Holo Pockets to Electron Density: GPT-style Drug Design with Density

Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative components such as the filler (ligands and solvent). Here, we leverage low-resolution electron density (ED) derived from the filler as a physically grounded condition for \textit{de novo} drug design. We consider two types of ED, calculated and cryo-EM/X-ray, obtainable from computational or experimental sources, supporting unified pre-training and experimental integration. Compared with rigid pocket representations, experimental ED naturally captures conformational flexibility and provides a more faithful description of the binding environment. Based on this, we introduce EDMolGPT, a decoder-only autoregressive framework that generates molecules from low-resolution ED point clouds. By grounding generation in physically meaningful density signals, EDMolGPT mitigates structural bias and produces molecules with 3D conformations. Evaluations on 101 biological targets verify the effectiveness. Our project page: https://jiahaochen1.github.io/EDMolGPT_Page/.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Statistical inference for the logarithmic spatial heteroskedasticity model with exogenous variables

The spatial dependence in mean has been well studied by plenty of models in a large strand of literature, however, the investigation of spatial dependence in variance is lagging significantly behind. The existing models for the spatial dependence in variance are scarce, with neither probabilistic structure nor statistical inference procedure being explored. To circumvent this deficiency, this paper proposes a new generalized logarithmic spatial heteroscedasticity model with exogenous variables (denoted by the log-SHE model) to study the spatial dependence in variance. For the log-SHE model, its spatial near-epoch dependence (NED) property is investigated, and a systematic statistical inference procedure is provided, including the maximum likelihood and generalized method of moments estimators, the Wald, Lagrange multiplier and likelihood-ratio-type D tests for model parameter constraints, and the overidentification test for the model diagnostic checking. Using the tool of spatial NED, the asymptotics of all proposed estimators and tests are established under regular conditions. The usefulness of the proposed methodology is illustrated by simulation results and a real data example on the house selling price.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language

Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality. Since the hierarchy of molecular knowledge is profound, even humans learn from different modalities including both intuitive diagrams and professional texts to assist their understanding. Inspired by this, we propose a molecular multimodal foundation model which is pretrained from molecular graphs and their semantically related textual data (crawled from published Scientific Citation Index papers) via contrastive learning. This AI model represents a critical attempt that directly bridges molecular graphs and natural language. Importantly, through capturing the specific and complementary information of the two modalities, our proposed model can better grasp molecular expertise. Experimental results show that our model not only exhibits promising performance in cross-modal tasks such as cross-modal retrieval and molecule caption, but also enhances molecular property prediction and possesses capability to generate meaningful molecular graphs from natural language descriptions. We believe that our model would have a broad impact on AI-empowered fields across disciplines such as biology, chemistry, materials, environment, and medicine, among others.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

An efficient polynomial-time approximation scheme for parallel multi-stage open shops

Various new scheduling problems have been arising from practical production processes and spawning new research areas in the scheduling field. We study the parallel multi-stage open shops problem, which generalizes the classic open shop scheduling and parallel machine scheduling problems. Given m identical k-stage open shops and a set of n jobs, we aim to process all jobs on these open shops with the minimum makespan, i.e., the completion time of the last job, under the constraint that job preemption is not allowed. We present an efficient polynomial-time approximation scheme (EPTAS) for the case when both m and k are constant. The main idea for our EPTAS is the combination of several categorization, scaling, and linear programming rounding techniques. Jobs and/or operations are first scaled and then categorized carefully into multiple types so that different types of jobs and/or operations are scheduled appropriately without increasing the makespan too much.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Interventional Contrastive Learning with Meta Semantic Regularizer

Contrastive learning (CL)-based self-supervised learning models learn visual representations in a pairwise manner. Although the prevailing CL model has achieved great progress, in this paper, we uncover an ever-overlooked phenomenon: When the CL model is trained with full images, the performance tested in full images is better than that in foreground areas; when the CL model is trained with foreground areas, the performance tested in full images is worse than that in foreground areas. This observation reveals that backgrounds in images may interfere with the model learning semantic information and their influence has not been fully eliminated. To tackle this issue, we build a Structural Causal Model (SCM) to model the background as a confounder. We propose a backdoor adjustment-based regularization method, namely Interventional Contrastive Learning with Meta Semantic Regularizer (ICL-MSR), to perform causal intervention towards the proposed SCM. ICL-MSR can be incorporated into any existing CL methods to alleviate background distractions from representation learning. Theoretically, we prove that ICL-MSR achieves a tighter error bound. Empirically, our experiments on multiple benchmark datasets demonstrate that ICL-MSR is able to improve the performances of different state-of-the-art CL methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Preformer: Predictive Transformer with Multi-Scale Segment-wise Correlations for Long-Term Time Series Forecasting

Transformer-based methods have shown great potential in long-term time series forecasting. However, most of these methods adopt the standard point-wise self-attention mechanism, which not only becomes intractable for long-term forecasting since its complexity increases quadratically with the length of time series, but also cannot explicitly capture the predictive dependencies from contexts since the corresponding key and value are transformed from the same point. This paper proposes a predictive Transformer-based model called {\em Preformer}. Preformer introduces a novel efficient {\em Multi-Scale Segment-Correlation} mechanism that divides time series into segments and utilizes segment-wise correlation-based attention for encoding time series. A multi-scale structure is developed to aggregate dependencies at different temporal scales and facilitate the selection of segment length. Preformer further designs a predictive paradigm for decoding, where the key and value come from two successive segments rather than the same segment. In this way, if a key segment has a high correlation score with the query segment, its successive segment contributes more to the prediction of the query segment. Extensive experiments demonstrate that our Preformer outperforms other Transformer-based methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Robust Local Preserving and Global Aligning Network for Adversarial Domain Adaptation

Unsupervised domain adaptation (UDA) requires source domain samples with clean ground truth labels during training. Accurately labeling a large number of source domain samples is time-consuming and laborious. An alternative is to utilize samples with noisy labels for training. However, training with noisy labels can greatly reduce the performance of UDA. In this paper, we address the problem that learning UDA models only with access to noisy labels and propose a novel method called robust local preserving and global aligning network (RLPGA). RLPGA improves the robustness of the label noise from two aspects. One is learning a classifier by a robust informative-theoretic-based loss function. The other is constructing two adjacency weight matrices and two negative weight matrices by the proposed local preserving module to preserve the local topology structures of input data. We conduct theoretical analysis on the robustness of the proposed RLPGA and prove that the robust informative-theoretic-based loss and the local preserving module are beneficial to reduce the empirical risk of the target domain. A series of empirical studies show the effectiveness of our proposed RLPGA.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Semi-WTC: A Practical Semi-supervised Framework for Attack Categorization through Weight-Task Consistency

Supervised learning has been widely used for attack categorization, requiring high-quality data and labels. However, the data is often imbalanced and it is difficult to obtain sufficient annotations. Moreover, supervised models are subject to real-world deployment issues, such as defending against unseen artificial attacks. To tackle the challenges, we propose a semi-supervised fine-grained attack categorization framework consisting of an encoder and a two-branch structure and this framework can be generalized to different supervised models. The multilayer perceptron with residual connection is used as the encoder to extract features and reduce the complexity. The Recurrent Prototype Module (RPM) is proposed to train the encoder effectively in a semi-supervised manner. To alleviate the data imbalance problem, we introduce the Weight-Task Consistency (WTC) into the iterative process of RPM by assigning larger weights to classes with fewer samples in the loss function. In addition, to cope with new attacks in real-world deployment, we propose an Active Adaption Resampling (AAR) method, which can better discover the distribution of unseen sample data and adapt the parameters of encoder. Experimental results show that our model outperforms the state-of-the-art semi-supervised attack detection methods with a 3% improvement in classification accuracy and a 90% reduction in training time.

0 citations0 reviewsNo code linkedOpen access