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Researcher profile

Jiangbin Zheng

Jiangbin Zheng contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer VisionMachine LearningArtificial IntelligenceBiomoleculeseess.IVQuantitative Methods

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Published work

5 published item(s)

preprint2026arXiv

MetaGEM: Bottom-Up Reconstruction of Genome-Scale Metabolic Networks via Deep Enzyme-Metabolite Anchoring

Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark matter unresolved. Direct reconstruction from metabolomics is also difficult because mapping observed metabolites to reactions is an ill-posed inverse problem with combinatorial ambiguity and possible spurious networks. Here we present MetaGEM, a bottom-up framework that uses enzymes as physical anchors to convert system-level network inference into enzyme-metabolite interaction prediction. MetaGEM uses a multimodal dual-tower architecture that combines protein evolutionary semantics from a protein language model with three-dimensional metabolite representations. It further introduces contrastive learning with hard negative mining to separate structurally similar metabolites and reduce false positive interactions. On a de-homologized benchmark, MetaGEM achieves state-of-the-art enzyme-metabolite prediction performance, with AUROC of 0.9701 and MCC of 0.8033, and remains robust under low sequence identity splits. In downstream reconstruction, MetaGEM generates functional genome-scale metabolic models for Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. The reconstructed models improve network connectivity, capture promiscuous enzymes, and show strong agreement with experimental phenotype microarray and gene essentiality data. These results indicate that MetaGEM provides a practical route from metabolomic evidence to computable metabolic networks and offers a foundation for automated AI-driven virtual cell reconstruction.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

Graph-level Protein Representation Learning by Structure Knowledge Refinement

This paper focuses on learning representation on the whole graph level in an unsupervised manner. Learning graph-level representation plays an important role in a variety of real-world issues such as molecule property prediction, protein structure feature extraction, and social network analysis. The mainstream method is utilizing contrastive learning to facilitate graph feature extraction, known as Graph Contrastive Learning (GCL). GCL, although effective, suffers from some complications in contrastive learning, such as the effect of false negative pairs. Moreover, augmentation strategies in GCL are weakly adaptive to diverse graph datasets. Motivated by these problems, we propose a novel framework called Structure Knowledge Refinement (SKR) which uses data structure to determine the probability of whether a pair is positive or negative. Meanwhile, we propose an augmentation strategy that naturally preserves the semantic meaning of the original data and is compatible with our SKR framework. Furthermore, we illustrate the effectiveness of our SKR framework through intuition and experiments. The experimental results on the tasks of graph-level classification demonstrate that our SKR framework is superior to most state-of-the-art baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Survey on Masked Facial Detection Methods and Datasets for Fighting Against COVID-19

Coronavirus disease 2019 (COVID-19) continues to pose a great challenge to the world since its outbreak. To fight against the disease, a series of artificial intelligence (AI) techniques are developed and applied to real-world scenarios such as safety monitoring, disease diagnosis, infection risk assessment, lesion segmentation of COVID-19 CT scans,etc. The coronavirus epidemics have forced people wear masks to counteract the transmission of virus, which also brings difficulties to monitor large groups of people wearing masks. In this paper, we primarily focus on the AI techniques of masked facial detection and related datasets. We survey the recent advances, beginning with the descriptions of masked facial detection datasets. Thirteen available datasets are described and discussed in details. Then, the methods are roughly categorized into two classes: conventional methods and neural network-based methods. Conventional methods are usually trained by boosting algorithms with hand-crafted features, which accounts for a small proportion. Neural network-based methods are further classified as three parts according to the number of processing stages. Representative algorithms are described in detail, coupled with some typical techniques that are described briefly. Finally, we summarize the recent benchmarking results, give the discussions on the limitations of datasets and methods, and expand future research directions. To our knowledge, this is the first survey about masked facial detection methods and datasets. Hopefully our survey could provide some help to fight against epidemics.

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preprint2020arXiv

Fuzzy SLIC: Fuzzy Simple Linear Iterative Clustering

Most superpixel methods are sensitive to noise and cannot control the superpixel number precisely. To solve these problems, in this paper, we propose a robust superpixel method called fuzzy simple linear iterative clustering (Fuzzy SLIC), which adopts a local spatial fuzzy C-means clustering and dynamic fuzzy superpixels. We develop a fast and precise superpixel number control algorithm called onion peeling (OP) algorithm. Fuzzy SLIC is insensitive to most types of noise, including Gaussian, salt and pepper, and multiplicative noise. The OP algorithm can control the superpixel number accurately without reducing much computational efficiency. In the validation experiments, we tested the Fuzzy SLIC and OP algorithm and compared them with state-of-the-art methods on the BSD500 and Pascal VOC2007 benchmarks. The experiment results show that our methods outperform state-of-the-art techniques in both noise-free and noisy environments.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

SparseFusion: Dynamic Human Avatar Modeling from Sparse RGBD Images

In this paper, we propose a novel approach to reconstruct 3D human body shapes based on a sparse set of RGBD frames using a single RGBD camera. We specifically focus on the realistic settings where human subjects move freely during the capture. The main challenge is how to robustly fuse these sparse frames into a canonical 3D model, under pose changes and surface occlusions. This is addressed by our new framework consisting of the following steps. First, based on a generative human template, for every two frames having sufficient overlap, an initial pairwise alignment is performed; It is followed by a global non-rigid registration procedure, in which partial results from RGBD frames are collected into a unified 3D shape, under the guidance of correspondences from the pairwise alignment; Finally, the texture map of the reconstructed human model is optimized to deliver a clear and spatially consistent texture. Empirical evaluations on synthetic and real datasets demonstrate both quantitatively and qualitatively the superior performance of our framework in reconstructing complete 3D human models with high fidelity. It is worth noting that our framework is flexible, with potential applications going beyond shape reconstruction. As an example, we showcase its use in reshaping and reposing to a new avatar.

0 citations0 reviewsNo code linkedOpen access