Jianxin Wang
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View article: PyrMol: A Knowledge-Structured Pyramid Graph Framework for Generalizable Molecular Property Prediction
PyrMol: A Knowledge-Structured Pyramid Graph Framework for Generalizable Molecular Property Prediction Open
Accurate prediction of molecular properties is essential for accelerating drug discovery. While graph neural networks (GNNs) have achieved impressive progress, most models rely on atomic graphs with limited chemical semantics, leading to s…
View article: ChromNet: A Multi‐Task Learning Framework for Cross‐Cell Type Prediction of 3D Chromatin Interactions Using Epigenetic Signals
ChromNet: A Multi‐Task Learning Framework for Cross‐Cell Type Prediction of 3D Chromatin Interactions Using Epigenetic Signals Open
The 3D organization of chromatin plays a fundamental role in gene regulation, cellular function, and disease mechanisms. However, current experimental techniques, such as Hi‐C, remain costly and labor‐intensive, limiting their application …
View article: Suction cup denture for restoration of maxillary edentulousness with hemilateral maxillary defects: a case report
Suction cup denture for restoration of maxillary edentulousness with hemilateral maxillary defects: a case report Open
This single case report describes the rehabilitation of a 71-year-old man with a hemimaxillary defect following resection of maxillary gingival carcinoma and reconstruction with a pedicled submental island flap. Conventional prosthetic reh…
View article: Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing
Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing Open
View article: Whole-genome analysis of CVA4 in children with herpangina in two cities of China
Whole-genome analysis of CVA4 in children with herpangina in two cities of China Open
Sporadic epidemics of coxsackievirus A4 (CVA4) have been reported worldwide, but there are relatively few studies on CVA4. This study successfully obtained 60 VP1 region sequences and 50 complete genome sequences of CVA4. Phylogenetic anal…
View article: MultiGRNFormer: A Transformer-Based Multi-Omics GRN Inference Framework
MultiGRNFormer: A Transformer-Based Multi-Omics GRN Inference Framework Open
Gene Regulatory Network (GRN) describes the regulatory interactions between transcription factors (TFs) and their target genes, playing a crucial role in understanding developmental biology, disease mechanisms, and drug target discovery. H…
View article: Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of sex chromosomes
Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of sex chromosomes Open
Dioscorea alata L., the most widely cultivated yam species, exhibits dioecy (XY system) and a strong male-biased sex ratio. These two major constraints limit parental combinations and hinder breeding progress. To get insight into the sex c…
View article: Molecular dynamics-guided design of 2-aminoimidazole derived lipid nanoparticles for efficient muscle transfection
Molecular dynamics-guided design of 2-aminoimidazole derived lipid nanoparticles for efficient muscle transfection Open
View article: Inversion Analysis of Stress Fields Based on the LSTM–Attention Neural Network
Inversion Analysis of Stress Fields Based on the LSTM–Attention Neural Network Open
Conventional geostress methods of measurement cannot reveal an accurate geostress field distribution in an engineering area, limited by both cost and prevailing geological conditions. This study introduces an improved LSTM–Attention neural…
View article: diPaRIS: Dynamic and Interpretable Protein‐RNA Interactions Prediction With U‐Shaped Network and Novel Structure Encoding
diPaRIS: Dynamic and Interpretable Protein‐RNA Interactions Prediction With U‐Shaped Network and Novel Structure Encoding Open
Protein‐RNA interactions play a critical role in various biological processes and disease development. Proteins interact with RNAs through dynamic binding sites that exhibit specific structural patterns under various cellular conditions. W…
View article: SwitchTop- <i>k</i> : Scaling Top- <i>k</i> Compression on Programmable Switches
SwitchTop- <i>k</i> : Scaling Top- <i>k</i> Compression on Programmable Switches Open
View article: TopoLa: A Universal Framework to Enhance Cell Representations for Single-cell and Spatial Omics through Topology-encoded Latent Hyperbolic Geometry
TopoLa: A Universal Framework to Enhance Cell Representations for Single-cell and Spatial Omics through Topology-encoded Latent Hyperbolic Geometry Open
Recent advances in cellular research demonstrate that scRNA-seq characterizes cellular heterogeneity, while spatial transcriptomics reveals the spatial distribution of gene expression. Cell representation is the fundamental issue in the tw…
View article: Bipartite Patient-Modality Graph Learning with Event-Conditional Modelling of Censoring for Cancer Survival Prediction
Bipartite Patient-Modality Graph Learning with Event-Conditional Modelling of Censoring for Cancer Survival Prediction Open
Accurately predicting the survival of cancer patients is crucial for personalized treatment. However, existing studies focus solely on the relationships between samples with known survival risks, without fully leveraging the value of censo…
View article: Identifying DNA methylation types and methylated base positions from bacteria using nanopore sequencing with multi-scale neural network
Identifying DNA methylation types and methylated base positions from bacteria using nanopore sequencing with multi-scale neural network Open
Motivation DNA methylation plays important roles in various cellular physiological processes in bacteria. Nanopore sequencing has shown the ability to identify different types of DNA methylation from individual bacteria directly. However, …
View article: Effectively Integrating CNN and Low-Complexity Transformer for Lung Cancer Tumor Prediction After Neoadjuvant Chemoimmunotherapy
Effectively Integrating CNN and Low-Complexity Transformer for Lung Cancer Tumor Prediction After Neoadjuvant Chemoimmunotherapy Open
A novel hybrid model combining a convolutional neural network (CNN) and a low-complexity Transformer network is introduced for predicting lung cancer response to neoadjuvant chemoimmunotherapy using computed tomography scans. This approach…
View article: ColdstartCPI: Induced-fit theory-guided DTI predictive model with improved generalization performance
ColdstartCPI: Induced-fit theory-guided DTI predictive model with improved generalization performance Open
Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for…
View article: Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein–Protein Interaction Networks
Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein–Protein Interaction Networks Open
Virulence factors (VFs), produced by pathogens, facilitate pathogenic microorganisms to invade, colonize, and damage the host cells. Accurate VF identification advances pathogenic mechanism understanding and provides novel anti-virulence t…
View article: CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily Open
Motivation Protein–protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic stu…
View article: PartInstruct: Part-level Instruction Following for Fine-grained Robot Manipulation
PartInstruct: Part-level Instruction Following for Fine-grained Robot Manipulation Open
View article: O2Former:Direction-Aware and Multi-Scale Query Enhancement for SAR Ship Instance Segmentation
O2Former:Direction-Aware and Multi-Scale Query Enhancement for SAR Ship Instance Segmentation Open
Instance segmentation of ships in synthetic aperture radar (SAR) imagery is critical for applications such as maritime monitoring, environmental analysis, and national security. SAR ship images present challenges including scale variation,…
View article: Baseline cell cycle and immune profiles indicate CDK4/6 inhibitor response in metastatic HR + /HER2- breast cancer
Baseline cell cycle and immune profiles indicate CDK4/6 inhibitor response in metastatic HR + /HER2- breast cancer Open
View article: Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein-Protein Interaction Networks
Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein-Protein Interaction Networks Open
Virulence factors (VFs), produced by pathogens, facilitate pathogenic microorganisms to invade, colonize, and damage the host cells. Accurate VF identification advances pathogenic mechanism understanding and provides novel anti-virulence t…
View article: MADSP: predicting anti-cancer drug synergy through multi-source integration and attention-based representation learning
MADSP: predicting anti-cancer drug synergy through multi-source integration and attention-based representation learning Open
Motivation Drug combination therapy is an effective strategy for cancer treatment, enhancing drug efficacy and reducing toxic side effects. However, in vitro drug screening experiments are time-consuming and expensive, necessitating the de…
View article: P.142 Development and validation of a molecular classifier of meningiomas
P.142 Development and validation of a molecular classifier of meningiomas Open
Background: Meningiomas exhibit considerable heterogeneity. We previously identified four distinct molecular groups ( immunogenic, NF2-wildtype, hypermetabolic, proliferative) which address much of this heterogeneity. Despite their utility…
View article: Thermal Runaway Prediction of Lithium-ion Battery based on Dynamic Pruned LSTM
Thermal Runaway Prediction of Lithium-ion Battery based on Dynamic Pruned LSTM Open
This research raised a dynamic pruned long short-term memory (LSTM) architecture for predicting thermal runaway of lithium-ion battery in real time, and thus dealt with the key demand for high-precision anomaly detection under strict laten…
View article: PartInstruct: Part-level Instruction Following for Fine-grained Robot Manipulation
PartInstruct: Part-level Instruction Following for Fine-grained Robot Manipulation Open
Fine-grained robot manipulation, such as lifting and rotating a bottle to display the label on the cap, requires robust reasoning about object parts and their relationships with intended tasks. Despite recent advances in training general-p…
View article: A deep learning-based method for predicting the frequency classes of drug side effects based on multi-source similarity fusion
A deep learning-based method for predicting the frequency classes of drug side effects based on multi-source similarity fusion Open
Motivation Drug side effects refer to harmful or adverse reactions that occur during drug use, unrelated to the therapeutic purpose. A core issue in drug side effect prediction is determining the frequency of these drug side effects in the…
View article: Towards Protein Functions Prediction: An Inclusive Literature Review of Artificial Intelligent Techniques and Future Research Guidelines
Towards Protein Functions Prediction: An Inclusive Literature Review of Artificial Intelligent Techniques and Future Research Guidelines Open
Proteins perform critical functions, and their role is closely associated with their composition. Reliable prediction of protein function using computational techniques is becoming necessary because experimental limitations make it challen…
View article: Multimodal Representation Learning Based on Personalized Graph-Based Fusion for Mortality Prediction Using Electronic Medical Records
Multimodal Representation Learning Based on Personalized Graph-Based Fusion for Mortality Prediction Using Electronic Medical Records Open
Predicting mortality risk in the Intensive Care Unit (ICU) using Electronic Medical Records (EMR) is crucial for identifying patients in need of immediate attention. However, the incompleteness and the variability of EMR features for each …
View article: Quantitative methylation reference datasets of Quartet DNA reference materials for benchmarking genome-wide epigenome sequencing
Quantitative methylation reference datasets of Quartet DNA reference materials for benchmarking genome-wide epigenome sequencing Open
The absence of cross-lab and cross-replicate reproducibility assessments and the lack of quantitative methylation reference datasets (ground truth) impedes benchmarking genome-wide epigenome sequencing for its intended use in clinical sett…