yusuke1997/dblp-id-title huggingface dataset:
Comorbidity Scoring with Causal Disease Networks
Combining Context and Knowledge Representations for Chemical-Disease Relation Extraction
Checking Phylogenetics Decisiveness in Theory and in Practice
Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology
Guest Editor's Introduction: Selected Papers from ACM-BCB 2014
Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential
GIFDTI: Prediction of Drug-Target Interactions Based on Global Molecular and Intermolecular Interaction Representation Learning
CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression
Orientation Determination of Cryo-EM Projection Images Using Reliable Common Lines and Spherical Embeddings
Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis
A Gene Selection Method Based on Outliers for Breast Cancer Subtype Classification
Fuzzy-Adaptive-Subspace-Iteration-Based Two-Way Clustering of Microarray Data
Carcinoma Type Classification From High-Resolution Breast Microscopy Images Using a Hybrid Ensemble of Deep Convolutional Features and Gradient Boosting Trees Classifiers
A Class-Information-Based Sparse Component Analysis Method to Identify Differentially Expressed Genes on RNA-Seq Data
Predicting DNA Methylation States with Hybrid Information Based Deep-Learning Model
Controlling the Effects of External Perturbations on a Gene Regulatory Network Using Proportional-Integral-Derivative Controller
predML-Site: Predicting Multiple Lysine PTM Sites With Optimal Feature Representation and Data Imbalance Minimization
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree
Control of Gene Regulatory Networks Using Bayesian Inverse Reinforcement Learning
Identifying Spatial Domains From Spatial Multi-Omics Data With Graph Mutual Information and Deep Subspace Learning
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment
An Enhanced Random Forests Approach to Predict Heart Failure From Small Imbalanced Gene Expression Data
Detection of Driver Modules with Rarely Mutated Genes in Cancers
Semantic Meta-Path Enhanced Global and Local Topology Learning for lncRNA-Disease Association Prediction
Local Exact Pattern Matching for Non-FixedRNA Structures
Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics - Part 1
Pre-Training and Ensembling of Deep Neural Networks for Target Gene Expression Prediction From Landmark Genes
Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model
Jointly Composite Feature Learning and Autism Spectrum Disorder Classification Using Deep Multi-Output Takagi-Sugeno-Kang Fuzzy Inference Systems
Biomarker Identification and Cancer Classification Based on Microarray Data Using Laplace Naive Bayes Model with Mean Shrinkage
Identification of Protein Complexes from Tandem Affinity Purification/Mass Spectrometry Data via Biased Random Walk
BERTPVP: Identifying and Classifying Phage Virion Proteins Using Bidirectional Encoder Representations-Based Transformers
Encoding Molecular Motions in Voxel Maps
Expectile Neural Networks for Genetic Data Analysis of Complex Diseases
Mathematical Properties of the Deep Coalescence Cost
GPFN: Prior-Data Fitted Networks for Genomic Prediction
Comparison of Deep-Learning Models for Classification of Cellular Phenotype From Flow Cytometry Data
Deep Transfer Learning for Cross-Species Plant Disease Diagnosis Adapting Mixed Subdomains
Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem
A 2-Approximation Scheme for Sorting Signed Permutations by Reversals, Transpositions, Transreversals, and Block-Interchanges
A Secure High-Order Gene Interaction Detection Algorithm Based on Deep Neural Network
Prompt Deep Light-Weight Vessel Segmentation Network (PLVS-Net)
Computational Modeling of Gene-Specific Transcriptional Repression, Activation and Chromatin Interactions in Leukemogenesis by LASSO-Regularized Logistic Regression
Improving Biochemical Named Entity Recognition Using PSO Classifier Selection and Bayesian Combination Methods
Associative Clustering for Exploring Dependencies between Functional Genomics Data Sets
Cell Mechanics Based Computational Classification of Red Blood Cells Via Machine Intelligence Applied to Morpho-Rheological Markers
Mem-mEN: Predicting Multi-Functional Types of Membrane Proteins by Interpretable Elastic Nets
A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction
Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data
Multi-View Kernel Learning for Identification of Disease Genes
scDVAE:Single-Cell Data Clustering Based on Variational Autoencoder With Disentangled Latent Representations
Applying Monte Carlo Simulation to Biomedical Literature to Approximate Genetic Network
Adaptive Fuzzy Consensus Clustering Framework for Clustering Analysis of Cancer Data
OnAI-Comp: An Online AI Experts Competing Framework for Early Sepsis Detection
Scalable Non-Linear Graph Fusion for Prioritizing Cancer-Causing Genes
A Convolutional Deep Clustering Framework for Gene Expression Time Series
A Novel Drug Repositioning Approach Based on Collaborative Metric Learning
Structure-Guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm
The Depth Problem: Identifying the Most Representative Units in a Data Group
ScCCL: Single-Cell Data Clustering Based on Self-Supervised Contrastive Learning
Stacked Graph Attention Network With Temporal Modeling for lncRNA-miRNA Association Network
Discovering Motifs in Biological Sequences Using the Micron Automata Processor
Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles
NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction
Tanglegrams: A Reduction Tool for Mathematical Phylogenetics
Pathway Analysis with Signaling Hypergraphs
Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System
Celiac Disease Detection From Videocapsule Endoscopy Images Using Strip Principal Component Analysis
Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2
A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model
Detection of Lungs Tumors in CT Scan Images Using Convolutional Neural Networks
Guest Editors' Introduction to the Special Section on the 14th International Conference on Computational Methods in Systems Biology (CMSB 2016)
A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit
txCoords: A Novel Web Application for Transcriptomic Peak Re-Mapping
Deletion Detection Method Using the Distribution of Insert Size and a Precise Alignment Strategy
Synchronizing Detection and Removal of Smoke in Endoscopic Images With Cyclic Consistency Adversarial Nets
Reviewer Appreciation Editorial
SNeCT: Scalable Network Constrained Tucker Decomposition for Multi-Platform Data Profiling
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach
Protecting Privacy and Security of Genomic Data in i2b2 with Homomorphic Encryption and Differential Privacy
PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks
Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets
Spatial Pyramid Pooling With 3D Convolution Improves Lung Cancer Detection
Brute Force Virtual Drug Screening with Molecular Dynamics Simulation and MM/PBSA to Find Potent Inhibitors of METTL16
PLMAM-PLA: A Method Using Pretrained Language Models and Attention Mechanisms for Protein-Ligand Binding Affinity Prediction
RNA Search with Decision Trees and Partial Covariance Models
A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms
MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks on Multicore Clusters
Supervised Variational Relevance Learning, An Analytic Geometric Feature Selection with Applications to Omic Datasets
RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms
Identification of Essential Proteins Based on Edge Clustering Coefficient
Escaping the Drug-Bias Trap: Using Debiasing Design to Improve Interpretability and Generalization of Drug-Target Interaction Prediction
Aberrant Static and Dynamic Functional Brain Network in Depression Based on EEG Source Localization
Object Weighting: A New Clustering Approach to Deal with Outliers and Cluster Overlap in Computational Biology
Essential Protein Detection by Random Walk on Weighted Protein-Protein Interaction Networks
A YOLOX-Based Deep Instance Segmentation Neural Network for Cardiac Anatomical Structures in Fetal Ultrasound Images
Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints
Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci
Prediction of Membrane Protein Amphiphilic Helix Based on Horizontal Visibility Graph and Graph Convolution Network
KungFQ: A Simple and Powerful Approach to Compress fastq Files
Predicting the Antigenic Relationship of Foot-and-Mouth Disease Virus for Vaccine Selection Through a Computational Model
WMMDCA: Prediction of Drug Responses by Weight-Based Modular Mapping in Cancer Cell Lines
A Graph-Theoretical Approach for Motif Discovery in Protein Sequences
Deep Spatio-Temporal Network for Low-SNR Cryo-EM Movie Frame Enhancement
PyMut: A Web Tool for Overlapping Gene Loss-of-Function Mutation Design
Efficient Local Search for Euclidean Path-Difference Median Trees
Genome Rearrangement with ILP
Predicting Human Intention-Behavior Through EEG Signal Analysis Using Multi-Scale CNN
Guest Editors Introduction to the Special Issue on Software and Databases
Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Based on Conditional Mutual Information
Predicting MiRNA-Disease Associations by Graph Representation Learning Based on Jumping Knowledge Networks
Guest editorial for the 12th Asia Pacific Bioinformatics Conference
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction
A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier
The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds
A Gaussian Mixture-Model Exploiting Pathway Knowledge for Dissecting Cancer Heterogeneity
RNA-Seq Analysis Pipeline Based on Oshell Environment
A Closed-Loop Control Scheme for Steering Steady States of Glycolysis and Glycogenolysis Pathway
EPMDA: Edge Perturbation Based Method for miRNA-Disease Association Prediction
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement
A Spectral Approach to Protein Structure Alignment
HetRCNA: A Novel Method to Identify Recurrent Copy Number Alternations from Heterogeneous Tumor Samples Based on Matrix Decomposition Framework
Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram for Detecting DNA Copy Number Aberrations
PreTP-Stack: Prediction of Therapeutic Peptides Based on the Stacked Ensemble Learing
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
Early Diagnosis of Alzheimer's Disease Based on Resting-State Brain Networks and Deep Learning
Integration of Imaging (epi)Genomics Data for the Study of Schizophrenia Using Group Sparse Joint Nonnegative Matrix Factorization
Optimal Bayesian Filtering for Biomarker Discovery: Performance and Robustness
Efficient Detection of Communities in Biological Bipartite Networks
Rapid Assessment of Adverse Drug Reactions by Statistical Solution of Gene Association Network
DBNX: A Machine Learning Method for Ensembling Polygenic Risk Scores and Non-Genetic Factors
Cell Population Tracking in a Honeycomb Structure Using an IMM Filter Based 3D Local Graph Matching Model
Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach
An Adaptive Hybrid Algorithm for Global Network Alignment
Reconstruction of Gene Regulatory Networks Using Multiple Datasets
Mitotic Index Determination on Live Cells From Label-Free Acquired Quantitative Phase Images Using a Supervised Autoencoder
Predicting Drug-Target Interaction Via Self-Supervised Learning
Functional Neural Networks for High-Dimensional Genetic Data Analysis
Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information
Bi-convex Optimization to Learn Classifiers from Multiple Biomedical Annotations
Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering
Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application
Classical Mechanics Approach Applied to Analysis of Genetic Oscillators
Stability Analysis of Biological Networks' Diffusion State
Macromolecules Structural Classification With a 3D Dilated Dense Network in Cryo-Electron Tomography
Chinese EMR Named Entity Recognition Using Fused Label Relations Based on Machine Reading Comprehension Framework
A Biologically Inspired Validity Measure for Comparison of Clustering Methods over Metabolic Data Sets
TANGO: A GO-Term Embedding Based Method for Protein Semantic Similarity Prediction
Discriminant Projection Shared Dictionary Learning for Classification of Tumors Using Gene Expression Data
Cascaded Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction
Prioritizing Type 2 Diabetes Genes by Weighted PageRank on Bilayer Heterogeneous Networks
Building Specific Signals from Frequency Chaos Game and Revealing Periodicities Using a Smoothed Fourier Analysis
Stochastic Gene Expression Modeling with Hill Function for Switch-Like Gene Responses
Robust Microbial Markers for Non-Invasive Inflammatory Bowel Disease Identification
Modeling and Identification of Amnioserosa Cell Mechanical Behavior by Using Mass-Spring Lattices
Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features
RFLP-Inator: Interactive Web Platform for In Silico Simulation and Complementary Tools of the PCR-RFLP Technique
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction
Phylogenetic Reconstruction for Copy-Number Evolution Problems
Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks
Dynamics in Epistasis Analysis
Semiglobal Sequence Alignment with Gaps Using GPU
An Efficient and Explainable Ensemble-learning Framework for Early Lung Cancer Biomarkers Detection
Protein Structure Prediction Using Population-Based Algorithm Guided by Information Entropy
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants
Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation
Layer-Specific Modules Detection in Cancer Multi-Layer Networks
G Protein-Coupled Receptor Interaction Prediction Based on Deep Transfer Learning
Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures
Predicting FAD Interacting Residues with Feature Selection and Comprehensive Sequence Descriptors
Stochastic-Deterministic Modeling of Immune Responses and Tumor Evolution Under Therapeutic Influence: Intelligent Predictive Supervised Exogenous Networks
Linear Time Algorithms to Construct Populations Fitting Multiple Constraint Distributions at Genomic Scales
CDPath: Cooperative Driver Pathways Discovery Using Integer Linear Programming and Markov Clustering
The Relevance of Topology in Parallel Simulation of Biological Networks
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics
A General Framework for Analyzing Data from Two Short Time-Series Microarray Experiments
Construction of Refined Protein Interaction Network for Predicting Essential Proteins
Predicting Essential Proteins by Integrating Network Topology, Subcellular Localization Information, Gene Expression Profile and GO Annotation Data
Extracting ROI-Based Contourlet Subband Energy Feature From the sMRI Image for Alzheimer's Disease Classification
Probabilistic Boolean Network Modelling and Analysis Framework for mRNA Translation
MiniDBG: A Novel and Minimal De Bruijn Graph for Read Mapping
Deep Learning for Automated Feature Discovery and Classification of Sleep Stages
A Novel Wavelet-Based Approach for Predicting Nucleosome Positions Using DNAS tructural Information
Inferring Gene Regulatory Networks via Ensemble Path Consistency Algorithm Based on Conditional Mutual Information
Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm
A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory
Supervised, Unsupervised, and Semi-Supervised Feature Selection: A Review on Gene Selection
Deep Factor Learning for Accurate Brain Neuroimaging Data Analysis on Discrimination for Structural MRI and Functional MRI
Prediction of Drug-Target Interactions Based on Network Representation Learning and Ensemble Learning
A New ECG Denoising Framework Using Generative Adversarial Network
A Top-r Feature Selection Algorithm for Microarray Gene Expression Data
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization
A New Efficient Algorithm for the Frequent Gene Team Problem
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction
A Visual Interface for Querying Heterogeneous Phylogenetic Databases
Dual-Layer Strengthened Collaborative Topic Regression Modeling for Predicting Drug Sensitivity
Conditioning-Based Modeling of Contextual Genomic Regulation
DCHap: A Divide-and-Conquer Haplotype Phasing Algorithm for Third-Generation Sequences
ESNet: End-to-End Chromosome Instance Segmentation Method Based on Edge Supervised Network
Q-BAFNet: A Hybrid Quantum Classical Approach for Drug-Target Binding Affinity Prediction
Relating Translation Efficiency to Protein Networks Provides Evolutionary Insights in Shewanella and Its Implications for Extracellular Electron Transfer
A Protein-Context Enhanced Master Slave Framework for Zero-Shot Drug Target Interaction Prediction
A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models
Bioactive Peptide Recognition Based on NLP Pre-Train Algorithm
The Latent Process Decomposition of cDNA Microarray Data Sets
Mining Gene Expression Data Focusing Cancer Therapeutics: A Digest
Common Neighbors Extension of the Sticky Model for PPI Networks Evaluated by Global and Local Graphlet Similarity
Colored de Bruijn Graphs and the Genome Halving Problem
Superiority of Spaced Seeds for Homology Search
Identifying Cancer Driver Genes Using a Neural Network Framework With Cross-Attention Mechanism
An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework
Virsearcher: Identifying Bacteriophages from Metagenomes by Combining Convolutional Neural Network and Gene Information
Pareto Dominance Archive and Coordinated Selection Strategy-Based Many-Objective Optimizer for Protein Structure Prediction
Reinforce: An Ensemble Approach for Inferring PPI Network from AP-MS Data
Mining Relationships among Multiple Entities in Biological Networks
Fourier Transform and Kolmogorov-Arnold Network Enhanced Relation-Aware Generative and Adversarial Network for miRNA-Disease Association Prediction
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants
Time-Aware Multi-Type Data Fusion Representation Learning Framework for Risk Prediction of Cardiovascular Diseases
Resolving Colliding Larvae by Fitting ASM to Random Walker-Based Pre-Segmentations
Unsupervised Discovery of Geometrically Common Structural Motifs and Long-Range Contacts in Protein 3D Structures
Improving Strand Pairing Prediction through Exploring Folding Cooperativity
Predicting miRNA-Disease Associations via Node-Level Attention Graph Auto-Encoder
Joint Extraction of Biomedical Events Based on Dynamic Path Planning Strategy and Hybrid Neural Network
An Efficient Targeted Drug Design Method Using Framework of Multiscale Encoder-Decoder
Post-Processing Fairness Evaluation of Federated Models: An Unsupervised Approach in Healthcare
A Dissimilarity Measure for Semidirected Networks
GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency
DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding
A Continuous-Time, Discrete-State Method for Simulating the Dynamics of Biochemical Systems
Molecular Dynamics Trajectory Compression with a Coarse-Grained Model
Rough-Fuzzy Clustering for Grouping Functionally Similar Genes from Microarray Data
Tractable Cases of (*, 2)-Bounded Parsimony Haplotyping
MCWS-Transformers: Towards an Efficient Modeling of Protein Sequences via Multi Context-Window Based Scaled Self-Attention
A Multimodal Deep Neural Network for Human Breast Cancer Prognosis Prediction by Integrating Multi-Dimensional Data
Hierarchical Hybrid Networks for Automatic Pulmonary Blood Vessel Segmentation in Computed Tomography Images
Post-Structuring Radiology Reports of Breast Cancer Patients for Clinical Quality Assurance
Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing
Tissue-Specific Subcellular Localization Prediction Using Multi-Label Markov Random Fields
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network
Algorithms for Reticulate Networks of Multiple Phylogenetic Trees
iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure
Particle Restoration: A Novel Image Processing Framework for Improving Real Cryo-EM Image Quality in Single Particle Analysis
Accurately Detecting Protein Complexes by Graph Embedding and Combining Functions with Interactions
Accurate Tracking of Arabidopsis Root Cortex Cell Nuclei in 3D Time-Lapse Microscopy Images Based on Genetic Algorithm
Multiscale Motif-Aware Relation Graph Structure for Drug-Target Binding Affinity Prediction
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer
Minimum-Flip Supertrees: Complexity and Algorithms
Protein2Vec: Aligning Multiple PPI Networks with Representation Learning
Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
Neural Network and Random Forest Models in Protein Function Prediction
SpeedHap: An Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA
Accurate Construction of Consensus Genetic Maps via Integer Linear Programming
Stepwise Tikhonov Regularisation: Application to the Prediction of HIV-1 Drug Resistance
A Multi-Omics Data Integration Framework for Gene Regulatory Network Inference Based on Contrastive Learning
Non-Negative Low-Rank Representation With Similarity Correction for Cell Type Identification in scRNA-Seq Data
AGTR2, One Possible Novel Key Gene for the Entry of SARS-CoV-2 Into Human Cells
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion
Integration of Multi-Omics Data for Gene Regulatory Network Inference and Application to Breast Cancer