yusuke1997/dblp-id-title huggingface dataset:
Autocorrelation-based noise subtraction method with smoothing, overestimation, energy, and cepstral mean and variance normalization for noisy speech recognition
Estimation and quantization of ICC-dependent phase parameters for parametric stereo audio coding
Prosodic mapping of text font based on the dimensional theory of emotions: a case study on style and size
Performance vs. hardware requirements in state-of-the-art automatic speech recognition
Nonlinear residual echo suppression based on dual-stream DPRNN
Automatic detection of attachment style in married couples through conversation analysis
Continuous lipreading based on acoustic temporal alignments
Hybrid lightweight temporal-frequency analysis network for multi-channel speech enhancement
A depthwise separable convolutional neural network for keyword spotting on an embedded system
The Ethnic Lyrics Fetcher tool
Data-based spatial audio processing
Language agnostic missing subtitle detection
Production and perception of velar stop (de)voicing in European Portuguese and Italian
Voice activity detection algorithm based on long-term pitch information
Relevance-based quantization of scattering features for unsupervised mining of environmental audio
Semantic Labeling of Nonspeech Audio Clips
A new joint CTC-attention-based speech recognition model with multi-level multi-head attention
ALBAYZIN 2018 spoken term detection evaluation: a multi-domain international evaluation in Spanish
Performance evaluation of perceptible impulsive noise detection methods based on auditory models
SVQ-MAE: an efficient speech pre-training framework with constrained computational resources
Multiple-Description Multistage Vector Quantization
Correlation-Based Amplitude Estimation of Coincident Partials in Monaural Musical Signals
Bio-ontologies: current trends and future directions
A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology
BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data
A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data
Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice
Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs
GO-function: deriving biologically relevant functions from statistically significant functions
DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms
Editorial: Orthology and applications
Deep learning-based fusion of nuclear segmentation features for microsatellite instability and tumor mutational burden prediction in digestive tract cancers: a multicenter validation study
ScFold: a GNN-based model for efficient inverse folding of short-chain proteins via spatial reduction
Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance
Detection of alternative splicing: deep sequencing or deep learning?
Weak-binding molecules are not drugs? - toward a systematic strategy for finding effective weak-binding drugs
Immune infiltration and clinical significance analyses of the coagulation-related genes in hepatocellular carcinoma
Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs
Searching the Expressed Sequence Tag (EST) Databases: Panning for Genes
Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network
Deep learning in bioinformatics and biomedicine
SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data
A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps
GraphCDR: a graph neural network method with contrastive learning for cancer drug response prediction
Genome-wide hierarchical mixed model association analysis
Cloud-based introduction to BASH programming for biologists
MMP3C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles
Gene Swin transformer: new deep learning method for colorectal cancer prognosis using transcriptomic data
Metabolomics technology and bioinformatics for precision medicine
Recent advances in user-friendly computational tools to engineer protein function
FLED: a full-length eccDNA detector for long-reads sequencing data
eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data
Deciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF
NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning
Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq
Accurate TCR-pMHC interaction prediction using a BERT-based transfer learning method
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys
What is the probability of replicating a statistically significant association in genome-wide association studies?
A new thinking: extended application of genomic selection to screen multiomics data for development of novel hypoxia-immune biomarkers and target therapy of clear cell renal cell carcinoma
GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field
Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
Mining the pharmacogenomics literature - a survey of the state of the art
Modeling biological problems in computer science: a case study in genome assembly
A review of ensemble methods for de novo motif discovery in ChIP-Seq data
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference
Optimization of miRNA-seq data preprocessing
Expression of Concern: Bioinformatics in Russia: history and present-day landscape
Taming the complexity of biological pathways through parallel computing
Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors
Multimodal deep learning approaches for precision oncology: a comprehensive review
Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools
Technologies for Integrating Biological Data
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning
Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types
NGPINT: a next-generation protein-protein interaction software
Machine learning approach to gene essentiality prediction: a review
Genotype imputation and reference panel: a systematic evaluation on haplotype size and diversity
DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data
SMG: self-supervised masked graph learning for cancer gene identification
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data
IBRAP: integrated benchmarking single-cell RNA-sequencing analytical pipeline
Consensus clustering of single-cell RNA-seq data by enhancing network affinity
Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features
TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine
A model for Bioinformatics training: the marine biological laboratory
An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction
Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions
HiBrowser: an interactive and dynamic browser for synchronous Hi-C data visualization
Therapeutic gene target prediction using novel deep hypergraph representation learning
A Comparison of Microarray Databases
A broken promise: microbiome differential abundance methods do not control the false discovery rate
Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework
Some comments on certain statistical aspects of the study of the microbiome
A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions
Simultaneous Modelling of Metabolic, Genetic and Product-interaction Networks
Benchmarking differential expression, imputation and quantification methods for proteomics data
spaCI: deciphering spatial cellular communications through adaptive graph model
A novel generation adversarial network framework with characteristics aggregation and diffusion for brain disease classification and feature selection
Biological activities of drug inactive ingredients
Evolutionary algorithms simulating molecular evolution: a new field proposal
Enhancing reinforcement learning for de novo molecular design applying self-attention mechanisms
A first course in computing with applications to biology
Robust signalling entropy estimation for biological process characterisation
Education resources of the National Center for Biotechnology Information
DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequences
CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation
An introduction to artificial neural networks in bioinformatics - application to complex microarray and mass spectrometry datasets in cancer studies
Cancer gene identification through integrating causal prompting large language model with omics data-driven causal inference
A practical guide for the computational selection of residues to be experimentally characterized in protein families
Optimization of in silico tools for predicting genetic variants: individualizing for genes with molecular sub-regional stratification
Detecting short tandem repeats from genome data: opening the software black box
Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug-drug interactions prediction
ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody-antigen computational docking
Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling
DIST: spatial transcriptomics enhancement using deep learning
CMOMO: a deep multi-objective optimization framework for constrained molecular multi-property optimization
Classification of PTEN missense VUS through exascale simulations
Deep learning-enhanced clustering and classification of protein molecule tertiary structures using weighted distance matrices
Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers
scSAMAC: saliency-adjusted masking induced attention contrastive learning for single-cell clustering
A review of machine learning approaches for drug synergy prediction in cancer
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction
Computational methods and data resources for predicting tumor neoantigens
Ensemble classification based signature discovery for cancer diagnosis in RNA expression profiles across different platforms
Exploring the potential of compound-protein complex structure-free models in virtual screening using BlendNet
Assessing protein model quality based on deep graph coupled networks using protein language model
Deciphering oncogenic drivers: from single genes to integrated pathways
Elementary methods provide more replicable results in microbial differential abundance analysis
pathMap: a path-based mapping tool for long noisy reads with high sensitivity
MVSGDR: multi-view stacked graph convolutional network for drug repositioning
Fully connected autoencoder and convolutional neural network with attention-based method for inferring disease-related lncRNAs
In silico clinical trials: concepts and early adoptions
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening
Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges
A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning
Comprehensive pathway enrichment analysis workflows: COVID-19 case study
Potential Bias in GO: : TermFinder
Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA
Predicting lncRNA-disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation
Exploration of databases and methods supporting drug repurposing: a comprehensive survey
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective
IBPGNET: lung adenocarcinoma recurrence prediction based on neural network interpretability
A network embedding framework based on integrating multiplex network for drug combination prediction
Multi contact-based folding method for de novo protein structure prediction
Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction
Sequencing technologies and tools for short tandem repeat variation detection
A survey of circular RNAs in complex diseases: databases, tools and computational methods
A novel strategy for designing the magic shotguns for distantly related target pairs
CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data
HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data
scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data
Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes
RNMFLP: Predicting circRNA-disease associations based on robust nonnegative matrix factorization and label propagation
TransGCN: a semi-supervised graph convolution network-based framework to infer protein translocations in spatio-temporal proteomics
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
PreTP-EL: prediction of therapeutic peptides based on ensemble learning
Predicting metabolite-disease associations based on auto-encoder and non-negative matrix factorization
Omics data analysis and integration for COVID-19 patients - editorial
Calculating transcription factor binding maps for chromatin
Bioinformatics: scalability, capabilities and training in the data-driven era
Machine learning-enabled virtual screening indicates the anti-tuberculosis activity of aldoxorubicin and quarfloxin with verification by molecular docking, molecular dynamics simulations, and biological evaluations
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning
Prediction of RNA secondary structure including pseudoknots for long sequences
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation
Leveraging trans-ethnic genetic risk scores to improve association power for complex traits in underrepresented populations
Hybrid modelling of biological systems: current progress and future prospects
Enteropathway: the metabolic pathway database for the human gut microbiota
Inferring single-cell resolution spatial gene expression via fusing spot-based spatial transcriptomics, location, and histology using GCN
E -value: a superior alternative to P -value and its adjustments in DNA methylation studies
PRES: a webserver for decoding the functional perturbations of RNA editing sites
LDER-GE estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information
A comprehensive benchmarking of WGS-based deletion structural variant callers
Spatom: a graph neural network for structure-based protein-protein interaction site prediction
Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods
Anticancer peptides prediction with deep representation learning features
FusionPub, a therapeutic landscape of human fusion genes
Microarray Probe Selection Strategies
ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction
Computational analyses of bacterial strains from shotgun reads
Comparison of haplotype-based statistical tests for disease association with rare and common variants
Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
Graphormer supervised de novo protein design method and function validation
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity
Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era
Mining literature for systems biology
Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method
Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks
DLF-Sul: a multi-module deep learning framework for prediction of S-sulfinylation sites in proteins
MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys
LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing
SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples
Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment
A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation
DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data
Understanding and identifying amino acid repeats
HLAncPred: a method for predicting promiscuous non-classical HLA binding sites
Open tools for quantitative anonymization of tabular phenotype data: literature review
Design patterns for the construction of computational biological models
A novel privacy-preserving federated genome-wide association study framework and its application in identifying potential risk variants in ankylosing spondylitis
DTI-HETA: prediction of drug-target interactions based on GCN and GAT on heterogeneous graph
CRESSP: a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins
Computational methods for the comparative quantification of proteins in label-free LC n -MS experiments
Deep learning approaches for resolving genomic discrepancies in cancer: a systematic review and clinical perspective
BBATProt: a framework predicting biological function with enhanced feature extraction via interpretable deep learning
PharmBERT: a domain-specific BERT model for drug labels
DTSyn: a dual-transformer-based neural network to predict synergistic drug combinations
Carmna: classification and regression models for nitrogenase activity based on a pretrained large protein language model
A machine learning framework using urinary biomarkers for pancreatic ductal adenocarcinoma prediction with post hoc validation via single-cell transcriptomics
MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph
DKADE: a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications
The application of Hadoop in structural bioinformatics
Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL
Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer
Challenges in integrating Escherichia coli molecular biology data
Recent omics-based computational methods for COVID-19 drug discovery and repurposing
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins
Design of RNAs: comparing programs for inverse RNA folding
Computational models, databases and tools for antibiotic combinations
SpliceWiz: interactive analysis and visualization of alternative splicing in R
Heritability jointly explained by host genotype and microbiome: will improve traits prediction?
BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution
Integrating bioinformatics into senior high school: design principles and implications
AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody-antigen interaction prediction
Analysis of super-enhancer using machine learning and its application to medical biology
EXPERT: transfer learning-enabled context-aware microbial community classification
NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers
Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions
SpotLink enables sensitive and precise identification of site nonspecific cross-links at the proteome scale
Resources and tools for the high-throughput, multi-omic study of intestinal microbiota
Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues
Disease prediction by cell-free DNA methylation
Old friends in new guise: repositioning of known drugs with structural bioinformatics
OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials
Computer Prediction of Sites Associated with Various Elements of the Nuclear Matrix
Synthetic lethal connectivity and graph transformer improve synthetic lethality prediction
Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?
Challenges in gene-oriented approaches for pangenome content discovery
Correction to: DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences
What makes a gene name? Named entity recognition in the biomedical literature
Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data
Inference of dynamic spatial GRN models with multi-GPU evolutionary computation
Accelerating the discovery of anticancer peptides targeting lung and breast cancers with the Wasserstein autoencoder model and PSO algorithm