yusuke1997/dblp-id-title huggingface dataset:
Protein Classification using Modified N-Gram and Skip-Gram Models: Extended Abstract
ULTRA: A Model Based Tool to Detect Tandem Repeats
Med-PRSIMD: Enhanced Complex Disease Risk Prediction through Integrative Analysis of Multi-Type Data and Medical History Records
Computational Modeling of Protein-RNA Interactions
General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept
MetaphorPrompt - An Analogical Reasoning Approach for Extracting Causal Links from Biological Text
Mining Novel Knowledge from Biomedical Literature using Statistical Measures and Domain Knowledge
AlphaEpi: Enhancing B Cell Epitope Prediction with AlphaFold 3
Leveraging Large Language Models for Automatic Hypotheses Testing over Heterogeneous Biological Databases
The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological function
Decoy Ensemble Reduction in Template-free Protein Structure Prediction
Using quantitative dose-response data to benchmark B-cell epitope prediction for antipeptide antibodies
Cloud4SNP: Distributed Analysis of SNP Microarray Data on the Cloud
Enforcing Minimum Necessary Access in Healthcare Through Integrated Audit and Access Control
Integrating Co-Evolutionary Information in Monte Carlo Based Method for Proteins Trajectory Simulation
NINJA: boolean modelling and formal verification of tiered-rate chemical reaction networks (extended abstract)
Mixture of logistic models and an ensemble approach for protein-protein interaction extraction
Integrated Visualization Tool for Differentially Expressed Genes and Gene Ontology Analysis
The 2017 Computational Structural Bioinformatics Workshop: CSBW 2017
Entropy-based evaluation function for the investigation of genetic code adaptability
Reconstructing transcriptional regulatory networks by probabilistic network component analysis
Computational Intractability Generates the Topology of Biological Networks
Investigating genome similarity through cross mapping percentage
Fusion In Breast Cancer Histology Classification
Optimal bayesian feature filtering
Intelligent F-information for genetic swarm algorithm based fuzzy expert system
Joint learning for biomedical NER and entity normalization: encoding schemes, counterfactual examples, and zero-shot evaluation
ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. ACM-BCB 2013, Washington, DC, USA, September 22-25, 2013
Modeling the competitive effects of nucleosomes on transcription factors binding
A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and Networks
Protein Structure Refinement by Iterative Fragment Exchange
QSEA for fuzzy subgraph querying of KEGG pathways
Detecting Divergent Subpopulations in Phenomics Data using Interesting Flares
Resolving healthcare forum posts via similar thread retrieval
SMILES-BERT: Large Scale Unsupervised Pre-Training for Molecular Property Prediction
ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants in silico
Copy Number Variation Detection Using Total Variation
Network-Based Prediction of Polygenic Disease Genes Involved in Cell Motility: Extended Abstract
Differential Compound Prioritization via Bi-Directional Selectivity Push with Power
A Privacy Preserving Markov Model for Sequence Classification
Analysis of ß-strand Twist from the 3-dimensional Image of a Protein
Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model
A pattern mining based integrative framework for biomarker discovery
Decoding TDP-43 Dependent Cryptic Splicing in Amyotrophic Lateral Sclerosis and Identifying Novel Disease-causing Genes
Complexity reduction of stochastic master equation simulation based on Kronecker product analysis
Knowledge Rich Natural Language Queries over Structured Biological Databases
Distribution-based sketching of single-cell samples
Haplotype-aware variant selection for genome graphs
Deep-Learning Based Cell Segmentation and Deconvolution in Spatial Transcriptomics
Practical Universal k-mer Sets for Minimizer Schemes
Unsupervised mapping of sentences to biomedical concepts based on integrated information retrieval model and clustering
Automating risk of bias assessment for clinical trials
Protein structure alignment using elastic shape analysis
Statistical analysis of GC-biased gene conversion and recombination hotspots in eukaryotic genomes: a phylogenetic hidden Markov model-based approach
Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines
Assessing Fairness of AlphaFold2 Prediction of Protein 3D Structures
Scalable Algorithms at Genomic Resolution to fit LD Distributions
Model-Agnostic Interpretation of Cancer Classification with Multi-Platform Genomic Data
Cross-Global Attention Graph Kernel Network Prediction of Drug Prescription
Inference of tumor phylogenies from genomic assays on heterogeneous samples
RBVS: Database of the Receptor-Based Virtual Screening
Feature Selection Model for Diagnosis, Electronic Medical Records and Geographical Data Correlation
Prediction of Biological Protein-protein Interaction Types Using Short-Linear Motifs
Breast-Density Semantic Segmentation with Probability Scaling for BI-RADS Assessment using DeepLabV3
Modeling climate-dependent population dynamics of mosquitoes to guide public health policies
One feature doesn't fit all: characterizing topological features of targets in signaling networks
CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low Expression
Three-Dimensional Spot Detection in Ratiometric Fluorescence Imaging For Measurement of Subcellular Organelles
A fast method for large-scale multichromosomal breakpoint median problems
STAPFormer: A New 3D Human Pose Estimation Framework in Sports and Health
Integration of Multiple Data Sources for Gene Network Inference using Genetic Perturbation Data: Extended Abstract
Rational design of orthogonal libraries of protein coding genes
Large highly connected clusters in protein-protein interaction networks
Large-scale Analysis of Drug Combinations by Integrating Multiple Heterogeneous Information Networks
Impact of the Networking Infrastructure on the Performance of Variant Calling on Human Genomes in Commodity Clusters
Balancing Confidentiality and Sharing of Genomic and Phenotypic Data in a Clinical Research System
ngALL database: a flexible framework for the management and integration of childhood leukemia next generation sequencing data
A Deep Learning Approach to Phase-Space Analysis for Seizure Detection
B-cell epitope prediction for antipeptide paratopes with the HAPTIC2/HEPTAD user toolkit (HUT)
Understanding user intents in online health forums
Gene Expression Based Computation Methods for Alzheimer's Disease Progression using Hippocampal Volume Loss and MMSE Scores
De novo identification of cell type hierarchy with application to compound marker detection
Classifying Immunophenotypes With Templates From Flow Cytometry
SNP2Structure: A public database for mapping and modeling nsSNPs on human protein structures
EDISON: a web application for computational health informatics at scale
mm2-gb: GPU Accelerated Minimap2 for Long Read DNA Mapping
Informatics-driven Protein-protein Docking
SMILE: A Novel Procedure for Subcellular Module Identification with Localization Expansion
Optimal cancer prognosis under network uncertainty
De novo proteomics of neuronal ischemic tolerance
Binary Response Models for Recognition of Antimicrobial Peptides
TOMAS: A novel TOpology-aware Meta-Analysis approach applied to System biology
eClaim System based on IHE XDR
Modeling ebola outbreak: a case study on 2014 outbreak in sierra leone
ELITE: Efficiently Locating Insertions of Transposable Elements
Integrated Identification of Disease-Gene Links and their Utility in Next-Generation Sequencing Interpretation
Unconstrained gene tree diameters for deep coalescence
Reconstructing Neuronal Signaling Pathways With the Potential for Disruption in Schizophrenia
Multi-Resolution Rigidity-Based Sampling of Protein Conformational Paths
Challenges of Drug Design
Majority Vote Cascading: A Semi-Supervised Framework for Improving Protein Function Prediction
MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search
Measuring Relatedness Between Scientific Entities in Annotation Datasets
The Forward Stem Matrix: An Efficient Data Structure for Finding Hairpins in RNA Secondary Structures
A Practical and Efficient Algorithm for the k-mismatch Shortest Unique Substring Finding Problem
Computational modeling of the effects of oxidative stress on the IGF-1 signaling pathway in human articular chondrocytes
Using 2-node hypergraph clustering coefficients to analyze disease-gene networks
RNA-Seq analyses to reveal the human transcriptome landscape
Mitigating health disparities in EHR via deconfounder
Predicting the need for blood transfusion in intensive care units with reinforcement learning
Overlap Graph Reduction for Genome Assembly using Apache Spark
MIA: Multi-cohort Integrated Analysis for Biomarker Identification
GapsMis: flexible sequence alignment with a bounded number of gaps
A maximum-likelihood approach to absolute protein quantification in mass spectrometry
Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes
Empirical metabolite identification via GA feature selection and Bayes classification
Immunoglobulin functional motions and their effects on the complementarity determining regions
Fuse: towards multi-level functional summarization of protein interaction networks
Drug Target Prioritization Based on Ligand Binding Pocket and Disease-Target Association Scores
A systems biology approach for the identification of significantly perturbed genes
Quantitative trait loci mapping with microarray marker intensities
Feature Selection to Predict Compound's Effect on Aging
Copy number variation detection using single cell sequencing data
clustQ: Efficient Protein Decoy Clustering Using Superposition-free Weighted Internal Distance Comparisons
F-statistics algorithm for gene clustering evaluation
GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data
DeepAnnotator: Genome Annotation with Deep Learning
Phylogenetic Consensus for Exact Median Trees
Community detection-based features for sequence classification
Simulation of Random Network of Hodgkin and Huxley Neurons with Exponential Synaptic Conductances on an FPGA Platform
Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database
Network-regularized bi-clique finding for tumor stratification
Heuristics for the Sorting by Length-Weighted Inversion Problem
3D Biological/Biomedical Image Registration with enhanced Feature Extraction and Outlier Detection
Designing Autocorrelated Genes
GLProbs: Aligning multiple sequences adaptively
Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser
Chromatin structure fully determines replication timing program in human cells
Decoding dendritic cell function through module and network analysis
The genetics of human aging: predicting age and age-related diseases by deep mining high dimensional biomarker data
Root Causal Inference from Single Cell RNA Sequencing with the Negative Binomial
PPPred: Classifying Protein-phenotype Co-mentions Extracted from Biomedical Literature
MICA: MicroRNA integration for active module discovery
GRAPPEL: A Graph-based Approach for Early Risk Assessment of Acute Hypertension in Critical Care
LDEncoder: reference deep learning-based feature detector for transfer learning in the field of epigenomics
Reverse Engineering Gene Networks: A Comparative Study at Genome-scale
Immunological response in normal healthy twins across age
On the Minimum Copy Number Generation Problem in Cancer Genomics
Improving Validity of Cause of Death on Death Certificates
Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2023, Houston, TX, USA, September 3-6, 2023
Efficient query evaluation for DAG-shaped hierarchies
Biomarkers in Immunology: from Concepts to Applications
Pattern analysis : a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression data
Topology aware coloring of gene regulatory networks
Interoperable Healthcare with Blockchain: A Data Transfer Model
Cloud-assisted distributed private data sharing
ANCA: Alignment-based Network Construction Algorithm
MitoMut: An Efficient Approach to Detecting Mitochondrial DNA Deletions from Paired-end Next-generation Sequencing Data
Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intake
Large-scale Dataset and Effective Model for Variant-Disease Associations Extraction
Dynamic visualization and comparative analysis of multiple collinear genomic data
On Conformations of Peptides Bound to Class I Major Histocompatibility Complexes
Relating mammalian replication program to large-scale chromatin folding
Capturing Solvent-System Effects in B-Cell Epitope Prediction with the HAPTIC3/HEPTAD2 User Toolkit (HUT2)
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis
A Multi-Layered GRU Model for COVID-19 Patient Representation and Phenotyping from Large-Scale EHR Data
Modularity and community detection in Semantic Similarity Networks trough Spectral Based Transformation and Markov Clustering
ngPhylo: N-Gram Modeled Proteins with Substitution Matrices for Phylogenetic Analysis
Phylogenetic and mutational analysis of 2008, 2009 & 2010 neuraminidase of H1N1 influenza A
Using Combined Features to Analyze Atomic Structures derived from Cryo-EM Density Maps
An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads
Learning Electronic Health Records through Hyperbolic Embedding of Medical Ontologies
A novel framework for large scale metabolic network alignments by compression
Multi-target integration and annotation of single-cell RNA-sequencing data
PaReCat: Patient Record Subcategorization for Precision Traditional Chinese Medicine
Library-Based Microbial Source Tracking via Strain Identification
RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep Learning
Determining miRNA-disease associations using bipartite graph modelling
Overlapping Functional Modules Detection in PPI Network with Pairwise Constrained Nonnegative Matrix Tri-Factorization
Seq3seq Fingerprint: Towards End-to-end Semi-supervised Deep Drug Discovery
SparkGA: A Spark Framework for Cost Effective, Fast and Accurate DNA Analysis at Scale
Preconditioned Random Forest Regression: Application to Genome-Wide Study for Radiotherapy Toxicity Prediction
TREEMENT: Interpretable Patient-Trial Matching via Personalized Dynamic Tree-based Memory Network
An evolutionary search framework to efficiently sample local minima in the protein conformational space
Text Classification with Topic-based Word Embedding and Convolutional Neural Networks
Markov clustering of protein interaction networks with improved balance and scalability
A data assurance model for syndromic monitoring infectious diseases in developing countries
Visualization of biological shape transformation by 3D model morphing
Towards the characterization of normal peripheral immune cells with data from ImmPort
Efficient computation of distance incorporated codon autocorrelation (DICA) score using fast Fourier transform
Robust Actor-Critic Contextual Bandit for Mobile Health (mHealth) Interventions
Detecting various types of differential splicing events using RNA-Seq data
An integrated approach to predictive genomic analytics
Evaluation of multi-feature machine-learning models for analyzing electrochemical signals for drug monitoring
miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer
T-cell epitope prediction based on self-tolerance
Measuring the Mappability Spectrum of Reference Genome Assemblies
Compositional modelling of signalling pathways in timed concurrent constraint programming
Counting motifs in probabilistic biological networks
Cancer stem cell based adjuvant for oncoantingen-driven vaccination
Cancer molecular subtype classification by graph convolutional networks on multi-omics data
Universal immune system simulator framework (UISS)
Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis
Bioinformatic Analysis of Nucleotide Cyclase Functional Centers and Development of ACPred Webserver
Microarray vs. RNA-Seq: a comparison for active subnetwork discovery
GANDALF: Peptide Generation for Drug Design using Sequential and Structural Generative Adversarial Networks
Signed network propagation for detecting differential gene expressions and DNA copy number variations
Comparative analysis of network algorithms to address modularity with gene expression temporal data
Senior health management through internet of things and real-time big data analytics
Refinement of G protein-coupled receptor structure models: Improving the prediction of loop conformations and the virtual ligand screening performances
Deep learning for assembly of haplotypes and viral quasispecies from short and long sequencing reads
Disease Subtyping using Somatic Variant Data
Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton
Efficiently mining rich subgraphs from vertex-attributed graphs
EMNets: A Convolutional Autoencoder for Protein Surface Retrieval Based on Cryo-Electron Microscopy Imaging
A comparison of dimensionality reduction methods for large biological data
Poster: Pangenome-Wide Association Studies with Frequented Regions
Consolidated CDA-based care record summary definition and HIE system tools
iDNA-EBT: An ensemble model based on multi-scale secondary fine-tuned BERT
A graph-based cluster ensemble method to detect protein functional modules from multiple information sources
Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex Evolutionary Origins
expHTS: analysis of high throughput sequence data in an experimental framework
Privacy preserving neural networks for electronic health records de-identification
A Multi-view Deep Learning Method for Epileptic Seizure Detection using Short-time Fourier Transform
EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information
Clinical Trial Active Learning
Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis
Structural diversity measures for RNA
RegMIL: Phenotype Classification from Metagenomic Data
Predicting G-Quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks
Analyzing metabolite measurements for automated prediction of underlying biological mechanisms
An extensible software infrastructure for testing the evolutionary consequences of developmental interactions
Predictive model of the treatment effect for patients with major depressive disorder
HEMnet: Integration of Electronic Medical Records with Molecular Interaction Networks and Domain Knowledge for Survival Analysis
Automated Verification of Phenotypes using PubMed
Identification of protein stability patches that pinpoint key structural or functional sites
Community Based Cancer Biomarker Identification from Gene Co-expression Network
Performance Model Selection for Learning-based Biological Image Analysis on a Cluster
Co-evolving Patterns in Temporal Networks of Varying Evolution
MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks
Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads
Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation Graphs
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers
DNA Vaccine Design for Chikungunya Virus Based On the Conserved Epitopes Derived from Structural Protein
Pathway analysis with signaling hypergraphs
ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools
Using Network Alignment for Analysis of Connectomes: Experiences from a Clinical Dataset
Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches
Low-Dimensional Representation of Genomic Sequences
DeepViFi: detecting oncoviral infections in cancer genomes using transformers
A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps
Evaluation of Five Sentence Similarity Models on Electronic Medical Records
Fast dendrogram-based OTU clustering using sequence embedding
Mining Faces from Biomedical Literature using Deep Learning
Non-overlapping clone pooling for high-throughput sequencing
KGDAL: knowledge graph guided double attention LSTM for rolling mortality prediction for AKI-D patients
The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction
A Distributed Constrained Non-negative Matrix Factorization Algorithm for Time-Series Gene Expression Data
Pathway Enrichment Analysis for Untargeted Metabolomics
A Multi-task Learning Approach for Predicting Spatio-temporal Patient Variables
In silico identification of microRNAs from expressed sequence tags of three earthworm species
Weakly Supervised Deep Learning for Thoracic Disease Classification and Localization on Chest X-rays
A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy
Sectioning biomedical abstracts using pointer networks
Early Prediction of Risk Adjustment Factor (RAF) for Medicare Advantage (MA) and Evaluation of its Benefits
Experimentation of an automatic resolution method for protein abbreviations in full-text papers
Detection of a fusion gene using soft-clipping reads in exome-sequencing data
RepFrag: a graph based method for finding repeats and transposons from fragmented genomes
Doxorubicin Efficacy Prediction for Glioblastomas Using Deep Learning and Differnetial Equations
ArcheGEO: towards improving relevance of gene expression omnibus search results
A Sequence-Based Prediction Model of Vesicular Transport Proteins Using Ensemble Deep Learning
Reference-Free Imputation of Targeted Next-Generation Sequence Datasets
Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases
Signal quality detection towards practical non-touch vital sign monitoring
Leveraging Sentiment Analysis for Classifying Patient Complaints
ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets
Bias and Noise Cancellation for Robust Copy Number Variation Detection
Identifying patient-specific root causes of disease
Recovering Bound Forms of Protein Structures Using the Elastic Network Model and Molecular Interaction Fields
Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses
GWAS analysis to compute genetic markers of progression to Alzheimer's disease
Cutting-Edge Algorithms in Genomics: From Theory to Practice
Mapping Free Text into MedDRA by Natural Language Processing: A Modular Approach in Designing and Evaluating Software Extensions
Cross-Population Analysis for Functional Characterization of Type II Diabetes Variants
TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back
In silico predicted essential genes required for zebrafish ( Danio rerio ) steroid hormone production
A Multithreaded Algorithm for Mining Maximal Cohesive Dense Modules from Interaction Networks with Gene Profiles
Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection
Gene Co-Adaboost: a semi-supervised approach for classifying gene expression data
On the border length minimization problem (BLMP) on a square array
PANACEA: Towards Influence-driven Profiling of Drug Target Combinations in Cancer Signaling Networks
Spectrally resolved bioluminescence tomography with Huber-Markov random-field regularization
Microbiome Dynamics as Predictors of Lung Transplant Rejection