ISBRA 2023: THE 19TH INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS RESEARCH AND APPLICATIONS

This page contains an index consisting of author-provided keywords.

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$k$-mer	Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection
A
Adaptive exploitation	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Adversarial Attack	Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences
alternative polyadenylation	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
Analysis of brain functional connectivity	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
and LSTM	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Answer Set Programming	Inferring Boolean networks from single-cell human embryo datasets
Antibody	Sequence-Based Nanobody-Antigen Binding Prediction
Antigen	Sequence-Based Nanobody-Antigen Binding Prediction
Arrhythmia classification	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
Artificial bee colony	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Asymmetric convolution	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Attention mechanism	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
B
benchmarking	Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
Bidirectional encoder-decoder	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion
Bidirectional Recurrent neural network	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Binary Classification	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer
biological network analysis	A Brief Study of Gene Co-Expression Thresholding Algorithms
Biomarker	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
Boolean networks	Inferring Boolean networks from single-cell human embryo datasets
breast cancer	The effect of transcriptomic annotations in breast cancer DGE study
Brightfield Mi-croscopy	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
C
Cell Segmentation	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
cell type clustering	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
Cell Type Identification	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
chemical reaction network	On the Realisability of Chemical Pathways
Chemical structure identifiers	Reconciling Inconsistent Molecular Structures from Biochemical Databases
cheminformatics	Reconciling Inconsistent Molecular Structures from Biochemical Databases On the Realisability of Chemical Pathways
chromatin hubs	Clique-based topological characterization of chromatin interaction hubs
chromatin interaction graphs	Clique-based topological characterization of chromatin interaction hubs
Chromatin loops	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
circRNA-protein interaction	PCPI: Prediction of circRNA and protein interaction using machine learning method
Circular DNA	CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
circular RNA	PCPI: Prediction of circRNA and protein interaction using machine learning method Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Classification	Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences PDB2Vec: Using 3D Structural Information For Improved Protein Analysis
Clustering	scGASI: A graph autoencoder-based single-cell integration clustering method
Complex disease	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Consensus Learning	scGASI: A graph autoencoder-based single-cell integration clustering method
consensus structure	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Context Gating-aware	Radiology Report Generation via Visual Recalibration and Context Gating-aware
Convolutional Layer	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
Convolutional Networks	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
copy number aberrations	Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
Correntropy	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Cryo-EM	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
D
Data imbalance	DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
de Bruijn graph	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
De Novo Protein Sequencing	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
decision algorithm	On Sorting by Flanked Transpositions
Deep Learning	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Denoising Autoencoder	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
directed multi-hypergraph	On the Realisability of Chemical Pathways
Distance Geometry	The Ordered Covering Problem in Distance Geometry
DropMessage	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
Drug-drug interaction	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Drug-drug interaction event type prediction	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Drug-drug interactions	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
E
ECG	DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
Embedding	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
ensemble Hi-C data	Clique-based topological characterization of chromatin interaction hubs
Epistasis network	Genetic Algorithm with Evolutionary Jumps
Epistatic interaction	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Evolution	Genetic Algorithm with Evolutionary Jumps
F
Feature Engineering	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer
Feature interaction	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Feature Selection	Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms
flanked transpositions	On Sorting by Flanked Transpositions
Flavonols	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
G
Gaussian kernel	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Gaussian Kernel Function	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
Gene Expression	Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms
Gene regulation	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Gene tree reconstruction	Reducing the impact of domain rearrangement on sequence alignment and phylogeny reconstruction
Generating Functions	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Generative adversarial networks	DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
Genetic algorithm	Genetic Algorithm with Evolutionary Jumps
Genome Dynamics	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Genome rearrangement	On Sorting by Flanked Transpositions
genomic annotations	The effect of transcriptomic annotations in breast cancer DGE study
Global average pooling	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
graph attention network	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Graph Autoencoder	scGASI: A graph autoencoder-based single-cell integration clustering method
Graph covering	The Ordered Covering Problem in Distance Geometry
Graph neural network	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
graph theoretical algorithms	A Brief Study of Gene Co-Expression Thresholding Algorithms
Graph theory	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
H
Hashing	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification
heterogeneous data	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Histogram	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
Holonomic Functions	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Human preimplantation development	Inferring Boolean networks from single-cell human embryo datasets
Hypergraph Regularization	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
I
identity calculation	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Image Denoising	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
Intergenic Regions	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
iPS Cell Reprogramming	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
J
Jaro similarity	On Computing the Jaro Similarity Between Two Strings
Jumping Knowledge	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
K
K-mer counts	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
K-mer set	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
k-mers	Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences
K-mers compression	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
kernel	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
Kernel Methods	Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection
Kidney renal clear cell carcinoma	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
Knapsack problem	Genetic Algorithm with Evolutionary Jumps
L
Linear time algorithm	On Computing the Jaro Similarity Between Two Strings
M
Machine Learning	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry
machine learning methods	PCPI: Prediction of circRNA and protein interaction using machine learning method
Magnetic signed Laplacian	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Major depressive disorder	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
Markovian Processes	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Mass Spectrometry	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry
medical images	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Medical Visual Recalibration	Radiology Report Generation via Visual Recalibration and Context Gating-aware
MHC	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry
Microbiome	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
Minimizer	Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection
miRNA	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
MiRNA-disease association	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
mobile element variants	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Molecular Structures	The Ordered Covering Problem in Distance Geometry
Multi-layer Kernel Self-expression Integration	scGASI: A graph autoencoder-based single-cell integration clustering method
Multi-layer Similarity Fusion	scGASI: A graph autoencoder-based single-cell integration clustering method
multi-modal	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Multi-modality	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Multi-perspective	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion
Multimodal data	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Multiple Alignment	CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
Multiple instance learning	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Multiple sequence alignment	Reducing the impact of domain rearrangement on sequence alignment and phylogeny reconstruction
Mutation	Genetic Algorithm with Evolutionary Jumps
N
Nanobody	Sequence-Based Nanobody-Antigen Binding Prediction
Neoepitope	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry
network biology	Clique-based topological characterization of chromatin interaction hubs
Neural Networks	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer
neuroblastoma	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Next Generation Sequencing	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
Noise Simulation	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
NP-hard	On Sorting by Flanked Transpositions
O
One hot encoding	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
P
Partition	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
pathway	On the Realisability of Chemical Pathways
PCA	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
pentose phosphate pathway	On the Realisability of Chemical Pathways
petri net	On the Realisability of Chemical Pathways
Phage display	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
Phylogenetics	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Principal Component Analysis	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Prognosis	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
protein 3D structure	PDB2Vec: Using 3D Structural Information For Improved Protein Analysis
protein analysis	PDB2Vec: Using 3D Structural Information For Improved Protein Analysis
protein disorder	PDFll: Intrinsic protein disorder and function prediction from the language of life
Protein domain rearrangement	Reducing the impact of domain rearrangement on sequence alignment and phylogeny reconstruction
protein function prediction	PDFll: Intrinsic protein disorder and function prediction from the language of life
protein language model	PDFll: Intrinsic protein disorder and function prediction from the language of life
Protein Scaffold Filling	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
Protein Sequence	Sequence-Based Nanobody-Antigen Binding Prediction PDB2Vec: Using 3D Structural Information For Improved Protein Analysis
Protein Sequences	Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences
protein structure prediction	PDFll: Intrinsic protein disorder and function prediction from the language of life
Proteins	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification
pseudo-energies	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Pseudoprogression	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Q
Quadruple-negative breast cancer (QNBC) Androgen receptor (AR)	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer
R
Racial Disparity	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms
RBP	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Rearrangement Distance	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
Record linkage	On Computing the Jaro Similarity Between Two Strings
Regulatory motif	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
Report Generation	Radiology Report Generation via Visual Recalibration and Context Gating-aware
representation learning	Sequence-Based Nanobody-Antigen Binding Prediction TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
resting-state fMRI	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
Reversal	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
RNA secondary structure	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
S
SARS-CoV-2 Spike Sequences	Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection
scRNA-seq	scGASI: A graph autoencoder-based single-cell integration clustering method
scRNAseq modeling	Inferring Boolean networks from single-cell human embryo datasets
self-supervised learning	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Sequence Analysis	Sequence-Based Nanobody-Antigen Binding Prediction
Sequence classification	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
sequence realignment	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Signed and directed graph	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Simple Graph Convolution	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
single-cell RNA-seq	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
single-cell sequencing	Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
single-nucleotide variants (SNVs)	Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
Small-molecule databases	Reconciling Inconsistent Molecular Structures from Biochemical Databases
smallest path cover	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
Sparsity Constraint	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Spike Sequences	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification
Standardisation	Reconciling Inconsistent Molecular Structures from Biochemical Databases
String distance	On Computing the Jaro Similarity Between Two Strings
String similarity	On Computing the Jaro Similarity Between Two Strings
Subgraph neural network	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
synergistic drug combinations	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
T
t-SNE	Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection
Text Indexing	CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
third-generation sequencing data	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
thresholding methodology	A Brief Study of Gene Co-Expression Thresholding Algorithms
TKTL1	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
transcript expression profiling	The effect of transcriptomic annotations in breast cancer DGE study
transcription factory	Clique-based topological characterization of chromatin interaction hubs
Transformer	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
translation	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Triple-Negative Breast Cancer	Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms
Tumor infiltration lymphocytes	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
tumor phylogeny	Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
W
Watershed Segmentation	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
Whole slide image	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Word2vec	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Y
YY1	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops

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