Topic 26

learning deep machine bioinformatics neural prediction accuracy trained training convolutional network performance networks classification methods predict method models data based art images datasets predicting dataset features algorithms accurate model approach image algorithm information train computational supervised proposed predictions approaches paper propose state segmentation using problem feature can predictive automated cnn accurately large set classifier techniques existing learn outperforms used classify on interpretable improve dimensional applied framework tasks biological unsupervised representations experimental space challenging task learned input applications automatically available apply introduce sequence developed novel automatic sets artificial test application better classifiers knowledge then manual validation able achieves consuming use learns

892 items. Top items listed below.

Annotating Gene Ontology terms for protein sequences with the Transformer model 105 26 4

Detection of pre-microRNA with Convolutional Neural Networks 105 26 4

A Deep Learning Framework for Predicting Human Essential Genes by Integrating Sequence and Functional data 105 26 4

Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets 26 4

CoCoNet: Boosting RNA contact prediction by convolutional neural networks 105 26 13 4

A comparative study of supervised machine learning algorithms for the prediction of long-range chromatin interactions 105 26 4

DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning 105 26 13 4

A deep learning framework for characterization of genotype data 26 4

Structure-Based Function Prediction using Graph Convolutional Networks 105 26 4

Towards CNN Representations for Small Mass Spectrometry Data Classification: From Transfer Learning to Cumulative Learning 26 4

A deep learning framework for high-throughput mechanism-driven phenotype compound screening 26 4

Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology 112 26 4

Imputing missing RNA-seq data from DNA methylation by using transfer learning based-deep neural network 105 26 4

DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity 105 26 4

Evaluating Representations for Gene Ontology Terms 105 26 4

The impact of different negative training data on regulatory sequence predictions 26 4

Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks 105 26 4 2

HistoFlow: Label-Efficient and Interactive Deep Learning Cell Analysis 26 4

Bayesian Neural Networks for Cellular Image Classification and Uncertainty Analysis 26 4

Terminitor: Cleavage Site Prediction Using Deep Learning Models 105 26 4

Identifying Genomic Islands with Deep Neural Networks 26 4

Using Single Protein/Ligand Binding Models to Predict Active Ligands for Unseen Proteins 105 26 4

A High Accurate Machine Learning Meta-Strategy for the Prediction of Intrinsically Disorder Proteins 105 26 4

A novel single-cell based method for breast cancer prognosis 43 26 4

A deep learning approach for staging embryonic tissue isolates with small data 26 4

Sequence representations and their utility for predicting protein-protein interactions 105 26 4

A deep learning approach for tissue spatial quantification and genomic correlations of histopathological images 131 26 9 4

An automated framework for efficiently designing deep convolutional neural networks in genomics 26 4

Predicting Cortical Signatures of Consciousness using Dynamic Functional Connectivity Graph-Convolutional Neural Networks 26 22 2

IAV-CNN: a 2D convolutional neural network model to predict antigenic variants of influenza A virus 105 26 4

Learning, Visualizing and Exploring 16S rRNA Structure Using an Attention-based Deep Neural Network 105 26 13 4

Cross-Subject EEG-Based Emotion Recognition through Neural Networks with Stratified Normalization 26 4 2

Evolutionary context-integrated deep sequence modeling for protein engineering 105 26 4

In situ classification of cell types in human kidney tissue using 3D nuclear staining 26 4

Deep Feature Extraction for Resting-State Functional MRI by Self-Supervised Learning and Application to Schizophrenia Diagnosis 26 22 2

A meta-learning approach for genomic survival analysis 26 4

ECMarker: Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages 105 26 13 4

DeepPheno: Predicting single gene loss of function phenotypes 105 26 13 4

Functional assessments of PTEN variants using machine-assisted phenotype scoring 26 4

Signal-to-signal Neural Networks for Improved Spike Estimation from Calcium Imaging Data 26 4 2

A transfer-learning approach for first-year developmental infant brain segmentation using deep neural networks 26 22 2

Leveraging prior concept learning improves ability to generalize from few examples in computational models of human object recognition 100 26 23 2

Generalization in data-driven models of primary visual cortex 100 26 2

Related Topics of a Novel TCR-based Cancer Detection Approach 26 4

iMDA-BN: Identification of miRNA-Disease Associations based on the Biological Network and Graph Embedding Algorithm 105 26 4

A composite method to infer drug resistance with mixed genomic data 26 4

Learned SPARCOM: Unfolded Deep Super-Resolution Microscopy 184 70 26 18 4

SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction 105 26 4

Improving brain age estimates with deep learning leads to identification of novel genetic factors associated with brain aging 19 7 4 2

A convolutional neural network for common coordinate registration of high-resolution histology images 26 4

Deep Learning Based Segmentation of Brain Tissue from Diffusion MRI 59 26 4 2

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

Optimized sgRNA design by deep learning to balance the off-target effects and on-target activity of CRISPR/Cas9 26 4

Transferability of Brain decoding using GraphConvolutional Networks 100 26 22 2

Quantitative comparison of Drosophila behavior annotations by human observers and a machine learning algorithm 26 7 4 2

A Genome-based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates 26 4

RNA secondary structure prediction using deep learning with thermodynamic integration 105 26 4

Transformer neural network for protein-specific de novo drug generation as a machine translation problem 105 26 4

Improved Prediction of Smoking Status via Isoform-Aware RNA-seq Deep Learning Models 26 4

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement 43 26 4

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function 105 26 13 4

Image-based patch selection for deep learning to improve automated Gleason grading in histopathological slides 131 26 4

Probing machine-learning classifiers using noise, bubbles, and reverse correlation 26 4 2

Fluorescence Microscopy Datasets for Training Deep Neural Networks 26 4

Network-based Machine Learning Approach for Structural Domain Identification in Proteins 105 26 4

Denoising large-scale biological data using network filters 26 4

Deep learning models for lipid-nanoparticle-based drug delivery 26 4

Aggregation of Cohorts for Histopathological Diagnosis with Deep Morphological Analysis 26 4

Epitope Prediction of Antigen Protein using Attention-Based LSTM Network 105 26 24 4

Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide 37 26 1

NetQuilt: Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity 105 26 4

GraphProt2: A novel deep learning-based method for predicting binding sites of RNA-binding proteins 105 26 4

Predicting drug sensitivity of cancer cells based on DNA methylation levels 112 26 4

Metabolic pathway inference using multi-label classification with rich pathway features 26 4

Current challenges for epitope-agnostic TCR interaction prediction and a new perspective derived from image classification 105 26 4

Predicting Alignment Distances via Continuous Sequence Matching 140 26 4

DeepPPPred: An Ensemble of BERT, CNN, and RNN for Classifying Co-mentions of Proteins and Phenotypes 105 26 4

Protein sequence design with a learned potential 105 26 4

Leveraging non-structural data to predict structures of protein-ligand complexes 105 26 4

Struct2Graph: A graph attention network for structure based predictions of protein-protein interactions 105 26 13 4

Multi-tissue transcriptome-wide association studies 19 4

CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations 26 4

Supervised Adversarial Alignment of scRNA-seq Data 147 43 26 4

PhenomNet: Bridging Phenotype-Genotype Gap: A CNN-LSTM Based Automatic Plant Root Anatomization System. 26 4

Graph convolutional networks for drug response prediction 105 26 13 4

Predicting molecular subtypes of breast cancer using pathological images by deep convolutional neural network from public dataset 131 26 4

Predicting Residues Involved in Anti-DNA Autoantibodies with Limited Neural Networks 105 26 4

miTAR: a hybrid deep learning-based approach for predicting miRNA targets 105 26 13 4

Deep Homology-Based Protein Contact-Map Prediction 105 26 4

Scalable hierarchical clustering by composition rank vector encoding and tree structure 26 4

Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity 105 26 4

Bayesian neural networks for the optimisation of biological clocks in humans 26 4

Meta-Signer: Metagenomic Signature Identifier based on Rank Aggregation of Features 26 4

Optimizing the use of gene expression data to predict plant metabolic pathway memberships 105 26 4

Learning Patterns of the Ageing Brain in MRI using Deep Convolutional Networks 26 4 2

Fully unsupervised deep mode of action learning for phenotyping high-content cellular images 26 4

T4SE-XGB: interpretable sequence-based prediction of type IV secreted effectors using eXtreme gradient boosting algorithm 105 13 4

DNA methylation changes with age as a complex system: a parenclitic network approach to a family-based cohort of patients with Down Syndrome 26 4

Exploration of Chemical Space with Partial Labeled Noisy Student Self-Training for Improving Deep Learning: Application to Drug Metabolism 105 26 13 4

Wide and Deep Learning for Automatic Cell Type Identification 26 4