Topic 184

text interest competing declared statementthe authors full bioinformatics view performance available no trained freely github algorithm prediction algorithms art methods consuming accuracy tasks set often deep cost datasets efficient optimal predicting classification parameters learning convolutional dimensional models training package medical paper introduce use sequences network methodology fast bert biomedical popular com language neural difficult gold uses https approaches bioengineering computational standard researchers predictive extraction trainable usually state regression images baselines networks operators make convex yields robustness machine achieving accurate lasso have data classical statistical base python literature approach speedups distance accuracies being descent method fista nesterov unsmoothed representation scale validation

41 items. Top items listed below.

PRER: A Patient Representation with Pairwise Relative Expression of Proteins on Biological Networks 184 7 4

Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins 184 105 13 4

AE-LGBM: Sequence-Based Novel Approach To Detect Interacting Protein Pairs via Ensemble of Autoencoder and LightGBM. 184 105 26 7 4

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

Accurate plant pathogen effector protein classification ab initio with deepredeff, an ensemble of convolutional neural networks 184 26 7 4

Frame-by-frame annotation of video recordings using deep neural networks 184 7 4 2

ADMIXPIPE: Population analyses in ADMIXTURE for non-model organisms 184 13 4

Automatic Generation of Personalised Models of the Lower Limb from Three-Dimensional Bone Geometries: A Validation Study 184 7 4

A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text 184 7 4

Building a tRNA thermometer to access the world's biochemical diversity 184 7 4

RNAxplorer: Harnessing the Power of Guiding Potentials for Sampling of RNA Landscapes 184 13 7 4

Frequency-independent biological signal identification (FIBSI): A free program that simplifies intensive analysis of non-stationary time series data 184 123 4

DeepForest: A Python package for RGB deep learning tree crown delineation 184 7 4

BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text 184 7 4

Improved characterisation of clinical text through ontology-based vocabulary expansion 184 7 4

Deep learning and computer vision will transform entomology 184 26 4

An improved 3DMax algorithm to reconstruct the three-dimensional structure of the chromosome 184 4

MORONET: Multi-omics Integration via Graph Convolutional Networks for Biomedical Data Classification 7 4

DeepCDR: a hybrid graph convolutional network for predicting cancer drug response 184 13 7 4

Proteomic fingerprint identification of Neotropical hard tick species (Acari: Ixodidae) using a self-curated mass spectra reference library 184 7 4

i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results 184 62 7 4

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities 165 62 13 7 4

A framework to efficiently smooth L1 penalties for linear regression 184 123 4

On the effectiveness of small, discriminatively pre-trained language representation models for biomedical text mining 184 26 4

Viral Sequence Identification in Metagenomes using Natural Language Processing Techniques 184 162 26 4

A fast and efficient smoothing approach to Lasso regression and an application in statistical genetics: polygenic risk scores for chronic obstructive pulmonary disease (COPD) 184 123 19 4

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

Nested Stochastic Block Models Applied to the Analysis of Single Cell Data 7 4

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

Evaluating Representations for Gene Ontology Terms 105 26 4

SPRDA: a matrix completion approach based on the structural perturbation to infer disease-associated Piwi-Interacting RNAs 7 4

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

FastSK: Fast Sequence Analysis with Gapped String Kernels 184 26 4

A consensus-based ensemble approach to improve de novo transcriptome assembly 25 4

Measuring both microbial load and diversity with a single amplicon sequencing library 7 4

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

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

The challenge of RNA branching prediction: a parametric analysis of multiloop initiation under thermodynamic optimization 184 105 4

Bootstrap aggregating improves the generalizability of Connectome Predictive Modelling 123 7 4 2

A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes 7 4

SchroŐądinger's phenotypes: herbarium specimens show two-dimensional images are both good and (not so) bad sources of morphological data 7 4

Estimating intracranial pressure via low-dimensional models: toward a practical tool for clinical decision support at multi-hour timescales 7 4

Obtaining leaner deep neural networks for decoding brain functional connectome in a single shot 184 13 4 2

PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments 169 7 4

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

Simulating bout-and-pause patterns with reinforcement learning 7 2

Segmentation-less, automated vascular vectorization robustly extracts neurovascular network statistics from in vivo two-photon images 184 26 4

scASK: A novel ensemble framework for classifying cell types based on single-cell RNA-seq data 147 13 7 4

Thin Film Metallization Stacks Serve as Reliable Conductors on Ceramic-based Substrates for Active Implants 184 7

Errors in Predicting Muscle Fiber Lengths from Joint Kinematics Point to the Need to Include Tendon Tension in Computational Neuromuscular Models 184 7 4

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

A Pseudo-Temporal Causality Approach to Identifying miRNA-mRNA Interactions During Biological Processes 7 4

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

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

Antithetic integral feedback for the robust control of monostable and oscillatory biomolecular circuits 7 4

Predicting Alignment Distances via Continuous Sequence Matching 140 26 4

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data 31 7 4

PAN: Personalized Annotation-based Networks for the Prediction of Breast Cancer Relapse 112 13 4

The Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning 7 4

A machine learning based approach to the segmentation of micro CT data in archaeological and evolutionary sciences 184 26 4

Granger-Causal Testing for Irregularly Sampled Time Series with Application to Nitrogen Signaling in Arabidopsis 7 4

Probabilistic divergence of a TBM methodology from the ideal protocol 7 4

gapseq: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models 7 4

Kmer2SNP: reference-free SNP calling from raw reads based on matching 13 4

Lilikoi V2.0: a deep-learning enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data 7 4

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

Improving enzyme optimum temperature prediction with resampling strategies and ensemble learning 184 105 26 4

Optimal versus approximate channel selection methods for EEG decoding with application to topology-constrained neuro-sensor networks 184 123 38 4

A meta-learning approach for genomic survival analysis 26 4

A predictive model of gene expression reveals the role of regulatory motifs in the mating response of yeast 7

Balrog: A universal protein model for prokaryotic gene prediction 162 13 4

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

Method for identification of heme-binding proteins and quantification of their interactions 7 4

Computational Model of G2-M DNA Damage Checkpoint Regulation in Normal and p53-null Cancer Cells 7 3

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

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

Multiple Emulsions Able To Be Use For Oral Administration Of Actives Pharmaceutical Ingredients: Different Phases Physico-Chemical Parameters Study 184 115

Residual-matching: An efficient alternative to random sampling in human subjects research recruitment 7 4

Neuronal Population Models Reveal Specific Linear Conductance Controllers Sufficient to Rescue Preclinical Disease Phenotypes 7 4

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

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

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

Asymmetric representation of aversive prediction errors in Pavlovian threat conditioning 7 2

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections 162 13 4

Identifying Genomic Islands with Deep Neural Networks 26 4

A deep learning framework for characterization of genotype data 26 4

Persistence: Using Protein Turnover to Expand the Applications of Transcriptomics 7 4

DIY-NAMIC behavior: A high-throughput method to measure complex phenotypes in the homecage 7 4

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

Boundary-Forest Clustering: Large-Scale Consensus Clustering of Biological Sequences 145 4

XGSEA: CROSS-species Gene Set Enrichment Analysis via domain adaptation 13 4

On the automatic annotation of gene functions using observational data and phylogenetic trees 162 13 4

Improved detection of tumor suppressor events in single-cell RNA-Seq data 7 4

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

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding 7 1

AnnotatorJ: an ImageJ plugin to ease hand-annotation of cellular compartments 26 4

SubFeat: Feature Subspacing Ensemble Classifier for Function Prediction of DNA, RNA and Protein Sequences 13 4

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

A robust method for generating, quantifying and testing large amounts of Escherichia coli persisters 7 4

Scale-free structure of cancer networks and their vulnerability to hub-directed combination therapy 7