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UDSMProt: Universal Deep Sequence Models for Protein Classification

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.bbrc.2007.09.098openalex-snapshot

EzyPred: A top–down approach for predicting enzyme functional classes and subclasses

inferredcites →https://doi.org/10.1016/j.compbiolchem.2007.11.004openalex-snapshot

Subsequence-based feature map for protein function classification

inferredcites →https://doi.org/10.1016/j.ymeth.2015.08.009openalex-snapshot

GoFDR: A sequence alignment based method for predicting protein functions

inferredcites →https://doi.org/10.1016/s0022-2836(05)80134-2openalex-snapshot

SCOP: A structural classification of proteins database for the investigation of sequences and structures

inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot

EMBOSS: The European Molecular Biology Open Software Suite

inferredcites →https://doi.org/10.1038/nmeth.2340openalex-snapshot

A large-scale evaluation of computational protein function prediction

inferredcites →https://doi.org/10.1038/s41586-018-0124-0openalex-snapshot

Mutant phenotypes for thousands of bacterial genes of unknown function

inferredcites →https://doi.org/10.1038/s41587-021-01179-wopenalex-snapshot

Using deep learning to annotate the protein universe

inferredcites →https://doi.org/10.1038/s42256-019-0049-9openalex-snapshot

Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins

inferredcites →https://doi.org/10.1038/srep31865openalex-snapshot

FFPred 3: feature-based function prediction for all Gene Ontology domains

inferredcites →https://doi.org/10.1073/pnas.2016239118openalex-snapshot

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

inferredcites →https://doi.org/10.1093/bib/bbw108openalex-snapshot

A comprehensive review and comparison of different computational methods for protein remote homology detection

inferredcites →https://doi.org/10.1093/bioinformatics/btm247openalex-snapshot

Fast model-based protein homology detection without alignment

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btt228openalex-snapshot

Information-theoretic evaluation of predicted ontological annotations

inferredcites →https://doi.org/10.1093/bioinformatics/btx624openalex-snapshot

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier

inferredcites →https://doi.org/10.1093/bioinformatics/btx680openalex-snapshot

DEEPre: sequence-based enzyme EC number prediction by deep learning

inferredcites →https://doi.org/10.1093/bioinformatics/btz422openalex-snapshot

AlphaFold at CASP13

inferredcites →https://doi.org/10.1093/nar/gky1049openalex-snapshot

UniProt: a worldwide hub of protein knowledge

inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot

The Pfam protein families database in 2019

inferredcites →https://doi.org/10.1101/676825openalex-snapshot

Evaluating Protein Transfer Learning with TAPE

inferredcites →https://doi.org/10.1186/1471-2105-8-23openalex-snapshot

Motif kernel generated by genetic programming improves remote homology and fold detection

inferredcites →https://doi.org/10.1186/s12859-017-1842-2openalex-snapshot

Protein remote homology detection based on bidirectional long short-term memory

inferredcites →https://doi.org/10.1186/s12859-018-2368-yopenalex-snapshot

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

inferredcites →https://doi.org/10.1371/journal.pone.0141287openalex-snapshot

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

inferredcites →https://doi.org/10.18653/v1/n18-1202openalex-snapshot

Deep Contextualized Word Representations

inferredcites →https://doi.org/10.18653/v1/p16-1162openalex-snapshot

Neural Machine Translation of Rare Words with Subword Units

inferredcites →https://doi.org/10.18653/v1/p18-1031openalex-snapshot

Universal Language Model Fine-tuning for Text Classification

inferredcites →https://doi.org/10.4230/lipics.cosit.2022.18openalex-snapshot

AI-Assisted Pipeline for Dynamic Generation of Trustworthy Health Supplement Content at Scale

inferredcites →https://doi.org/10.4230/lipics.cp.2025.31openalex-snapshot

HISTORIAE, History of Socio-Cultural Transformation as Linguistic Data Science. A Humanities Use Case

inferredcites →https://doi.org/10.48550/arxiv.1412.6980openalex-snapshot

Adam: A Method for Stochastic Optimization

inferredcites →https://doi.org/10.48550/arxiv.1612.04426openalex-snapshot

Improving Neural Language Models with a Continuous Cache

inferredcites →https://doi.org/10.48550/arxiv.1708.02182openalex-snapshot

Regularizing and Optimizing LSTM Language Models

inferredcites →https://doi.org/10.48550/arxiv.1803.09820openalex-snapshot

A disciplined approach to neural network hyper-parameters: Part 1 -- learning rate, batch size, momentum, and weight decay

inferredcites →https://doi.org/10.48550/arxiv.1905.02450openalex-snapshot

MASS: Masked Sequence to Sequence Pre-training for Language Generation

inferredcites →https://doi.org/10.48550/arxiv.1906.08237openalex-snapshot

XLNet: Generalized Autoregressive Pretraining for Language Understanding

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2021.107596openalex-snapshot

Deep protein representations enable recombinant protein expression prediction

inferred← citeshttps://doi.org/10.1101/2020.04.17.047316openalex-snapshot

Transfer learning improves antibiotic resistance class prediction

inferred← citeshttps://doi.org/10.1101/2020.06.15.153643openalex-snapshot

Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks

inferred← citeshttps://doi.org/10.1186/s12859-020-03631-1openalex-snapshot

USMPep: universal sequence models for major histocompatibility complex binding affinity prediction

inferred← citeshttps://doi.org/10.3389/fcimb.2021.610348openalex-snapshot

Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data

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