Research graph
References from The language of proteins: NLP, machine learning & protein sequences. Local targets link to admitted publications; unresolved targets remain external evidence.
Evaluation of Database Search Programs for Accurate Detection of Neuropeptides in Tandem Mass Spectrometry Experiments
10.1021/pr3007123 · 2012 · External reference
Neural networks versus logistic regression for 30 days all-cause readmission prediction
10.1038/s41598-019-45685-z · 2019 · External reference
10.1038/s41592-019-0598-1
10.1038/s41592-019-0598-1 · External reference
10.1101/2020.03.09.983585
10.1101/2020.03.09.983585 · External reference
10.1093/bioinformatics/btx431
10.1093/bioinformatics/btx431 · External reference
Deep learning for computational biology
10.15252/msb.20156651 · 2016 · External reference
Unresolved reference
External reference
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
2019 · External reference
Continuous Distributed representation of biological sequences for deep proteomics and genomics
2015 · External reference
The complete peptide dictionary – a meta-proteomics resource
10.1002/pmic.201000270 · 2010 · External reference
Machine learning methods for predictive proteomics
10.1093/bib/bbn008 · 2008 · External reference
Protein Sequence Motifs: Highly Predictive Features of Protein Function
10.1007/978-3-540-35488-8_32 · 2006 · External reference
Unresolved reference
External reference
10.1093/nar/28.1.235
10.1093/nar/28.1.235 · External reference
Using deep learning to annotate the protein universe
2019 · External reference
Enriching word vectors with subword information
10.1162/tacl_a_00051 · 2017 · External reference
UniProtKB/Swiss-Prot: The manually annotated section of the uniprot knowledgebase
2007 · External reference
ASAP: A machine learning framework for local protein properties
10.1093/database/baw133 · 2016 · External reference
Unresolved reference
External reference
10.1073/pnas.0914097107
10.1073/pnas.0914097107 · External reference
Unresolved reference
External reference
10.3917/perri.fur.2015.01
10.3917/perri.fur.2015.01 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
10.1038/srep31865
10.1038/srep31865 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Speeding up Tandem Mass Spectrometry Database Search: Metric Embeddings and Fast near Neighbor Search
10.1093/bioinformatics/btl645 · 2007 · External reference
10.1101/2020.07.12.199554
10.1101/2020.07.12.199554 · External reference
Unresolved reference
External reference
10.1186/1471-2105-14-s3-s15
10.1186/1471-2105-14-s3-s15 · External reference
Word2vec explained: Deriving Mikolov et al’.s negative-sampling word-embedding method
2014 · External reference
The unreasonable effectiveness of data
10.1109/mis.2009.36 · 2009 · External reference
Modeling aspects of the language of life through transfer-learning protein sequences
10.1186/s12859-019-3220-8 · 2019 · External reference
10.1126/science.abd7331
10.1126/science.abd7331 · External reference
10.1162/neco.1997.9.8.1735
10.1162/neco.1997.9.8.1735 · External reference
10.1093/bioinformatics/btl002
10.1093/bioinformatics/btl002 · External reference
Universal language model fine-tuning for text classification
2018 · External reference
10.1002/prot.10381
10.1002/prot.10381 · External reference
10.1101/2020.09.17.301879
10.1101/2020.09.17.301879 · External reference
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
10.1186/s13059-016-1037-6 · 2016 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
2017 · External reference
10.1016/j.csbj.2020.06.017 · Admitted local publication
Imagenet classification with deep convolutional neural networks
2012 · External reference
Critical assessment of methods of protein structure prediction (casp)—round xiii
10.1002/prot.25823 · 2019 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
ALBERT: A lite BERT for self-supervised learning of language representations
2020 · External reference
10.1142/9789812799623_0053
10.1142/9789812799623_0053 · External reference
Mismatch string kernels for discriminative protein classification
2004 · External reference
Unresolved reference
External reference
10.1101/2020.09.04.282814
10.1101/2020.09.04.282814 · External reference
Unresolved reference
External reference
10.1101/2020.03.07.982272
10.1101/2020.03.07.982272 · External reference
Unresolved reference
External reference
One neuron is more informative than a deep neural network for aftershock pattern forecasting
2019 · External reference
Distributed representations of words and phrases and their compositionality
2013 · External reference
10.1093/bib/bbw068
10.1093/bib/bbw068 · External reference
Simplified amino acid alphabets for protein fold recognition and implications for folding
10.1093/protein/13.3.149 · 2000 · External reference
ClanTox: A classifier of short animal toxins
10.1093/nar/gkp299 · 2009 · External reference
Evaluating vector-space models of word representation, or, the unreasonable effectiveness of counting words near other words
2017 · External reference
10.1093/bioinformatics/btt725
10.1093/bioinformatics/btt725 · External reference
Unresolved reference
External reference
10.7490/f1000research.1110203.1
10.7490/f1000research.1110203.1 · External reference
10.1016/j.ymeth.2014.10.026
10.1016/j.ymeth.2014.10.026 · External reference
Unresolved reference
External reference
Proteomic Signatures: Amino Acid and Oligopeptide Compositions Differentiate among Phyla
10.1002/prot.10559 · 2004 · External reference
10.3115/v1/d14-1162
10.3115/v1/d14-1162 · External reference
Unresolved reference
External reference
10.1093/bioinformatics/btp164
10.1093/bioinformatics/btp164 · External reference
Aligning the pretraining and finetuning objectives of language models
2020 · External reference
10.1016/0014-5793(91)80799-9
10.1016/0014-5793(91)80799-9 · External reference
Deep Learning Embedder Method and Tool for Mass Spectra Similarity Search
10.1016/j.jprot.2020.104070 · 2021 · External reference
Unresolved reference
External reference
Exploring the limits of transfer learning with a unified text-to-text transformer
2020 · External reference
DeepType: Multilingual entity linking by neural type system evolution
2018 · External reference
10.1101/676825
10.1101/676825 · External reference
10.1101/2021.02.12.430858
10.1101/2021.02.12.430858 · External reference
Unresolved reference
2014 · External reference
10.1038/nmeth.1818
10.1038/nmeth.1818 · External reference
10.1101/622803
10.1101/622803 · External reference
10.1126/science.aan0693
10.1126/science.aan0693 · External reference
Unresolved reference
External reference
Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains
10.1093/bioinformatics/bti1035 · 2005 · External reference
Unresolved reference
External reference
10.1093/bioinformatics/btx818
10.1093/bioinformatics/btx818 · External reference
Biases in the experimental annotations of protein function and their effect on our understanding of protein function space
2013 · External reference
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data
10.1186/1745-6150-5-6 · 2010 · External reference
10.1038/s41586-019-1923-7
10.1038/s41586-019-1923-7 · External reference
10.18653/v1/p16-1162
10.18653/v1/p16-1162 · External reference
10.1002/j.1538-7305.1951.tb01366.x
10.1002/j.1538-7305.1951.tb01366.x · External reference
10.1101/2020.04.08.002378
10.1101/2020.04.08.002378 · External reference
Unresolved reference
External reference
10.1073/pnas.0409746102
10.1073/pnas.0409746102 · 2005 · External reference
10.1038/nbt.3988
10.1038/nbt.3988 · External reference
The shannon information entropy of protein sequences
10.1016/s0006-3495(96)79210-x · 1996 · External reference
UDSMProt: universal deep sequence models for protein classification
10.1093/bioinformatics/btaa003 · 2020 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
10.1016/j.resmic.2009.05.004
10.1016/j.resmic.2009.05.004 · External reference
10.1007/978-3-540-74126-8_3
10.1007/978-3-540-74126-8_3 · External reference
Attention is all you need
2017 · External reference
10.1101/2020.06.26.174417
10.1101/2020.06.26.174417 · External reference
Glue: A multi-task benchmark and analysis platform for natural language understanding
2018 · External reference
A high efficient biological language model for predicting protein-protein interactions
10.3390/cells8020122 · 2019 · External reference
Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein
10.1016/j.febslet.2004.09.036 · 2004 · External reference
Deep learning in proteomics
2020 · External reference
Signal peptides generated by attention-based neural networks
10.1021/acssynbio.0c00219 · 2020 · External reference
10.18653/v1/k19-1052
10.18653/v1/k19-1052 · External reference
10.1126/science.abb2762
10.1126/science.abb2762 · External reference
10.1093/bioinformatics/bty178
10.1093/bioinformatics/bty178 · External reference
XLNet: Generalized autoregressive pretraining for language understanding
2019 · External reference
Unresolved reference
External reference
Dilated residual networks
2017 · External reference
10.1073/pnas.1814684116
10.1073/pnas.1814684116 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Understanding deep learning requires rethinking generalization
2017 · External reference
