ProteinBERT: A universal deep-learning model of protein sequence and function

This page summarizes the projects mentioned and recommended in the original post on /r/bioinformatics

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  • protein_bert

  • tape

    Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (by songlab-cal)

  • We evaluated based on downstream tasks (multiple supervised benchmarks, including 4 from TAPE), not the LM performance.

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  • ProFET

    ProFET: Protein Feature Engineering Toolkit for Machine Learning

  • That should be trivial for it, attention models are good for "feature X exists somewhere in the text"/ That said, if your feature is just the presence of some short motif, why not just use n-gram/k-mer features? Those are invariant to location, and super fast/simple. I did some packages in the past for that, specially for proteins (PROFET, ASAP(for residue level)).

  • asap

    Amino-Acid Sequence Annotation Predictor (ASAP)

  • That should be trivial for it, attention models are good for "feature X exists somewhere in the text"/ That said, if your feature is just the presence of some short motif, why not just use n-gram/k-mer features? Those are invariant to location, and super fast/simple. I did some packages in the past for that, specially for proteins (PROFET, ASAP(for residue level)).

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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