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README.md

Paper12-PlosOne-DeepProteinMultitaskTagging

Y. Qi, M. Osh, J. Weston, W. Noble (2012) A unified multitask architecture for predicting local protein properties, PLoS ONE (March 2012) (URL),

Summary: Deep neural network architecture + Protein Sequence Labeling

(bibTex), @article{qi12plosone, author = {Qi, , Yanjun AND Oja, , Merja AND Weston, , Jason AND Noble, , William Stafford}, journal = {PLoS ONE}, publisher = {Public Library of Science}, title = {A Unified Multitask Architecture for Predicting Local Protein Properties}, year = {2012}, month = {03}, volume = {7}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0032235}, pages = {e32235}, abstract = {

A variety of functionally important protein properties, such as secondary structure, transmembrane topology and solvent accessibility, can be encoded as a labeling of amino acids. Indeed, the prediction of such properties from the primary amino acid sequence is one of the core projects of computational biology. Accordingly, a panoply of approaches have been developed for predicting such properties; however, most such approaches focus on solving a single task at a time. Motivated by recent, successful work in natural language processing, we propose to use multitask learning to train a single, joint model that exploits the dependencies among these various labeling tasks. We describe a deep neural network architecture that, given a protein sequence, outputs a host of predicted local properties, including secondary structure, solvent accessibility, transmembrane topology, signal peptides and DNA-binding residues. The network is trained jointly on all these tasks in a supervised fashion, augmented with a novel form of semi-supervised learning in which the model is trained to distinguish between local patterns from natural and synthetic protein sequences. The task-independent architecture of the network obviates the need for task-specific feature engineering. We demonstrate that, for all of the tasks that we considered, our approach leads to statistically significant improvements in performance, relative to a single task neural network approach, and that the resulting model achieves state-of-the-art performance.

}, number = {3}, doi = {10.1371/journal.pone.0032235} }


Paper URL: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032235


(SupplementWeb), all trained deep models have been shared @ http://noble.gs.washington.edu/proj/multitask/models/



RELATED SOFTWARE INSTALLATION:

---- (1) install BLAST from ncbi (NR filtered db)

  • http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html#1.1

  • setup using instrusction from : http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/

  • BLAST database is a key component of any BLAST search. Here we need to first download the NR database ==> ftp ftp.ncbi.nlm.nih.gov using "anonymous" ,
    then " cd blast/db ", then "get nr.*tar.gz" , then "tar zxvpf nr.*tar.gz" ==> nr.*tar.gz (non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq )

  • Configuration: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html#3.2

  • We can further filter nr database to nrf database using softwares provided by PSIPred

    • This step is optional !

    • Software PSIPred : http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README

    • A program called "pfilt" is included which will filter FASTA files before using the formatdb command to generate the encoded BLAST data bank files.

    • For example: pfilt nr.fasta > nrfilt formatdb -t nrfilt -i nrfilt cp nrfilt.p?? $BLASTDB

    • (The above command assumes you have already set the BLASTDB environment variable to the directory where you usually keep your BLAST data banks)


---- (2) install TORCH5 http://torch5.sourceforge.net/


---- (3) install viterbi package in your torch package

  • After the installation of TORCH5, copy the whole "viterbi" package directory under "your-path-to-torch-sources/dev/"
  • Then recompile and run commands ==> cd your-path-to-torch-sources/build cmake .. -DCMAKE_INSTALL_PREFIX=/my/install/path make make install


---- Please revise three variables before running ! ---- 1) "binDir" in "getPsiBlastNR.py" to your own BLAST local location
---- 2) "nrdb" in "getPsiBlastNR.py" to your own BLAST db local location
---- 3) "psipath" in "main.lua" to your local directory where psiblast profile features are generated in or have been generated in

---- RUN TO TEST

lua main.lua -h

Usage: main.lua [options]

Goal: to predict AA labels for certain task on input fasta file

Arguments: task: cb513ssp, dssalltaskdssp, dssalltaskssp, dssalltasksar, dssalltasksaa, coilcoil, dna-binding, ppi, sp, tm test fasta file to predict on a previously trained network model associated to your aimed task subdirectory to save the predictions in test fasta file to evaluate accuracy (if not exists, just put here psiExistFlag: [ 1 indicating psiBlast features exist, with system-defined dir ; 2 indicating psiBlast features exist, with user-defined dir in psipath; 0 indictating psiBlast features do not exist ]


==> You can try the following sample commands

---- lua main.lua -h

---- lua main.lua cb513ssp ./test/fasta/input.cb513ssp.seq.faa ./models4shareOnline/cb513ssp.model.asc ./test/ ./test/fasta/input.cb513ssp.lab.faa 1 > ./test/cb513test.log &

---- lua main.lua dssalltaskdssp ./test/fasta/input.dssp4task.seq.faa ./models4shareOnline/dssalltaskdssp.model.asc ./test/ ./test/fasta/input.dssp.lab.faa 0 > ./test/dssalltaskdssp.log &

---- lua main.lua dssalltaskssp ./test/fasta/input.dssp4task.seq.faa ./models4shareOnline/dssalltaskssp.model.asc ./test/ ./test/fasta/input.ssp.lab.faa 1 > ./test/dssalltaskssp.log

---- lua main.lua dssalltasksaa ./test/fasta/input.dssp4task.seq.faa ./models4shareOnline/dssalltasksaa.model.asc ./test/ ./test/fasta/input.saa.lab.faa 1 > ./test/dssalltasksaa.log

---- lua main.lua dssalltasksar ./test/fasta/input.dssp4task.seq.faa ./models4shareOnline/dssalltasksar.model.asc ./test/ ./test/fasta/input.sar.lab.faa 1 > ./test/dssalltasksar.log

==> similar commands are applied to other tasks (coilcoil, dna-binding, sp, tm)


==> For PPI task, we use it non-viterbi model since it performs better

---- lua main-nvit-ppi.lua ppi ./test/fasta/input.tppi.seq.faa ./models4shareOnline/TPPI-nonVit/tppi.psionly.model.asc.noviterbi ./test/ ./test/fasta/input.tppi.lab.faa 1 > ./test/log/ppi.log



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A Deep-Learning based Multi-Task Framework for Protein Sequence Labeling / Local Structural Property Prediction on biological Sequences

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