Biological sequence analysis and information processing by artificial neural networks

Pairvise alignment >carp Cyprinus carpio growth hormone 210 aa vs. >chicken Gallus gallus growth hormone 216 aa scoring matrix: BLOSUM50, gap penalties: -12/ % identity; Global alignment score: carp MA--RVLVLLSVVLVSLLVNQGRASDN-----QRLFNNAVIRVQHLHQLAAKMINDFEDSLLPEERRQLSKIFPLSFCNSD ::. :...:.:. : :.. :: :::.:.:::: :::...::..::..:.:.:: :. chicken MAPGSWFSPLLIAVVTLGLPQEAAATFPAMPLSNLFANAVLRAQHLHLLAAETYKEFERTYIPEDQRYTNKNSQAAFCYSE carp YIEAPAGKDETQKSSMLKLLRISFHLIESWEFPSQSLSGTVSNSLTVGNPNQLTEKLADLKMGISVLIQACLDGQPNMDDN : ::.:::..:..:..:::.:. ::.:: : : ::..:.:. :.... ::: ::. ::..:.. :.:. chicken TIPAPTGKDDAQQKSDMELLRFSLVLIQSWLTPVQYLSKVFTNNLVFGTSDRVFEKLKDLEEGIQALMRELEDRSPR---G carp DSLPLP-FEDFYLTM-GENNLRESFRLLACFKKDMHKVETYLRVANCRRSLDSNCTL.: :.. :...:. :... ::.:::::.:::::::.:.:::.::::. chicken PQLLRPTYDKFDIHLRNEDALLKNYGLLSCFKKDLHKVETYLKVMKCRRFGESNCTI

Biological Neural network

Biological neuron

Diversity of interactions in a network enables complex calculations Similar in biological and artificial systems Excitatory (+) and inhibitory (-) relations between compute units

Biological neuron structure

Transfer of biological principles to artificial neural network algorithms Non-linear relation between input and output Massively parallel information processing Data-driven construction of algorithms Ability to generalize to new data items

Simplest non-trivial classification problem CNHSYYP, HIETRRA, NWQSADY, NQYSEPR, WHITRCA, DYHSANY,... Two categories: positives and negatives Data described by features, e.g. charge, sidechain volume, molecular weight, number of atoms,...

Features of phosphorylations sites PKG cGMP- dep.kinase PKC CaM-II Ca++/cal- modulin-dep. kinase cdc2 Cyclin- dep.kinase 2 CK-II Casein kinase 2

Neural networks Neural networks can learn higher order correlations XOR function: 0 0 => => => => 0 (1,1) (1,0) (0,0) (0,1) No linear function can separate the points

Neural networks v1v1 v2v2 Linear function

Neural networks w 11 w 12 v1v1 w 21 w 22 v2v2 Higher order function

Neural networks. How does it work? w 12 v1v1 w 21 w 22 v2v2 w t2 w t1 w 11 vtvt Input 1 (Bias) {

Neural networks (0 0) Input 1 (Bias) { o 1 =-6 O 1 =0 o 2 =-2 O 2 =0 y 1 =-4.5 Y 1 =0

Neural networks (1 0 && 0 1) Input 1 (Bias) { o 1 =-2 O 1 =0 o 2 =4 O 2 =1 y 1 =4.5 Y 1 =1

Neural networks (1 1) Input 1 (Bias) { o 1 =2 O 1 =1 o 2 =10 O 2 =1 y 1 =-4.5 Y 1 =0

What is going on? XOR function: 0 0 => => => => Input 1 (Bias) { y2y2 y1y1

What is going on? (1,1) (1,0) (0,0) (0,1) x2x2 x1x1 y1y1 y2y2 (1,0) (2,2) (0,0)

DEMO

Training and error reduction

Transfer of biological principles to neural network algorithms Non-linear relation between input and output Massively parallel information processing Data-driven construction of algorithms

A Network contains a very large set of parameters –A network with 5 hidden neurons predicting binding for 9meric peptides has 9x20x5=900 weights Over fitting is a problem Stop training when test performance is optimal Neural network training years Temperature

Neural network training. Cross validation Cross validation Train on 4/5 of data Test on 1/5 => Produce 5 different neural networks each with a different prediction focus

Neural network training curve Maximum test set performance Most cable of generalizing

Network training Encoding of sequence data Sparse encoding Blosum encoding Sequence profile encoding

Sparse encoding of amino acid sequence windows

Sparse encoding Inp Neuron AAcid A R N D C Q E

Sparse encoding of nucleotide sequence windows Nucleotides 4 letter alphabet ACGTAGGCAATCTCAGACGTTTATC

BLOSUM encoding (Blosum50 matrix) A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V

Sequence encoding (continued) Sparse encoding V: L: V. L=0 (unrelated) Blosum encoding V: L: V. L = 0.88 (highly related) V. R = (close to unrelated)

Applications of artificial neural networks Talk recognition Prediction of protein secondary structure Prediction of Signal peptides Post translation modifications Glycosylation Phosphorylation Proteasomal cleavage MHC:peptide binding