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Saliency map on Cnns for protein secondary structure prediction

Saliency map on Cnns for protein secondary structure prediction
Saliency map on Cnns for protein secondary structure prediction
Deep learning, a powerful methodology for data-driven modelling, has been shown to be useful in tackling several problems in the biomedical domain. However, deep neural architectures lack interpretability of how predictions from them are made on any test input. While several approaches to "opening the black box" are being developed, their application to biological and medical data is very much as its infancy. Here, we consider the specific problem of protein secondary structure prediction using the techniques of saliency maps to explain decisions of a deep neural network. The analysis leads to two important observations: (a) one-hot-encoded amino-acids are irrelevant in the presence of PSSM values as extra features; and (b) in predicting α-helices at any position, amino-acids to the right are far more important than those to the left. The latter observation may have a biological basis relating to the synthesis of proteins by ribosome movement from left to right, sequentially adding amino-acids.
Interpretability, Saliency Maps, Protein Secondary Structure Prediction, Convolutional Neural Networks
2379-190X
1249-1253
IEEE
Romero Moreno, Guillermo
8c2f32d6-b0b5-4563-af22-c08b410b867f
Niranjan, Mahesan
5cbaeea8-7288-4b55-a89c-c43d212ddd4f
Prugel-Bennett, Adam
b107a151-1751-4d8b-b8db-2c395ac4e14e
Romero Moreno, Guillermo
8c2f32d6-b0b5-4563-af22-c08b410b867f
Niranjan, Mahesan
5cbaeea8-7288-4b55-a89c-c43d212ddd4f
Prugel-Bennett, Adam
b107a151-1751-4d8b-b8db-2c395ac4e14e

Romero Moreno, Guillermo, Niranjan, Mahesan and Prugel-Bennett, Adam (2019) Saliency map on Cnns for protein secondary structure prediction. In ICASSP 2019 - 2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE. pp. 1249-1253 . (doi:10.1109/ICASSP.2019.8683603).

Record type: Conference or Workshop Item (Paper)

Abstract

Deep learning, a powerful methodology for data-driven modelling, has been shown to be useful in tackling several problems in the biomedical domain. However, deep neural architectures lack interpretability of how predictions from them are made on any test input. While several approaches to "opening the black box" are being developed, their application to biological and medical data is very much as its infancy. Here, we consider the specific problem of protein secondary structure prediction using the techniques of saliency maps to explain decisions of a deep neural network. The analysis leads to two important observations: (a) one-hot-encoded amino-acids are irrelevant in the presence of PSSM values as extra features; and (b) in predicting α-helices at any position, amino-acids to the right are far more important than those to the left. The latter observation may have a biological basis relating to the synthesis of proteins by ribosome movement from left to right, sequentially adding amino-acids.

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Saliency Maps On CNNs For Protein Secondary Structure Prediction - Accepted Manuscript
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More information

e-pub ahead of print date: 17 April 2019
Published date: May 2019
Venue - Dates: ICASSP 2019: 2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Brighton Conference Centre, Brighton, United Kingdom, 2019-05-12 - 2019-05-17
Keywords: Interpretability, Saliency Maps, Protein Secondary Structure Prediction, Convolutional Neural Networks

Identifiers

Local EPrints ID: 430913
URI: http://eprints.soton.ac.uk/id/eprint/430913
ISSN: 2379-190X
PURE UUID: cc416c92-62a3-48e5-8a99-4a0a81d63747
ORCID for Guillermo Romero Moreno: ORCID iD orcid.org/0000-0002-0316-8306

Catalogue record

Date deposited: 17 May 2019 16:30
Last modified: 16 Sep 2021 01:59

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