Can a Sparse 29 x 29 Pixel Chaos Game Representation Predict Protein Binding Sites using Fine-Tuned State-of-the Art Deep Learning Semantic Segmentation Models?

Dick, K.; Green, J. R.

doi:10.1101/2023.08.04.410498

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bioRxiv · 10.1101/2023.08.04.410498

Can a Sparse 29 x 29 Pixel Chaos Game Representation Predict Protein Binding Sites using Fine-Tuned State-of-the Art Deep Learning Semantic Segmentation Models?

Dick, K.·Green, J. R.

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Abstract

No. While our experiments ultimately failed, this work was motivated by the seemingly reasonable hypothesis that encoding protein sequences as a fractal-based image in combination with a binary mask identifying those pixels representative of the protein binding interface could effectively be used to fine-tune a semantic segmentation model. We were wrong. Despite the shortcomings of this work, a number of insights were drawn, inspiring discussion about how this fractal-based space may be exploited to generate effective protein binding site predictors in the future. Furthermore, these realizations promise to orient complimentary studies leveraging fractal-based representations, whether in the field of bioinformatics, or more broadly within disparate fields leveraging sequence-type data, such as Natural Language Processing. In a non-traditional way, this work presents the experimental design undertaken and interleaves various insights and limitations. It is the hope of this work that those interested in leveraging fractal-based representations and deep learning architectures as part of their work will benefit from the insights arising from this work.

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Dick, K., Green, J. R.. 2023-08-04. Can a Sparse 29 x 29 Pixel Chaos Game Representation Predict Protein Binding Sites using Fine-Tuned State-of-the Art Deep Learning Semantic Segmentation Models?. https://doi.org/10.1101/2023.08.04.410498

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