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Joseph Szymborski

PhD - McGill University
Supervisor
Amin Emad
Research Topics
Computational Biology
Deep Learning
Website
GitHub

Publications

A flaw in using pre-trained pLLMs in protein-protein interaction inference models
Joseph Szymborski
Amin Emad
With the growing pervasiveness of pre-trained protein large language models (pLLMs), pLLM-based methods are increasingly being put forward f… (see more)or the protein-protein interaction (PPI) inference task. Here, we identify and confirm that existing pre-trained pLLMs are a source of data leakage for the downstream PPI task. We characterize the extent of the data leakage problem by training and comparing small and efficient pLLMs on a dataset that controls for data leakage (“strict”) with one that does not (“non-strict”). While data leakage from pre-trained pLLMs cause measurable inflation of testing scores, we find that this does not necessarily extend to other, non-paired biological tasks such as protein keyword annotation. Further, we find no connection between the context-lengths of pLLMs and the performance of pLLM-based PPI inference methods on proteins with sequence lengths that surpass it. Furthermore, we show that pLLM-based and non-pLLM-based models fail to generalize in tasks such as prediction of the human-SARS-CoV-2 PPIs or the effect of point mutations on binding-affinities. This study demonstrates the importance of extending existing protocols for the evaluation of pLLM-based models applied to paired biological datasets and identifies areas of weakness of current pLLM models.
2025-04-23
bioRxiv (preprint)
doi.org
INTREPPPID - An Orthologue-Informed Quintuplet Network for Cross-Species Prediction of Protein-Protein Interaction
Joseph Szymborski
Amin Emad
An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constrain… (see more)ts in time and cost of the associated “wet lab” experiments. In silico PPI inference methods are ideal tools to overcome these limitations, but often struggle with cross-species predictions. We present INTREPPPID, a method which incorporates orthology data using a new “quintuplet” neural network, which is constructed with five parallel encoders with shared parameters. INTREPPPID incorporates both a PPI classification task and an orthologous locality task. The latter learns embeddings of orthologues that have small Euclidean distances between them and large distances between embeddings of all other proteins. INTREPPPID outperforms all other leading PPI inference methods tested on both the intra-species and cross-species tasks using strict evaluation datasets. We show that INTREPPPID’s orthologous locality loss increases performance because of the biological relevance of the orthologue data, and not due to some other specious aspect of the architecture. Finally, we introduce PPI.bio and PPI Origami, a web server interface for INTREPPPID and a software tool for creating strict evaluation datasets, respectively. Together, these two initiatives aim to make both the use and development of PPI inference tools more accessible to the community. GRAPHICAL ABSTRACT
2024-01-01
Briefings Bioinform. (published)
doi.org