Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 11 of 11 for “"protein language models"”.
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Structure, Function, and Interaction in Protein Language Models
… This approach has been extended to the realm of protein sequences through pretrained protein language models, which have excelled in various protein engineering tasks. In this thesis, we investigate a pre-trained protein language model’s ability to predict protein structure and the effects of …
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Source identification for exosomal communication via protein language models
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01
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Harnessing Deep Learning with Protein Language Models to Unveil Microbial Enzyme Function in Health and Disease
… functions of enzymes are critical, as these proteins have important roles in catalysing essential biochemical reactions with high specificity and efficiency. Historically, functional annotation tools have relied on hidden Markov models (HMMs) that are built by aligning many amino acid …
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Integrating Functional Knowledge into Protein Design: A Novel Approach to Tokenization and Noise Injection for Function-Aware Protein Language Models
Designing novel proteins with specific biological functions remains a fundamental challenge in computational biology. While recent advances in protein language models have enabled powerful sequence-based representations, most models, including state-of-the-art systems like ESM3, fall short in …
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Learning the language of biomolecular interactions
Proteins are the primary functional unit of the cell, and their interactions drive cellular function. Interactions between proteins are responsible for a wide variety of functions raning from catalytic activity to cellular transport and signaling, and interactions between small molecules and …
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Learning the Language of Antibody Hypervariability Through Biological Property Prediction
Machine learning-based protein language models (PLMs) have proven to be successful in a variety of structure and function-prediction contexts. However, foundational PLMs (those trained on the corpus of all proteins) rely on evolutionary co-conservation of protein sub-sequences, but this …
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Protein Function Prediction Using Graph Convolutional Network
This project advances protein function prediction by integrating protein language models (PLMs) and graph convolutional networks (GCNs), addressing the limitations of traditional methods that rely heavily on sequence similarity. The proposed model leverages diverse protein features, including …
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Fine-tuning Boltz for Antibody-Antigen Binding Prediction
… most rapidly growing fields. Recent advances in protein language models and structure prediction have provided new tools for modeling, yet these approaches often fall short in capturing the fine-grained features that drive binding specificity in antibody and antigens. This thesis evaluates …
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Learning from pre-pandemic data to design and test future-proof therapeutics
… Nipah. We investigate both alignment-based and protein language models to explore the best model of mutation effects across pandemic-threat viral families. We demonstrate the utility of EVEscape in three critical applications: (1) Surveillance efforts flagging high escape SARS-CoV-2 variants …
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Assessing the Clinical Relevance of BRCA1 BRCT Domain Variants of Uncertain Significance
… best performance out of all trained supervised models, with 91.1% and 87.9% accuracy on the training and validation sets, respectively. Compared to individual in silico and AI protein language models, our model demonstrated the highest accuracy on the training set and comparable accuracy on the …
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Discovering Viral Hosts, Mutations, and Diseases using Machine Learning
… computational virology. (i) We develop a viral protein language model for predicting the host infected by a virus, given only the sequence of one of its proteins. Our approach, 'Hierarchical Attention for Viral protEin-based host iNference (HAVEN)', includes a novel architecture comprising …