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Post-Translational Modifications (PTMs) are a fundamental mechanism for regulating cellular functions and
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Post-Translational Modifications (PTMs) are a fundamental mechanism for regulating cellular functions and
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increasing the functional diversity of the proteome. Despite the identification of hundreds of unique PTMs
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through mass-spectrometry (MS) studies, accurately predicting many PTM types based on sequence data alone
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remains a significant challenge. Existing PTM prediction models predominantly focus on either single PTM
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types or employ ensemble methods that combine multiple models to predict different PTM types. This fragmentation
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is largely driven by the vast imbalance in data availability across PTM types making it difficult to predict
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multiple PTM types with a single model. To address this limitation, we present the Contrastively Learned
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Attention-Based Stratified PTM Predictor (CLASPP), a unified PTM prediction model. CLASPP overcomes
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data imbalance challenges by leveraging unsupervised clustering-based under-sampling and incorporating a novel
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contrastive learning framework tailored to PTM data. Drawing inspiration from advancements in image and
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natural language processing, the CLASPP model employs a multi-stage training strategy and utilizes a
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high-quality curated training dataset to improve PTM prediction accuracy compared to existing multi-PTM prediction
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models. Existing PTM prediction models predominantly focus on either single PTM types or employ ensemble methods
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that combine multiple models to predict different PTM types. This fragmentation is largely driven by the
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vast imbalance in data availability across PTM types making it difficult to predict multiple PTM types
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with a single model. To address this limitation, we present the
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Contrastively Learned Attention-Based Stratified PTM Predictor (CLASPP), a unified PTM prediction model.
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