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Semi-supervised Retrieval of Functional Residues Through the Integration of Protein Language Models and Gene Ontology Data
Dickson, A. M., Mouline, S., Tamadon, A., Mofrad, M.
bioRxiv·2025
MotivationExperimental studies of protein function often focus on mechanistic descriptions, characterizing how specific sites and residues contribute to activity. Abstractions such as domains and active sites enable quantitative descriptions of how protein features act biologically. Thanks to the abundance of high-quality sequence and function data, machine learning has achieved great success in directly predicting protein function. However, translating functional characterizations into mechanistic ones on the level of the domains, binding sites, or motifs remains challenging. This represents a semi-supervised problem: sequences and global functional labels are available, but local annotations must be inferred.
ResultsWe investigate the unsupervised discovery of functionally active protein regions by integrating protein sequence models with functional information. We first formalize the residue-level functional annotation problem by constructing unified evaluation datasets linking Gene Ontology functions to annotated residues. Eight datasets are assembled, spanning levels of specificity from single active-site residues to domains covering up to 60% of a protein. We then introduce a new class of function-conditioned generative models that more accurately predict functionally important residues than existing approaches, including interpretability methods and PSSM entropy estimation, across multiple benchmark datasets.
Availabilitygithub.com/mofradlab/go_interp
Contactmofrad@berkeley.edu
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View paper →Organized Hypocrisy and the Logic of Coloniality. Explaining the EU's Divergent Response to Grave Violations of International Law in Russia/Ukraine and Israel/Palestine
Daniela Verena Huber
JCMS: Journal of Common Market Studies·2025·6 citations
‘Organized hypocrisy’ has been mainly explained in IR by the logic of consequentiality operating against the logic of appropriateness. The literature has largely ignored the role of a third logic, the logic of coloniality, which highlights that organized hypocrisy appears persistently in international relations due to omissions in the field of knowledge: It features a double absence of the ‘other’ on their own normative terms and as a rights‐bearing subject. Pursuing a comparative analysis of EU policies to ensure accountability in the face of grave violations of international law in Russia/Ukraine and Israel/Palestine, this research finds patterned discrepancies, particularly towards Palestine which are explained by imaginations in official EU discourse where Russia, Ukraine and Israel figure in a Eurocentric temporal–spatial relation to Europe, while Palestine is dispossessed of its history, not set into any relationship to Europe and figures as a partially rights‐less subject in official EU discourse.
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