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Sazan Mahbub

Publications and source records attributed to Sazan Mahbub.

4 recordsLinked to original sources

Retrieval-Augmented Interpretable Learning: Towards Task-Specific Zero-Shot Models in Healthcare

We introduce Retrieval-Augmented Interpretable Learning (RAIL), a probabilistic meta-learning framework for zero-shot generation of task-specific interpretable models that synthesizes coefficient-space structure from natural-language task descriptions and a memory of previously learned task-specific predictors. RAIL retrieves related source tasks, transfers structure through coefficient space, and generates a new predictor in the original diagnostic-feature space, enabling zero-shot and few-shot clinical procedure prediction with feature-level explanations. Its probabilistic formulation provides uncertainty over retrieval, model coefficients, and predictions, supporting reliability-aware deployment: uncertain predictions or unstable explanations can be flagged for additional clinical review rather than treated as automatic decisions. This makes RAIL particularly suited for healthcare settings, where prediction tasks are highly long-tailed, new clinical targets arise frequently, and models must remain inspectable, uncertainty-aware, and compatible with human oversight. Across long-tailed clinical procedure prediction tasks, RAIL maintains reliable performance across data-availability regimes: it achieves 73.4% accuracy in the held-out zero-shot settings, where no supervised task-specific model can be trained, and remains near 73.2% accuracy in the extreme few-shot regime with only 2-4 examples, where supervised task-specific models perform close to chance. RAIL further benefits from clinically informed task representations and yields retrieval, uncertainty, and coefficient-level diagnostics that make model behavior more transparent. These results suggest a path toward scalable clinical prediction systems that can adapt to new tasks while preserving interpretability and reliability.

cs.LG

PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations

Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local structural constraints. Existing deep learning approaches achieve strong recovery rates, however, lack explicit mechanisms to reuse fine-grained structure-sequence patterns conserved across natural proteins. To mitigate this, we present PRISM a multimodal retrieval-augmented generation framework for inverse folding. PRISM retrieves fine-grained representations of potential motifs from known proteins and integrates them with a hybrid self-cross attention decoder. PRISM is formulated as a latent-variable probabilistic model and implemented with an efficient approximation, combining theoretical grounding with practical scalability. Experiments across multiple benchmarks, including CATH-4.2, TS50, TS500, CAMEO 2022, and the PDB date split, demonstrate the fine-grained multimodal retrieval efficacy of PRISM in yielding SoTA perplexity and amino acid recovery, while also improving the foldability metrics (RMSD, TM-score, pLDDT).

q-bio.QM

Recent Advances, Applications and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2024 Symposium

The fourth Machine Learning for Health (ML4H) symposium was held in person on December 15th and 16th, 2024, in the traditional, ancestral, and unceded territories of the Musqueam, Squamish, and Tsleil-Waututh Nations in Vancouver, British Columbia, Canada. The symposium included research roundtable sessions to foster discussions between participants and senior researchers on timely and relevant topics for the ML4H community. The organization of the research roundtables at the conference involved 13 senior and 27 junior chairs across 13 tables. Each roundtable session included an invited senior chair (with substantial experience in the field), junior chairs (responsible for facilitating the discussion), and attendees from diverse backgrounds with an interest in the session's topic.

cs.LG

Review4Repair: Code Review Aided Automatic Program Repairing

Context: Learning-based automatic program repair techniques are showing promise to provide quality fix suggestions for detected bugs in the source code of the software. These tools mostly exploit historical data of buggy and fixed code changes and are heavily dependent on bug localizers while applying to a new piece of code. With the increasing popularity of code review, dependency on bug localizers can be reduced. Besides, the code review-based bug localization is more trustworthy since reviewers' expertise and experience are reflected in these suggestions. Objective: The natural language instructions scripted on the review comments are enormous sources of information about the bug's nature and expected solutions. However, none of the learning-based tools has utilized the review comments to fix programming bugs to the best of our knowledge. In this study, we investigate the performance improvement of repair techniques using code review comments. Method: We train a sequence-to-sequence model on 55,060 code reviews and associated code changes. We also introduce new tokenization and preprocessing approaches that help to achieve significant improvement over state-of-the-art learning-based repair techniques. Results: We boost the top-1 accuracy by 20.33% and top-10 accuracy by 34.82%. We could provide a suggestion for stylistics and non-code errors unaddressed by prior techniques. Conclusion: We believe that the automatic fix suggestions along with code review generated by our approach would help developers address the review comment quickly and correctly and thus save their time and effort.

cs.SE