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Abstract BackgroundProtein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signaling of all main classes of protein. It is involved in several biological processes including immune response, protein stability, transcription regulation, post translational regulation, DNA damage repair, redox regulation, and is an emerging paradigm of redox signaling for protection against oxidative stress. The development of robust computational tools to predict protein SNO sites would contribute to further interpretation of the pathological and physiological mechanisms of SNO. ResultsUsing an intermediate fusion-based stacked generalization approach, we integrated embeddings from supervised embedding layer and contextualized protein language model (ProtT5) and developed a tool called pLMSNOSite (protein language model-based SNO site predictor). On an independent test set of experimentally identified SNO sites, pLMSNOSite achieved values of 0.340, 0.735 and 0.773 for MCC, sensitivity and specificity respectively. These results show that pLMSNOSite performs better than the compared approaches for the prediction of S-nitrosylation sites. ConclusionTogether, the experimental results suggest that pLMSNOSite achieves significant improvement in the prediction performance of S-nitrosylation sites and represents a robust computational approach for predicting protein S-nitrosylation sites. pLMSNOSite could be a useful resource for further elucidation of SNO and is publicly available athttps://github.com/KCLabMTU/pLMSNOSite.
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DIRECT: Dual Interpretable Recommendation with Multi-aspect Word Attribution
Recommending products to users with intuitive explanations helps improve the system in transparency, persuasiveness, and satisfaction. Existing interpretation techniques include post-hoc methods and interpretable modeling. The former category could quantitatively analyze input contribution to model prediction but has limited interpretation faithfulness, while the latter could explain model internal mechanisms but may not directly attribute model predictions to input features. In this study, we propose a novelDualInterpretableRecommendation model called DIRECT, which integrates ideas of the two interpretation categories to inherit their advantages and avoid limitations. Specifically, DIRECT makes use of item descriptions as explainable evidence for recommendation. First, similar to the post-hoc interpretation, DIRECT could attribute the prediction of a user preference score to textual words of the item descriptions. The attribution of each word is related to its sentiment polarity and word importance, where a word is important if it corresponds to an item aspect that the user is interested in. Second, to improve the interpretability of embedding space, we propose to extract high-level concepts from embeddings, where each concept corresponds to an item aspect. To learn discriminative concepts, we employ a concept-bottleneck layer, and maximize the coding rate reduction on word-aspect embeddings by leveraging a word-word affinity graph extracted from a pre-trained language model. In this way, DIRECT simultaneously achieves faithful attribution and usable interpretation of embedding space. We also show that DIRECT achieves linear inference time complexity regarding the length of item reviews. We conduct experiments including ablation studies on five real-world datasets. Quantitative analysis, visualizations, and case studies verify the interpretability of DIRECT. Our code is available at:https://github.com/JacksonWuxs/DIRECT.
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- Award ID(s):
- 2223768
- PAR ID:
- 10520420
- Publisher / Repository:
- ACM
- Date Published:
- Journal Name:
- ACM Transactions on Intelligent Systems and Technology
- ISSN:
- 2157-6904
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1145/3663483
