Historically, two primary criticisms statisticians have of machine learning and deep neural models is their lack of uncertainty quantification and the inability to do inference (i.e., to explain what inputs are important). Explainable AI has developed in the last few years as a sub-discipline of computer science and machine learning to mitigate these concerns (as well as concerns of fairness and transparency in deep modeling). In this article, our focus is on explaining which inputs are important in models for predicting environmental data. In particular, we focus on three general methods for explainability that are model agnostic and thus applicable across a breadth of models without internal explainability: "feature shuffling", "interpretable local surrogates", and "occlusion analysis". We describe particular implementations of each of these and illustrate their use with a variety of models, all applied to the problem of long-lead forecasting monthly soil moisture in the North American corn belt given sea surface temperature anomalies in the Pacific Ocean.
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http://dx.doi.org/10.1002/env.2772 | DOI Listing |
Transl Oncol
January 2025
Tango Therapeutics, Tango Therapeutics, 201 Brookline Avenue, Boston, 02215, MA, United States.
TNG908 is a clinical stage PRMT5 inhibitor with an MTA-cooperative binding mechanism designed to leverage the synthetic lethal interaction between PRMT5 inhibition and MTAP deletion. MTAP deletion occurs in 10-15 % of all human cancer representing multiple histologies. MTA is a negative regulator of PRMT5 that accumulates as a result of MTAP deletion.
View Article and Find Full Text PDFScience
January 2025
Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
The most advanced monoclonal antibodies (mAbs) and vaccines against malaria target the central repeat region or closely related sequences within the circumsporozoite protein (PfCSP). Here, using an antigen-agnostic strategy to investigate human antibody responses to whole sporozoites, we identified a class of mAbs that target a cryptic PfCSP epitope that is only exposed after cleavage and subsequent pyroglutamylation (pGlu) of the newly formed N terminus. This pGlu-CSP epitope is not targeted by current anti-PfCSP mAbs and is not included in the licensed malaria vaccines.
View Article and Find Full Text PDFBiom J
February 2025
Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
Epidemiological research aims to investigate how multiple exposures affect health outcomes of interest, but observational studies often suffer from biases caused by unmeasured confounders. In this study, we develop a novel sensitivity model to investigate the effect of correlated multiple exposures on the continuous health outcomes of interest. The proposed sensitivity analysis is model-agnostic and can be applied to any machine learning algorithm.
View Article and Find Full Text PDFEcol Lett
January 2025
Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel.
Modelling the dynamics of biological processes is ubiquitous across the ecological and evolutionary disciplines. However, the increasing complexity of these models poses a challenge to the dissemination of model-derived results. Often only a small subset of model results are made available to the scientific community, with further exploration of the parameter space relying on local deployment of code supplied by the authors.
View Article and Find Full Text PDFBrief Bioinform
November 2024
In-Service Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, 250 Wuxing Street, 110, Taipei, Taiwan.
Accurate prediction of RNA modifications holds profound implications for elucidating RNA function and mechanism, with potential applications in drug development. Here, the RNA-ModX presents a highly precise predictive model designed to forecast post-transcriptional RNA modifications, complemented by a user-friendly web application tailored for seamless utilization by future researchers. To achieve exceptional accuracy, the RNA-ModX systematically explored a range of machine learning models, including Long Short-Term Memory (LSTM), Gated Recurrent Unit, and Transformer-based architectures.
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