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Chris Alvin

Publications and source records attributed to Chris Alvin.

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Benchmarking Artificial Intelligence Models for Daily Coastal Hypoxia Forecasting

Coastal hypoxia, especially in the northern part of Gulf of Mexico, presents a persistent ecological and economic concern. Seasonal models offer coarse forecasts that miss the fine-scale variability needed for daily, responsive ecosystem management. We present study that compares four deep learning architectures for daily hypoxia classification: Bidirectional Long Short-Term Memory (BiLSTM), Medformer (Medical Transformer), Spatio-Temporal Transformer (ST-Transformer), and Temporal Convolutional Network (TCN). We trained our models with twelve years of daily hindcast data from 2009-2020 Our training data consists of 2009-2020 hindcast data from a coupled hydrodynamic-biogeochemical model. Similarly, we use hindcast data from 2020 through 2024 as a test data. We constructed classification models incorporating water column stratification, sediment oxygen consumption, and temperature-dependent decomposition rates. We evaluated each architectures using the same data preprocessing, input/output formulation, and validation protocols. Each model achieved high classification accuracy and strong discriminative ability with ST-Transformer achieving the highest performance across all metrics and tests periods (AUC-ROC: 0.982-0.992). We also employed McNemar's method to identify statistically significant differences in model predictions. Our contribution is a reproducible framework for operational real-time hypoxia prediction that can support broader efforts in the environmental and ocean modeling systems community and in ecosystem resilience. The source code is available https://github.com/rmagesh148/hypoxia-ai/

cs.LG

A Multimodal Human Protein Embeddings Database: DeepDrug Protein Embeddings Bank (DPEB)

Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types: structural (AlphaFold2), transformer-based sequence (BioEmbeddings), contextual amino acid patterns (ESM-2: Evolutionary Scale Modeling), and sequence-based n-gram statistics (ProtVec]). AlphaFold2 protein structures are available through public databases (e.g., AlphaFold2 Protein Structure Database), but the internal neural network embeddings are not. DPEB addresses this gap by providing AlphaFold2-derived embeddings for computational modeling. Our benchmark evaluations show GraphSAGE with BioEmbedding achieved the highest PPI prediction performance (87.37% AUROC, 79.16% accuracy). The framework also achieved 77.42% accuracy for enzyme classification and 86.04% accuracy for protein family classification. DPEB supports multiple graph neural network methods for PPI prediction, enabling applications in systems biology, drug target identification, pathway analysis, and disease mechanism studies.

cs.LG

Simpson's Paradox and Lagging Progress in Completion Trends of Underrepresented Students in Computer Science

It is imperative for the Computer Science (CS) community to ensure active participation and success of students from diverse backgrounds. This work compares CS to other areas of study with respect to success of students from three underrepresented groups: Women, Black and Hispanic or Latino. Using a data-driven approach, we show that trends of success over the years for underrepresented groups in CS are lagging behind other disciplines. Completion of CS programs by Black students in particular shows an alarming regression in the years 2011 through 2019. This national level decline is most concentrated in the Southeast of the United States and seems to be driven mostly by a small number of institutes that produce a large number of graduates. We strongly believe that more data-driven studies in this area are necessary to make progress towards a more equitable and inclusive CS community. Without an understanding of underlying dynamics, policy makers and practitioners will be unable to make informed decisions about how and where to allocate resources to address the problem.

cs.CY

Automatic Synthesis of Geometry Problems for an Intelligent Tutoring System

This paper presents an intelligent tutoring system, GeoTutor, for Euclidean Geometry that is automatically able to synthesize proof problems and their respective solutions given a geometric figure together with a set of properties true of it. GeoTutor can provide personalized practice problems that address student deficiencies in the subject matter.

cs.AI