PROGRAM
Days: Sunday, January 12th Monday, January 13th Tuesday, January 14th
Sunday, January 12th
View this program: with abstractssession overviewtalk overview
09:30-10:30 Session 2: Keynote Talk (SCE Auditorium)
Yury Khudyakov Centers for Disease Control and Prevention (CDC)
Conceptual challenges of viral molecular epidemiology
Chair:
10:50-12:30 Session 3A: ICCABS 1 (SCE Auditorium)
Chair:
| 10:50 | Enhancing Protein Side Chain Packing Using Rotamer Clustering and Machine Learning (abstract) |
| 11:10 | Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes? (abstract)   PRESENTER: Ivan Makohon |
| 11:30 | Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model (abstract) PRESENTER: Ashwag Altayyar |
| 11:50 | Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms (abstract) |
| 12:10 | Unsupervised Learning for Tertiary Structure Prediction of Protein Molecules: Systematic Review (abstract) |
10:50-12:30 Session 3B: CAME 1 (SCE Room 203)
Chair:
| 10:50 | Antigenic cooperation and cross-immunoreactivity networks (abstract) |
| 11:10 | The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia. (abstract) |
| 11:30 | The evolution of cancer progression risk: a phylogenetic and machine learning analysis (abstract) |
13:30-14:30 Session 4: Keynote Talk (SCE Auditorium)
Srinivas Aluru School of Computational Science and Engineering, Georgia Institute of Technology
Genome graphs: Algorithms and applications
Chair:
14:40-16:00 Session 5A: ICCABS 2 (SCE Auditorium)
Chair:
| 14:40 | Resistance genes are distinct in protein-protein interaction networks according to drug class and gene mobility (abstract) |
| 15:00 | MetaEdit: Computational Identification of RNA editing in Microbiomes (abstract) |
| 15:20 | Improving inter-helical residue contact prediction in α-helical Transmembrane proteins using structural neighborhood crowdedness information (abstract) PRESENTER: Aman Sawhney |
| 15:40 | Novel Molecular Markers of the Inferior Colliculus identified via Single Nuclei Transcriptomics (abstract) |
14:40-16:00 Session 5B: CAME 2 (SCE Room 203)
Chair:
| 14:40 | Leveraging Multiple Dimensions of Public Data to Characterize the Evolution of a Staphylococcal Plasmid (abstract) |
| 15:00 | Phylogenetic inference of migration histories of viral populations under evolutionary and structural constraints (abstract) |
| 15:20 | Leveraging large language models for predicting viral subtypes from sequence data (abstract) |
| 15:40 | Mixed HCV Infection: A novel genetic marker for surveillance of high-risk populations (abstract) |
16:10-17:10 Session 6A: CANGS 1 (SCE Auditorium)
Chair:
| 16:10 | scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data (abstract) |
| 16:30 | A Multi-Model Ensemble Learning Framework with Uncertainty Quantification for Enhanced Poliovirus Surveillance (M-SURE) (abstract) |
| 16:50 | HAPLOQ: A simple strategy for correcting sequencing errors on viral amplicons (abstract) |
16:10-17:10 Session 6B: CASCODA (SCE Room 203)
Chair:
| 16:10 | Supervised Poisson Factorization for Uncovering Latent Gene Expression Patterns and Predicting Disease Risk (abstract) |
| 16:30 | A Fused Transformer-based Model for Gene Expression Prediction using Histopathology Images (abstract) |
| 16:50 | Cancer progression inference from single-cell data with recurrences and mutation losses (abstract) |
Monday, January 13th
View this program: with abstractssession overviewtalk overview
09:00-10:00 Session 7: Keynote Talk (SCE Auditorium)
Yana Bromberg Bromberg Lab, Departments of Biology and Computer Science, Emory University
Learning the language of functional signatures of Life
Chair:
10:20-12:00 Session 8A: ICCABS 3 (SCE Auditorium)
Chair:
| 10:20 | A Benchmarking Study of Random Projections and Principal Components for Dimensionality Reduction Strategies in Single Cell Analysis (abstract) PRESENTER: Mohamed Abdelnaby |
| 10:40 | DuoHash: fast hashing of spaced seeds with application to spaced k-mers counting (abstract) |
| 11:00 | Haplotype-based Parallel PBWT for Biobank Scale Data (abstract) PRESENTER: Kecong Tang |
| 11:20 | Fast and Succinct Compression of k-mer Sets with Plain Text Representation of Colored de Bruijn Graphs (abstract) |
| 11:40 | Phylodynamics Analysis of HIV Epidemic History in Belarus in 1987-2022 (abstract) |
10:20-12:00 Session 8B: CAME 3 (SCE Room 203)
Chair:
| 10:20 | Benchmarking metagenomic software with the new CAMI web portal (abstract) |
| 10:40 | Model Selection for Sparse Microbial Network Inference using Variational Approximation (abstract) |
| 11:00 | Mammo-Bench: A Large-scale Benchmark Dataset of Mammography Images (abstract) PRESENTER: Gaurav Bhole |
| 11:20 | A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater (abstract) PRESENTER: Victor Gordeev |
| 11:40 | Personalized health and genomics libraries for the analysis of long-term effects in COVID-19 patients (abstract) PRESENTER: Andrei Lobiuc |
13:20-15:00 Session 9A: CANGS 2 (SCE Auditorium)
Chair:
| 13:20 | Evaluation of methods for estimating information entropy from limited sequence data (abstract) |
| 13:40 | From Reads to Enzymes: Exploring Enzymatic Potential in Metagenomes with DNA Language Models (abstract) PRESENTER: R. Prabakaran |
| 14:00 | Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase (abstract) |
| 14:20 | DCCNV: Enhanced Copy Number Variation Detection in Single-Cell Sequencing Using Diffusion Processes and Contrastive Learning (abstract) |
| 14:40 | Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation (abstract) |
13:20-15:00 Session 9B: CAMeRA 1 (SCE Room 203)
Chair:
| 13:20 | Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces (abstract) |
| 13:40 | AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers (abstract) |
| 14:00 | Opening an icy black box: diversity and functioning of soil bacteria in Antarctica’s largest ice-free region (abstract) |
| 14:20 | Assessment of Host and Bacterial Depletion Methods to Enhance RNA Virus Detection by Next-Generation Sequencing (abstract) |
| 14:40 | Earth Mover's Distance to recognize duplicate datasets in an automated molecular epidemiology system (abstract) |
15:20-17:00 Session 10A: CAME 4 (SCE Auditorium)
Chair:
| 15:20 | Applying Genetic Algorithm with Saltations to MAX-3SAT (abstract) |
| 15:40 | Nearest Neighbor CCP-Based Molecular Sequence Analysis (abstract) |
| 16:00 | DANCE: Deep Learning-Assisted Analysis of ProteiN Sequences Using Chaos Enhanced Kaleidoscopic Images (abstract) |
| 16:20 | Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm (abstract) |
| 16:40 | Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences (abstract) |
15:20-17:00 Session 10B: CAMeRA 2 (SCE Room 203)
Chair:
| 15:20 | DeepGOMeta: Functional Insights into Microbial Communities through Deep Learning (abstract) |
| 15:40 | Assessing microbial genome representation across various reference databases: a comprehensive evaluation (abstract) |
| 16:00 | Innovative Tools and Strategies for Outbreak Preparedness: Integrating Environmental Microbiomes and Prospective Pathogen Collections in Hospital Settings (abstract) |
| 16:20 | Hidden Markov Model Analysis of Genetic Linkage (abstract) |
| 16:40 | Epistatic Density of Viral Variants in Acute and Chronic HCV patients (abstract) |
Tuesday, January 14th
View this program: with abstractssession overviewtalk overview
09:00-10:00 Session 11: Invited Talk (SCE Auditorium)
Hamed Karami Population Health Sciences, School of Public Health, Georgia State University
A Methodological Workflow for Epidemic Forecasting
Chair:
10:20-12:00 Session 12A: CAME 5 (SCE Auditorium)
Chair:
| 10:20 | EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis (abstract) |
| 10:40 | Improved Graph-Based Antibody-Aware Epitope Prediction with Protein Language Model-Based Embeddings (abstract) |
| 11:00 | Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based CT Scan Analysis (abstract) |
| 11:20 | Simulation of tumor evolution and metastasis at single-cell resolution (abstract) |
| 11:40 | Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach (abstract) |
10:20-12:00 Session 12B: CAMeRA 3 (SCE Room 203)
Chair:
| 10:20 | Diversity and Distinctive Characteristics of the Global RNA Virome in Urban Environments (abstract) |
| 10:40 | The study of the effects of the full-scale Russian-Ukrainian war on the epidemiological situation and respiratory and intestinal diseases in the Kharkiv region of Ukraine from 2022 to 2024 (abstract) |
| 11:00 | Drug-centric prior improves drug response modeling in partially overlapping pharmacogenomic screens (abstract) PRESENTER: Dharani Thirumalaisamy |
| 11:20 | Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations (abstract) |
| 11:40 | HLA class I escape drives the evolution of SARS-CoV-2 in human population (abstract) |