ASI2025: 3RD WORKSHOP ON ADVANCES IN SYSTEMS IMMUNOLOGY

This page contains an index consisting of author-provided keywords.

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1.systems immunology	Deep learning for immune network inference from single-cell omics data and modeling tumor-immune system interaction
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2.deep learning	Deep learning for immune network inference from single-cell omics data and modeling tumor-immune system interaction
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3.single-cell omics	Deep learning for immune network inference from single-cell omics data and modeling tumor-immune system interaction
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4.immune networks	Deep learning for immune network inference from single-cell omics data and modeling tumor-immune system interaction
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5. bioinformatics	Deep learning for immune network inference from single-cell omics data and modeling tumor-immune system interaction
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Aging and immune dysfunction	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
algorithms	Reconstructing the co-evolution of tumors and their microenvironment from multiomic data
Allogeneic Transplantation	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
Alzheimer’s disease	Multi-Agent LLM Frameworks for Multimodal Identification of Alzheimer’s Disease
Antigen Design	An Integrated Computational Antigen Discovery Pipeline with Hierarchical Filtering for Emerging Viral Variants
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Bioinformatics tools	GeNeo2: a suite of bioinformatics tools for identifying tumor-specific neoepitopes with enhanced features for personalized cancer immunotherapies
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cancer	Reconstructing the co-evolution of tumors and their microenvironment from multiomic data
cancer immunology	Cancer Immunology: Mechanisms, Clinical Impact, and Future Directions
Catastrophic Forgetting	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
CD4+ T cell response	Post-hoc Explanation for TCR-pMHC Prediction
ChatGPT	Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process
Class imbalance	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
Colon adenocarcinoma	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
Computational Biology	Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process
Computational complexity	On the Intractability of Evolutionary Dynamics in Layered Graphs
Computational Pipeline	An Integrated Computational Antigen Discovery Pipeline with Hierarchical Filtering for Emerging Viral Variants
Computational Saturation Mutagenesis	Computational and Experimental Integration Reveals Multi-scale Effects of Peroxidase Mutations
Conceptual Compositionality	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
Continual Learning	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
Contrastive learning	Multi-View Graph–Text Alignment for Immunology
CRISPR-engineered Drosophila	Computational and Experimental Integration Reveals Multi-scale Effects of Peroxidase Mutations
Cross-species validation	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
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DAG	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
Data quality	Evaluation of Nuclei Isolation Techniques for Single-Nucleus RNA Sequencing in Tissue and Cell Suspensions
deep learning	Post-hoc Explanation for TCR-pMHC Prediction Toward Automated and Scalable Hematopoietic Cell Sorting: A Deep Learning Approach
Directed acyclic graph	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
DNA methylation drift	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Donor Database	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
drug delivery	Understanding nano-bio interactions to enable next-generation vaccines and drug delivery systems
drug ranking	CoDER: A new framework for Consistent Drug Efficacy Ranking
drug repurposing	CoDER: A new framework for Consistent Drug Efficacy Ranking
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Ecological modeling	On the Intractability of Evolutionary Dynamics in Layered Graphs
efficacy ranking	CoDER: A new framework for Consistent Drug Efficacy Ranking
Enhancer-aware CpG annotation	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Epigenetic clocks	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
epitope prediction	Post-hoc Explanation for TCR-pMHC Prediction
Eptiope	An Integrated Computational Antigen Discovery Pipeline with Hierarchical Filtering for Emerging Viral Variants
Evolutionary conservation	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Evolutionary dynamics	On the Intractability of Evolutionary Dynamics in Layered Graphs Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process
explainable AI	Post-hoc Explanation for TCR-pMHC Prediction
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Fixation problem	On the Intractability of Evolutionary Dynamics in Layered Graphs
FOXO3 motif scanning	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
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Graph Database	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
graph neural network (GNN)	Efficient Encoding of TCR-pMHC Structure for Improved Structure-Based Binding Prediction
Graph neural networks	Multi-View Graph–Text Alignment for Immunology
GraphMatch	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
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HAIs in Solid Tumor patients	Predicting Healthcare-Associated Infections in Emergency Department Patients with Solid Tumor History
Hematopoietic Stem Cells (HSCs)	Toward Automated and Scalable Hematopoietic Cell Sorting: A Deep Learning Approach
Hierarchical clustering	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
Host-pathogen interaction modeling	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
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Immune aging biomarkers	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
immune surveillance	Cancer Immunology: Mechanisms, Clinical Impact, and Future Directions
Immunoinformatics	An Integrated Computational Antigen Discovery Pipeline with Hierarchical Filtering for Emerging Viral Variants
Immunological modeling	On the Intractability of Evolutionary Dynamics in Layered Graphs
immunology	Enhancing computational immunometabolomic analysis with domain knowledge
immunometabolomics	Enhancing computational immunometabolomic analysis with domain knowledge
Immunosenescence	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
index-free adjacency	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
Interpretable machine learning	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
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knowledge	Enhancing computational immunometabolomic analysis with domain knowledge
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large language models	Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process Multi-Agent LLM Frameworks for Multimodal Identification of Alzheimer’s Disease
Large Reasoning Models (LRMs)	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
Layered graphs	On the Intractability of Evolutionary Dynamics in Layered Graphs
LSTM	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
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metabolomics	Enhancing computational immunometabolomic analysis with domain knowledge
microenvironment	Reconstructing the co-evolution of tumors and their microenvironment from multiomic data
ML-based Risk Stratification	Predicting Healthcare-Associated Infections in Emergency Department Patients with Solid Tumor History
Moran Process	Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process
multi-agent system	Multi-Agent LLM Frameworks for Multimodal Identification of Alzheimer’s Disease
Multi-Channel Microscopy	Toward Automated and Scalable Hematopoietic Cell Sorting: A Deep Learning Approach
multi-modal data integration	scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data
Multi-omics integration	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Multi-View learning	Multi-View Graph–Text Alignment for Immunology
Multipotent Progenitors (MPPs)	Toward Automated and Scalable Hematopoietic Cell Sorting: A Deep Learning Approach
Myeloid lineage resilience	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
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nanoparticles	Understanding nano-bio interactions to enable next-generation vaccines and drug delivery systems
Neo4j	GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
Neoepitopes	GeNeo2: a suite of bioinformatics tools for identifying tumor-specific neoepitopes with enhanced features for personalized cancer immunotherapies
NF-κB regulatory logic	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
NP-completeness	On the Intractability of Evolutionary Dynamics in Layered Graphs
Nuclei isolation	Evaluation of Nuclei Isolation Techniques for Single-Nucleus RNA Sequencing in Tissue and Cell Suspensions
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optimal transport	scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data
optimization	Reconstructing the co-evolution of tumors and their microenvironment from multiomic data
Orthogonal Concept Representation	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
Orthogonal Gradient Projection	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
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Parameter Estimation	Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process
Peroxidases	Computational and Experimental Integration Reveals Multi-scale Effects of Peroxidase Mutations
Personalized cancer immunotherapy	GeNeo2: a suite of bioinformatics tools for identifying tumor-specific neoepitopes with enhanced features for personalized cancer immunotherapies
Planar graphs	On the Intractability of Evolutionary Dynamics in Layered Graphs
Population structure	On the Intractability of Evolutionary Dynamics in Layered Graphs
Protein Mutation	Computational and Experimental Integration Reveals Multi-scale Effects of Peroxidase Mutations
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Real-world Healthcare Data	Predicting Healthcare-Associated Infections in Emergency Department Patients with Solid Tumor History
Recurrent neural network	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
Regulatory genomics	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Retrospective Inference	Exploring Large Language Models for Parameter Estimation: Insights from the Moran Process
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Sars-cov2	An Integrated Computational Antigen Discovery Pipeline with Hierarchical Filtering for Emerging Viral Variants
SHAP feature attribution	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Simulation methods	On the Intractability of Evolutionary Dynamics in Layered Graphs
snRNA-seq	Evaluation of Nuclei Isolation Techniques for Single-Nucleus RNA Sequencing in Tissue and Cell Suspensions
somatic evolution	Reconstructing the co-evolution of tumors and their microenvironment from multiomic data
Systems immunology	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
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T-cell aging	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
TCR-pMHC binding	Efficient Encoding of TCR-pMHC Structure for Improved Structure-Based Binding Prediction
temporal single-cell analysis	scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data
tissue-specific consistency	CoDER: A new framework for Consistent Drug Efficacy Ranking
Traceable Deductive Reasoning	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology
Transcriptional co-option	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
Transcriptomic Profiling	Computational and Experimental Integration Reveals Multi-scale Effects of Peroxidase Mutations
Transcriptomics	Evaluation of Nuclei Isolation Techniques for Single-Nucleus RNA Sequencing in Tissue and Cell Suspensions
Transfer Learning	Toward Automated and Scalable Hematopoietic Cell Sorting: A Deep Learning Approach
transformer models	Post-hoc Explanation for TCR-pMHC Prediction
Tumor evolution	LSTM Prediction of Next-Gene Mutations Using Graph-Derived Orders in Colon Adenocarcinoma
tumor microenvironment	Cancer Immunology: Mechanisms, Clinical Impact, and Future Directions
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unseen peptide	Efficient Encoding of TCR-pMHC Structure for Improved Structure-Based Binding Prediction
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Vaccine response prediction	Regulatory Drift in Immune Aging: Enhancer Logic and Methylation-Based Predictors Across Species
vaccines	Understanding nano-bio interactions to enable next-generation vaccines and drug delivery systems
Virus	An Integrated Computational Antigen Discovery Pipeline with Hierarchical Filtering for Emerging Viral Variants
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Zernike Concept Vectors (ZCVs)	Orthogonal Concept Representation for Traceable Deductive Reasoning: A Neuro-Symbolic Framework for Continual Learning with Applications in Oncology

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