Evaluating ensemble learning approaches for horizontal gene transfer detection
This study examines ensemble machine learning for genomic island detection, a key driver of antimicrobial resistance spread. Combining diverse data represent...
Publication Categories
- Machine-Learning 13
- Bioinformatics 11
- Data-Visualization 4
- Genomics 4
- AI-Ethics 4
- AMR 3
- Explainable-AI 3
- Large-Language-Models 3
- User-Interfaces 2
- Time-series 2
- Molecular-Modeling 2
- Peptide-Classification 2
- Storage-Technologies 1
- Model-Evaluation 1
- Control-Systems 1
Machine-Learning
A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics
Genomic AI models like Nucleotide Transformer and Evo are advancing DNA and protein design, enabling breakthroughs such as AI-created bacteriophages. However...
The State of Peptide Detectability in Computational Proteomics and Guidelines for AI Applications
This review analyzes AI methods for peptide detectability prediction in proteomics, highlighting gaps in reproducibility and transparency. It proposes guidel...
Advocating the potential of artificial intelligence for syndrome discovery in syndromic surveillance systems: A scoping review
This scoping review examines the role of artificial intelligence in advancing syndromic surveillance, analyzing 15 key studies to provide eight strategic rec...
UbiQTree: Uncertainty quantification in XAI with tree ensembles
UbiQTree quantifies uncertainty in SHAP explanations for tree ensemble models, decomposing it into aleatoric (irreducible) and epistemic (reducible) componen...
Genomic data representations for horizontal gene transfer detection
RCKmer (k=7) + SVM representation achieves state-of-the-art HGT detection (F1=0.959, MCC=0.908) across 44 genomic encodings and 4 datasets, outperforming tra...
Persona Adaptable Strategies Make Large Language Models Tractable
Ten persona-adaptable strategies enable large language models to self-explain their functionality to everyday users, tailoring complexity/style to user arche...
Protocol for implementing the nested model for AI design and validation in compliance with AI regulations
Protocol for implementing the nested model to develop/validate AI systems compliant with regulations, spanning domain, data, model, and prediction layers wit...
Current state and future prospects of Horizontal Gene Transfer detection
Review reveals surging AI adoption in Horizontal Gene Transfer (HGT) detection—a key driver of prokaryotic evolution and antimicrobial resistance (AMR)—with ...
Kernel-based Learning for Safe Control of Discrete-Time Unknown Systems under Incomplete Observations
Kernel ridge regression enables safe tracking control for high-order dynamical systems with unknown dynamics and partial state observations. Our observer-int...
Interpretable Molecular Encodings and Representations for Machine Learning Tasks
iCAN delivers interpretable carbon-neighborhood encodings for organic molecules, outperforming prior methods in peptide/protein classification across large b...
Interactive polar diagrams for model comparison
polar-diagrams is an interactive library implementing Mutual Information and Taylor Diagrams to visualize multi-model performance across biology, medicine, c...
A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
We propose cmangoes, a parametric, carbon-chain-based encoding method for organic molecules that generates binary/numerical arrays (exportable as images) fro...
Bioinformatics
Evaluating ensemble learning approaches for horizontal gene transfer detection
This study examines ensemble machine learning for genomic island detection, a key driver of antimicrobial resistance spread. Combining diverse data represent...
The State of Peptide Detectability in Computational Proteomics and Guidelines for AI Applications
This review analyzes AI methods for peptide detectability prediction in proteomics, highlighting gaps in reproducibility and transparency. It proposes guidel...
UbiQTree: Uncertainty quantification in XAI with tree ensembles
UbiQTree quantifies uncertainty in SHAP explanations for tree ensemble models, decomposing it into aleatoric (irreducible) and epistemic (reducible) componen...
Genomic data representations for horizontal gene transfer detection
RCKmer (k=7) + SVM representation achieves state-of-the-art HGT detection (F1=0.959, MCC=0.908) across 44 genomic encodings and 4 datasets, outperforming tra...
Protocol for implementing the nested model for AI design and validation in compliance with AI regulations
Protocol for implementing the nested model to develop/validate AI systems compliant with regulations, spanning domain, data, model, and prediction layers wit...
Current state and future prospects of Horizontal Gene Transfer detection
Review reveals surging AI adoption in Horizontal Gene Transfer (HGT) detection—a key driver of prokaryotic evolution and antimicrobial resistance (AMR)—with ...
Interpretable Molecular Encodings and Representations for Machine Learning Tasks
iCAN delivers interpretable carbon-neighborhood encodings for organic molecules, outperforming prior methods in peptide/protein classification across large b...
Interactive polar diagrams for model comparison
polar-diagrams is an interactive library implementing Mutual Information and Taylor Diagrams to visualize multi-model performance across biology, medicine, c...
A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
We propose cmangoes, a parametric, carbon-chain-based encoding method for organic molecules that generates binary/numerical arrays (exportable as images) fro...
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks
MOVIS is a modular, web-based tool for exploring time-series multi-omics data, designed to make complex temporal, multi-modal datasets accessible to research...
The Visual Story of Data Storage: From Storage Properties to User Interfaces
Data creation is rapidly outpacing traditional storage, driving the need for new media such as DNA storage. This work surveys user requirements across key st...
Data-Visualization
Persona Adaptable Strategies Make Large Language Models Tractable
Ten persona-adaptable strategies enable large language models to self-explain their functionality to everyday users, tailoring complexity/style to user arche...
Interactive polar diagrams for model comparison
polar-diagrams is an interactive library implementing Mutual Information and Taylor Diagrams to visualize multi-model performance across biology, medicine, c...
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks
MOVIS is a modular, web-based tool for exploring time-series multi-omics data, designed to make complex temporal, multi-modal datasets accessible to research...
The Visual Story of Data Storage: From Storage Properties to User Interfaces
Data creation is rapidly outpacing traditional storage, driving the need for new media such as DNA storage. This work surveys user requirements across key st...
Genomics
Evaluating ensemble learning approaches for horizontal gene transfer detection
This study examines ensemble machine learning for genomic island detection, a key driver of antimicrobial resistance spread. Combining diverse data represent...
Genomic data representations for horizontal gene transfer detection
RCKmer (k=7) + SVM representation achieves state-of-the-art HGT detection (F1=0.959, MCC=0.908) across 44 genomic encodings and 4 datasets, outperforming tra...
Current state and future prospects of Horizontal Gene Transfer detection
Review reveals surging AI adoption in Horizontal Gene Transfer (HGT) detection—a key driver of prokaryotic evolution and antimicrobial resistance (AMR)—with ...
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks
MOVIS is a modular, web-based tool for exploring time-series multi-omics data, designed to make complex temporal, multi-modal datasets accessible to research...
AI-Ethics
A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics
Genomic AI models like Nucleotide Transformer and Evo are advancing DNA and protein design, enabling breakthroughs such as AI-created bacteriophages. However...
UbiQTree: Uncertainty quantification in XAI with tree ensembles
UbiQTree quantifies uncertainty in SHAP explanations for tree ensemble models, decomposing it into aleatoric (irreducible) and epistemic (reducible) componen...
Persona Adaptable Strategies Make Large Language Models Tractable
Ten persona-adaptable strategies enable large language models to self-explain their functionality to everyday users, tailoring complexity/style to user arche...
Protocol for implementing the nested model for AI design and validation in compliance with AI regulations
Protocol for implementing the nested model to develop/validate AI systems compliant with regulations, spanning domain, data, model, and prediction layers wit...
AMR
Evaluating ensemble learning approaches for horizontal gene transfer detection
This study examines ensemble machine learning for genomic island detection, a key driver of antimicrobial resistance spread. Combining diverse data represent...
Genomic data representations for horizontal gene transfer detection
RCKmer (k=7) + SVM representation achieves state-of-the-art HGT detection (F1=0.959, MCC=0.908) across 44 genomic encodings and 4 datasets, outperforming tra...
Current state and future prospects of Horizontal Gene Transfer detection
Review reveals surging AI adoption in Horizontal Gene Transfer (HGT) detection—a key driver of prokaryotic evolution and antimicrobial resistance (AMR)—with ...
Explainable-AI
A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics
Genomic AI models like Nucleotide Transformer and Evo are advancing DNA and protein design, enabling breakthroughs such as AI-created bacteriophages. However...
UbiQTree: Uncertainty quantification in XAI with tree ensembles
UbiQTree quantifies uncertainty in SHAP explanations for tree ensemble models, decomposing it into aleatoric (irreducible) and epistemic (reducible) componen...
Persona Adaptable Strategies Make Large Language Models Tractable
Ten persona-adaptable strategies enable large language models to self-explain their functionality to everyday users, tailoring complexity/style to user arche...
Large-Language-Models
A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics
Genomic AI models like Nucleotide Transformer and Evo are advancing DNA and protein design, enabling breakthroughs such as AI-created bacteriophages. However...
Advocating the potential of artificial intelligence for syndrome discovery in syndromic surveillance systems: A scoping review
This scoping review examines the role of artificial intelligence in advancing syndromic surveillance, analyzing 15 key studies to provide eight strategic rec...
Persona Adaptable Strategies Make Large Language Models Tractable
Ten persona-adaptable strategies enable large language models to self-explain their functionality to everyday users, tailoring complexity/style to user arche...
User-Interfaces
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks
MOVIS is a modular, web-based tool for exploring time-series multi-omics data, designed to make complex temporal, multi-modal datasets accessible to research...
The Visual Story of Data Storage: From Storage Properties to User Interfaces
Data creation is rapidly outpacing traditional storage, driving the need for new media such as DNA storage. This work surveys user requirements across key st...
Time-series
Interactive polar diagrams for model comparison
polar-diagrams is an interactive library implementing Mutual Information and Taylor Diagrams to visualize multi-model performance across biology, medicine, c...
MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks
MOVIS is a modular, web-based tool for exploring time-series multi-omics data, designed to make complex temporal, multi-modal datasets accessible to research...
Molecular-Modeling
Interpretable Molecular Encodings and Representations for Machine Learning Tasks
iCAN delivers interpretable carbon-neighborhood encodings for organic molecules, outperforming prior methods in peptide/protein classification across large b...
A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
We propose cmangoes, a parametric, carbon-chain-based encoding method for organic molecules that generates binary/numerical arrays (exportable as images) fro...
Peptide-Classification
Interpretable Molecular Encodings and Representations for Machine Learning Tasks
iCAN delivers interpretable carbon-neighborhood encodings for organic molecules, outperforming prior methods in peptide/protein classification across large b...
A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
We propose cmangoes, a parametric, carbon-chain-based encoding method for organic molecules that generates binary/numerical arrays (exportable as images) fro...
Storage-Technologies
The Visual Story of Data Storage: From Storage Properties to User Interfaces
Data creation is rapidly outpacing traditional storage, driving the need for new media such as DNA storage. This work surveys user requirements across key st...
Model-Evaluation
Interactive polar diagrams for model comparison
polar-diagrams is an interactive library implementing Mutual Information and Taylor Diagrams to visualize multi-model performance across biology, medicine, c...
Control-Systems
Kernel-based Learning for Safe Control of Discrete-Time Unknown Systems under Incomplete Observations
Kernel ridge regression enables safe tracking control for high-order dynamical systems with unknown dynamics and partial state observations. Our observer-int...