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Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal
Life SciencesMolecular & Cell BiologyAlgorithms & Theory

Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal

Researchers found that AI models used to analyze single-cell data may not capture regulatory signals, but instead just track gene co-expression patterns. This means these models may not provide meaningful biological insights.

preprint
Life SciencesGenetics & GenomicsAlgorithms & Theory

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures

Researchers developed a new way to model and understand DNA sequences using machine learning. This could lead to advances in areas like genetics and personalized medicine.

preprint
MolHIT: Advancing Molecular-Graph Generation with Hierarchical Discrete Diffusion Models
Life SciencesGenerative AIMolecular & Cell Biology

MolHIT: Advancing Molecular-Graph Generation with Hierarchical Discrete Diffusion Models

Researchers developed a new AI model that can generate molecular structures more efficiently for drug discovery and materials science. This advance could accelerate the pace of innovation in these critical fields.

preprint
Life SciencesBiotechnologyMicrobiology

PREFER: An Ontology for the PREcision FERmentation Community

Researchers developed an ontology, a structured way to describe and organize knowledge, to help streamline the growing field of precision fermentation. This could enable more efficient production of biofuels, pharmaceuticals, and sustainable foods.

preprint
Life SciencesGenerative AIMolecular & Cell Biology

Measuring Mid-2025 LLM-Assistance on Novice Performance in Biology

Generative AI is helping novices handle biology tasks more easily, raising concerns about dual-use risks as these skills could be misused.

preprint
AgriWorld:A World Tools Protocol Framework for Verifiable Agricultural Reasoning with Code-Executing LLM Agents
Life SciencesAgriculture & Food SystemsAlgorithms & Theory

AgriWorld:A World Tools Protocol Framework for Verifiable Agricultural Reasoning with Code-Executing LLM Agents

AI models can now help farmers monitor and plan agriculture more efficiently by analyzing large datasets on things like weather, soil, and crop yields. This could improve food production and sustainability, but the technology's reliability and safety must still be verified.

preprint
Retrieval Augmented Generation of Literature-derived Polymer Knowledge: The Example of a Biodegradable Polymer Expert System
Life SciencesPolymers & Soft MatterBiotechnology

Retrieval Augmented Generation of Literature-derived Polymer Knowledge: The Example of a Biodegradable Polymer Expert System

A new system can extract and combine information from polymer research papers to build better understanding of biodegradable plastics, which could lead to developing more sustainable materials.

preprint
Life SciencesAgriculture & Food Systems

Translating Dietary Standards into Healthy Meals with Minimal Substitutions

A new framework can create healthy meals that closely match dietary guidelines without requiring major substitutions or changes, making it easier for people to eat well.

preprint
Guide-Guard: Off-Target Predicting in CRISPR Applications
Life SciencesBiotechnologyGenetics & Genomics

Guide-Guard: Off-Target Predicting in CRISPR Applications

A new AI-powered tool can help predict and avoid unintended genetic changes when using CRISPR gene editing, potentially making this powerful biotech tool safer and more precise for medical and agricultural applications.

preprint
Genetic Generalized Additive Models
Life SciencesAlgorithms & TheoryGenetics & Genomics

Genetic Generalized Additive Models

Researchers have developed a new genetic algorithm that can automatically optimize complex predictive models, making it easier to understand how genes influence traits and health.

preprint
FairTabGen: High-Fidelity and Fair Synthetic Health Data Generation from Limited Samples
Life SciencesGenerative AIGenetics & Genomics

FairTabGen: High-Fidelity and Fair Synthetic Health Data Generation from Limited Samples

Researchers developed a tool called FairTabGen that can create realistic synthetic health data without private patient information, enabling medical research while protecting privacy.

preprint
Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models
Life SciencesAlgorithms & TheoryMolecular & Cell Biology

Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models

Researchers developed a new algorithm that can efficiently simulate rare molecular events, like chemical reactions or protein folding. This could lead to faster and more accurate computer models of complex biological processes.

preprint
Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal
Life SciencesMolecular & Cell BiologyAlgorithms & Theory

Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal

Researchers found that AI models used to analyze single-cell data may not capture regulatory signals, but instead just track gene co-expression patterns. This means these models may not provide meaningful biological insights.

preprint
Life SciencesGenetics & GenomicsAlgorithms & Theory

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures

Researchers developed a new way to model and understand DNA sequences using machine learning. This could lead to advances in areas like genetics and personalized medicine.

preprint
MolHIT: Advancing Molecular-Graph Generation with Hierarchical Discrete Diffusion Models
Life SciencesGenerative AIMolecular & Cell Biology

MolHIT: Advancing Molecular-Graph Generation with Hierarchical Discrete Diffusion Models

Researchers developed a new AI model that can generate molecular structures more efficiently for drug discovery and materials science. This advance could accelerate the pace of innovation in these critical fields.

preprint
Life SciencesBiotechnologyMicrobiology

PREFER: An Ontology for the PREcision FERmentation Community

Researchers developed an ontology, a structured way to describe and organize knowledge, to help streamline the growing field of precision fermentation. This could enable more efficient production of biofuels, pharmaceuticals, and sustainable foods.

preprint
Life SciencesGenerative AIMolecular & Cell Biology

Measuring Mid-2025 LLM-Assistance on Novice Performance in Biology

Generative AI is helping novices handle biology tasks more easily, raising concerns about dual-use risks as these skills could be misused.

preprint
AgriWorld:A World Tools Protocol Framework for Verifiable Agricultural Reasoning with Code-Executing LLM Agents
Life SciencesAgriculture & Food SystemsAlgorithms & Theory

AgriWorld:A World Tools Protocol Framework for Verifiable Agricultural Reasoning with Code-Executing LLM Agents

AI models can now help farmers monitor and plan agriculture more efficiently by analyzing large datasets on things like weather, soil, and crop yields. This could improve food production and sustainability, but the technology's reliability and safety must still be verified.

preprint
Retrieval Augmented Generation of Literature-derived Polymer Knowledge: The Example of a Biodegradable Polymer Expert System
Life SciencesPolymers & Soft MatterBiotechnology

Retrieval Augmented Generation of Literature-derived Polymer Knowledge: The Example of a Biodegradable Polymer Expert System

A new system can extract and combine information from polymer research papers to build better understanding of biodegradable plastics, which could lead to developing more sustainable materials.

preprint
Life SciencesAgriculture & Food Systems

Translating Dietary Standards into Healthy Meals with Minimal Substitutions

A new framework can create healthy meals that closely match dietary guidelines without requiring major substitutions or changes, making it easier for people to eat well.

preprint
Guide-Guard: Off-Target Predicting in CRISPR Applications
Life SciencesBiotechnologyGenetics & Genomics

Guide-Guard: Off-Target Predicting in CRISPR Applications

A new AI-powered tool can help predict and avoid unintended genetic changes when using CRISPR gene editing, potentially making this powerful biotech tool safer and more precise for medical and agricultural applications.

preprint
Genetic Generalized Additive Models
Life SciencesAlgorithms & TheoryGenetics & Genomics

Genetic Generalized Additive Models

Researchers have developed a new genetic algorithm that can automatically optimize complex predictive models, making it easier to understand how genes influence traits and health.

preprint
FairTabGen: High-Fidelity and Fair Synthetic Health Data Generation from Limited Samples
Life SciencesGenerative AIGenetics & Genomics

FairTabGen: High-Fidelity and Fair Synthetic Health Data Generation from Limited Samples

Researchers developed a tool called FairTabGen that can create realistic synthetic health data without private patient information, enabling medical research while protecting privacy.

preprint
Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models
Life SciencesAlgorithms & TheoryMolecular & Cell Biology

Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models

Researchers developed a new algorithm that can efficiently simulate rare molecular events, like chemical reactions or protein folding. This could lead to faster and more accurate computer models of complex biological processes.

preprint
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