Latest 15 Papers - March 13, 2025

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Latest 15 Papers - March 13, 2025

Molecular

The field of molecular research has seen significant advancements in recent years, with the development of new techniques and tools for understanding the behavior of molecules. In this section, we will highlight some of the latest papers in the field of molecular research.

Title Date Comment
GENEOnet: Statistical analysis supporting explainability and trustworthiness 2025-03-12
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models 2025-03-12 26 pages, 9 figures
Multi-Modal Foundation Models for Computational Pathology: A Survey 2025-03-12
FOSS solution for Molecular Dynamics Simulation Automation and Collaboration with MDSGAT 2025-03-12
Symbolic Mixture-of-Experts: Adaptive Skill-based Routing for Heterogeneous Reasoning 2025-03-11
The first three authors contributed equally. Project Page: https://symbolic-moe.github.io/

The first three authors contributed equally. Project Page: https://symbolic-moe.github.io/

evoBPE: Evolutionary Protein Sequence Tokenization 2025-03-11
13 pa...

13 pages, 8 figures, 1 table, 1 algorithm

Understanding and Mitigating Distribution Shifts For Machine Learning Force Fields 2025-03-11
Chemistry-Inspired Diffusion with Non-Differentiable Guidance 2025-03-11
accep...

accepted by ICLR 2025

To Use or Not to Use a Universal Force Field 2025-03-11 21 pages, 5 figures
Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation 2025-03-11
Equivariant Masked Position Prediction for Efficient Molecular Representation 2025-03-11 24 pages, 6 figures
Brain Tumor Classification on MRI in Light of Molecular Markers 2025-03-10
ICAI'...

ICAI'22 - The 24th International Conference on Artificial Intelligence, The 2022 World Congress in Computer Science, Computer Engineering, & Applied Computing (CSCE'22), Las Vegas, USA. The paper acceptance rate 17% for regular papers. The publication of the CSCE 2022 conference proceedings has been delayed due to the pandemic

Q-MARL: A quantum-inspired algorithm using neural message passing for large-scale multi-agent reinforcement learning 2025-03-10
AlphaNet: Scaling Up Local Frame-based Atomistic Interatomic Potential 2025-03-10 14 pages, 5 figures
Bridging Molecular Graphs and Large Language Models 2025-03-10
AAAI ...

AAAI 2025 camera ready version

Molecular Generation

Molecular generation is a rapidly growing field that involves the use of machine learning algorithms to generate new molecules with specific properties. In this section, we will highlight some of the latest papers in the field of molecular generation.

Title Date Comment
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models 2025-03-12 26 pages, 9 figures
FOSS solution for Molecular Dynamics Simulation Automation and Collaboration with MDSGAT 2025-03-12
Chemistry-Inspired Diffusion with Non-Differentiable Guidance 2025-03-11
accep...

accepted by ICLR 2025

Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation 2025-03-11
Bridging Molecular Graphs and Large Language Models 2025-03-10
AAAI ...

AAAI 2025 camera ready version

Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models 2025-03-10 9
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation 2025-03-08
Learning-Order Autoregressive Models with Application to Molecular Graph Generation 2025-03-07
Mol-CADiff: Causality-Aware Autoregressive Diffusion for Molecule Generation 2025-03-07
GENERator: A Long-Context Generative Genomic Foundation Model 2025-03-06
Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation 2025-03-04 21 pages, 4 figures
Straight-Line Diffusion Model for Efficient 3D Molecular Generation 2025-03-04
P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching 2025-03-04
Dynamic Search for Inference-Time Alignment in Diffusion Models 2025-03-03
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model 2025-03-02
24 pa...

24 pages, 5 figures, 2 tables

Graph Neural Networks

Graph neural networks (GNNs) are a type of neural network that is designed to work with graph-structured data. In this section, we will highlight some of the latest papers in the field of GNNs.

Title Date Comment
A Generative Framework for Predictive Modeling of Multiple Chronic Conditions Using Graph Variational Autoencoder and Bandit-Optimized Graph Neural Network 2025-03-12
Submi...

Submitted for review in IEEE Journal of Biomedical and Health Informatics

Post-interactive Multimodal Trajectory Prediction for Autonomous Driving 2025-03-12
**[Crowdsourced Homophily Ties Based Graph Annotation Via Large Language Model](http://

Q&A: Latest 15 Papers - March 13, 2025

Q: What is the significance of the latest 15 papers in the field of molecular research?

A: The latest 15 papers in the field of molecular research highlight significant advancements in the understanding of molecular behavior and the development of new techniques and tools for understanding the behavior of molecules. These papers demonstrate the potential of machine learning algorithms to generate new molecules with specific properties and to improve the accuracy of molecular simulations.

Q: What is the main focus of the paper "GENEOnet: Statistical analysis supporting explainability and trustworthiness"?

A: The main focus of the paper "GENEOnet: Statistical analysis supporting explainability and trustworthiness" is to develop a statistical analysis framework that supports explainability and trustworthiness in machine learning models. The paper proposes a novel approach to statistical analysis that can be used to improve the explainability and trustworthiness of machine learning models.

Q: What is the significance of the paper "ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models"?

A: The paper "ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models" proposes a novel approach to protein structure prediction and editing using large language models. The paper demonstrates the potential of large language models to improve the accuracy of protein structure prediction and editing.

Q: What is the main focus of the paper "Multi-Modal Foundation Models for Computational Pathology: A Survey"?

A: The main focus of the paper "Multi-Modal Foundation Models for Computational Pathology: A Survey" is to provide a comprehensive survey of multi-modal foundation models for computational pathology. The paper reviews the current state of the art in multi-modal foundation models for computational pathology and identifies areas for future research.

Q: What is the significance of the paper "FOSS solution for Molecular Dynamics Simulation Automation and Collaboration with MDSGAT"?

A: The paper "FOSS solution for Molecular Dynamics Simulation Automation and Collaboration with MDSGAT" proposes a novel approach to molecular dynamics simulation automation and collaboration using a FOSS (Free and Open-Source Software) solution. The paper demonstrates the potential of FOSS solutions to improve the efficiency and effectiveness of molecular dynamics simulations.

Q: What is the main focus of the paper "Symbolic Mixture-of-Experts: Adaptive Skill-based Routing for Heterogeneous Reasoning"?

A: The main focus of the paper "Symbolic Mixture-of-Experts: Adaptive Skill-based Routing for Heterogeneous Reasoning" is to develop a novel approach to heterogeneous reasoning using symbolic mixture-of-experts. The paper proposes a novel approach to adaptive skill-based routing for heterogeneous reasoning and demonstrates its potential to improve the accuracy and efficiency of heterogeneous reasoning.

Q: What is the significance of the paper "evoBPE: Evolutionary Protein Sequence Tokenization"?

A: The paper "evoBPE: Evolutionary Protein Sequence Tokenization" proposes a novel approach to protein sequence tokenization using evolutionary algorithms. The paper demonstrates the potential of evolutionary algorithms to improve the accuracy and efficiency of protein sequence tokenization.

Q: What is the main focus of the paper "Understanding and Mitigating Distribution Shifts For Machine Learning Force Fields"?

A: The main focus of the paper "Understanding and Mitigating Distribution Shifts For Machine Learning Force Fields" is to develop a novel approach to understanding and mitigating distribution shifts for machine learning force fields. The paper proposes a novel approach to distribution shift mitigation and demonstrates its potential to improve the accuracy and efficiency of machine learning force fields.

Q: What is the significance of the paper "Chemistry-Inspired Diffusion with Non-Differentiable Guidance"?

A: The paper "Chemistry-Inspired Diffusion with Non-Differentiable Guidance" proposes a novel approach to chemistry-inspired diffusion using non-differentiable guidance. The paper demonstrates the potential of non-differentiable guidance to improve the accuracy and efficiency of chemistry-inspired diffusion.

Q: What is the main focus of the paper "To Use or Not to Use a Universal Force Field"?

A: The main focus of the paper "To Use or Not to Use a Universal Force Field" is to investigate the use of universal force fields in molecular simulations. The paper proposes a novel approach to universal force field selection and demonstrates its potential to improve the accuracy and efficiency of molecular simulations.

Q: What is the significance of the paper "Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation"?

A: The paper "Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation" proposes a novel approach to protein-specific molecular generation using concept-driven deep learning. The paper demonstrates the potential of concept-driven deep learning to improve the accuracy and efficiency of protein-specific molecular generation.

Q: What is the main focus of the paper "Equivariant Masked Position Prediction for Efficient Molecular Representation"?

A: The main focus of the paper "Equivariant Masked Position Prediction for Efficient Molecular Representation" is to develop a novel approach to equivariant masked position prediction for efficient molecular representation. The paper proposes a novel approach to equivariant masked position prediction and demonstrates its potential to improve the accuracy and efficiency of molecular representation.

Q: What is the significance of the paper "Brain Tumor Classification on MRI in Light of Molecular Markers"?

A: The paper "Brain Tumor Classification on MRI in Light of Molecular Markers" proposes a novel approach to brain tumor classification on MRI using molecular markers. The paper demonstrates the potential of molecular markers to improve the accuracy and efficiency of brain tumor classification on MRI.

Q: What is the main focus of the paper "Q-MARL: A quantum-inspired algorithm using neural message passing for large-scale multi-agent reinforcement learning"?

A: The main focus of the paper "Q-MARL: A quantum-inspired algorithm using neural message passing for large-scale multi-agent reinforcement learning" is to develop a novel approach to quantum-inspired algorithms for large-scale multi-agent reinforcement learning. The paper proposes a novel approach to neural message passing for large-scale multi-agent reinforcement learning and demonstrates its potential to improve the accuracy and efficiency of multi-agent reinforcement learning.

Q: What is the significance of the paper "AlphaNet: Scaling Up Local Frame-based Atomistic Interatomic Potential"?

A: The paper "AlphaNet: Scaling Up Local Frame-based Atomistic Interatomic Potential" proposes a novel approach to scaling up local frame-based atomistic interatomic potential. The paper demonstrates the potential of local frame-based atomistic interatomic potential to improve the accuracy and efficiency of molecular simulations.

Q: What is the main focus of the paper "Bridging Molecular Graphs and Large Language Models"?

A: The main focus of the paper "Bridging Molecular Graphs and Large Language Models" is to develop a novel approach to bridging molecular graphs and large language models. The paper proposes a novel approach to bridging molecular graphs and large language models and demonstrates its potential to improve the accuracy and efficiency of molecular simulations.

Q: What is the significance of the paper "Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models"?

A: The paper "Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models" proposes a novel approach to property-enhanced instruction tuning for multi-task molecule generation with large language models. The paper demonstrates the potential of property-enhanced instruction tuning to improve the accuracy and efficiency of multi-task molecule generation.

Q: What is the main focus of the paper "Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation"?

A: The main focus of the paper "Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation" is to develop a novel approach to pretraining generative flow networks with inexpensive rewards for molecular graph generation. The paper proposes a novel approach to pretraining generative flow networks and demonstrates its potential to improve the accuracy and efficiency of molecular graph generation.

Q: What is the significance of the paper "Learning-Order Autoregressive Models with Application to Molecular Graph Generation"?

A: The paper "Learning-Order Autoregressive Models with Application to Molecular Graph Generation" proposes a novel approach to learning-order autoregressive models with application to molecular graph generation. The paper demonstrates the potential of learning-order autoregressive models to improve the accuracy and efficiency of molecular graph generation.

Q: What is the main focus of the paper "Mol-CADiff: Causality-Aware Autoregressive Diffusion for Molecule Generation"?

A: The main focus of the paper "Mol-CADiff: Causality-Aware Autoregressive Diffusion for Molecule Generation" is to develop a novel approach to causality-aware autoregressive diffusion for molecule generation. The paper proposes a novel approach to causality-aware autoregressive diffusion and demonstrates its potential to improve the accuracy and efficiency of molecule generation.

Q: What is the significance of the paper "GENERator: A Long-Context Generative Genomic Foundation Model"?

A: The paper "GENERator: A Long-Context Generative Genomic Foundation Model" proposes a novel approach to long-context generative genomic foundation models. The paper demonstrates the potential of long-context generative genomic foundation models to improve the accuracy and efficiency of genomic data analysis.

Q: What is the main focus of the paper "Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation"?

A: The main focus of the paper "Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation" is to develop a novel approach to smart reaction templating using a graph-based method for automated molecular dynamics input generation. The paper proposes a novel approach to smart reaction templating and demonstrates its potential to improve the accuracy and efficiency of molecular dynamics simulations.

Q: What is the significance of the paper "Straight-Line Diffusion Model for Efficient 3D Molecular Generation"?

A: The paper