Single Point Mutation

Single-point mutations, the alteration of a single nucleotide or amino acid, are a focus of intense research across diverse fields, aiming to understand their effects on diverse systems, from protein stability to the behavior of large language models. Current research employs various machine learning approaches, including graph neural networks, evolutionary algorithms (like genetic programming and Estimation of Distribution Algorithms), and deep learning models (such as those based on AlphaFold2 and large language models), to predict the impact of these mutations and optimize systems accordingly. These studies are crucial for advancing protein engineering, drug discovery, understanding disease mechanisms, improving AI model performance, and optimizing various computational processes.

Papers

November 12, 2024

Machines and Mathematical Mutations: Using GNNs to Characterize Quiver Mutation Classes
Jesse He, Helen Jenne, Herman Chau, Davis Brown, Mark Raugas, Sara Billey, Henry Kvinge
Graph Neural Network New Machine Gene Level GNN Single Point Mutation Quiver Representation Coefficient Mutation

October 30, 2024

MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering
Yizhen Luo, Zikun Nie, Massimo Hong, Suyuan Zhao, Hao Zhou, Zaiqing Nie
Protein Language Model Position Engineering Single Point Mutation Protein Representation Mutational Effect

October 29, 2024

Explainable convolutional neural network model provides an alternative genome-wide association perspective on mutations in SARS-CoV-2
Parisa Hatami, Richard Annan, Luis Urias Miranda, Jane Gorman, Mengjun Xie, Letu Qingge, Hong Qin
Biological Sequence Sars Cov 2 Single Point Mutation Genome Wide Association Study Explainable Deep

October 12, 2024

Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions
Xiaoran Jiao, Weian Mao, Wengong Jin, Peiyuan Yang, Hao Chen, Chunhua Shen
Mixed Effect Protein Protein Interaction Single Point Mutation Deodata Predictor

August 21, 2024

Mutagenesis screen to map the functions of parameters of Large Language Models
Yue Hu, Kai Hu, Patrick X. Zhao, Javed Khan, Chengming Xu
Many Parameter Single Point Mutation Functional Theory

July 11, 2024

Estimation of Distribution Algorithms with Matrix Transpose in Bayesian Learning
Dae-Won Kim, Song Ko, Bo-Yeong Kang
Estimation Task Bayesian Learning Evolutionary Optimization Single Point Mutation Mutation Operator Bayesian Structure Distribution Algorithm

July 9, 2024

HERMES: Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction
Gian Marco Visani, Michael N. Pun, William Galvin, Eric Daniel, Kevin Borisiak, Utheri Wagura, Armita Nourmohammad
Amino Acid Single Point Mutation Mutational Effect Scale Equivariant

June 13, 2024

ALPHAGMUT: A Rationale-Guided Alpha Shape Graph Neural Network to Evaluate Mutation Effects
Boshen Wang, Bowei Ye, Lin Xu, Jie Liang
Single Point Mutation Mutational Effect

May 16, 2024

Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V Chawla, Stan Z. Li
LeArning Abstract Prompt Learning Molecular Conformation Protein Protein Interaction Single Point Mutation Mutational Effect Mutational Effect Prediction

January 26, 2024

Predicting loss-of-function impact of genetic mutations: a machine learning approach
Arshmeet Kaur, Morteza Sarmadi
Machine Learning Approach Single Point Mutation Functional Outcome

December 29, 2023

A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1
Giulia Di Teodoro, Federico Siciliano, Valerio Guarrasi, Anne-Mieke Vandamme, Valeria Ghisetti, Anders Sönnerborg, Maurizio Zazzi, Fabrizio Silvestri, Laura Palagi
Graph Drawing Single Point Mutation Distribution Robustness

December 7, 2023

Efficiently Predicting Protein Stability Changes Upon Single-point Mutation with Large Language Models
Yijie Zhang, Zhangyang Gao, Cheng Tan, Stan Z. Li
Single Point Mutation Protein Stability

November 10, 2023

Genetic Algorithm enhanced by Deep Reinforcement Learning in parent selection mechanism and mutation : Minimizing makespan in permutation flow shop scheduling problems
Maissa Irmouli, Nourelhouda Benazzoug, Alaa Dania Adimi, Fatma Zohra Rezkellah, Imane Hamzaoui, Thanina Hamitouche, Malika Bessedik, Fatima Si Tayeb
Reinforcement Learning Deep Reinforcement Learning Genetic Algorithm Single Point Mutation Flow Shop Scheduling RL Method

November 8, 2023

Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1
Giulia Di Teodoro, Martin Pirkl, Francesca Incardona, Ilaria Vicenti, Anders Sönnerborg, Rolf Kaiser, Laura Palagi, Maurizio Zazzi, Thomas Lengauer
Temporal Dynamic Single Point Mutation Predictive Capability Treatment Outcome Viral Load

September 25, 2023

Multiple evolutionary pressures shape identical consonant avoidance in the world's languages
Chundra A. Cathcart
World Event Unknown Language Language Evolution Single Point Mutation Code Change Evolutionary Pressure

August 9, 2023

Directed differential equation discovery using modified mutation and cross-over operators
Elizaveta Ivanchik, Alexander Hvatov
Evolutionary Operator Equation Discovery Single Point Mutation Crossover Operator Differential Equation Discovery

May 22, 2023

Self-Replication, Spontaneous Mutations, and Exponential Genetic Drift in Neural Cellular Automata
Lana Sinapayen
Cellular Automaton Neural Cellular Automaton Single Point Mutation Self Replication

May 15, 2023

AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction
Zhongju Yuan, Tao Shen, Sheng Xu, Leiye Yu, Ruobing Ren, Siqi Sun
Protein Sequence Structure Prediction Adversarial Pattern Single Point Mutation AlphaFold2 Protein Structure Prediction

March 2, 2023

T-Cell Receptor Optimization with Reinforcement Learning and Mutation Policies for Precesion Immunotherapy
Ziqi Chen, Martin Renqiang Min, Hongyu Guo, Chao Cheng, Trevor Clancy, Xia Ning
Reinforcement Learning Single Point Mutation Adaptive Mutation Cell Receptor Subcutaneous Immunotherapy TCR Sequence

January 13, 2023

Mutation Testing of Deep Reinforcement Learning Based on Real Faults
Florian Tambon, Vahid Majdinasab, Amin Nikanjam, Foutse Khomh, Giuliano Antonio
Deep Reinforcement Learning Post Fault Trajectory Single Point Mutation Mutation Operator Deep Learning Testing Mutation Testing

Single Point Mutation

Papers

Machines and Mathematical Mutations: Using GNNs to Characterize Quiver Mutation Classes

MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering

Explainable convolutional neural network model provides an alternative genome-wide association perspective on mutations in SARS-CoV-2

Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions

Mutagenesis screen to map the functions of parameters of Large Language Models

Estimation of Distribution Algorithms with Matrix Transpose in Bayesian Learning

HERMES: Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction

ALPHAGMUT: A Rationale-Guided Alpha Shape Graph Neural Network to Evaluate Mutation Effects

Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning

Predicting loss-of-function impact of genetic mutations: a machine learning approach

A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1

Efficiently Predicting Protein Stability Changes Upon Single-point Mutation with Large Language Models

Genetic Algorithm enhanced by Deep Reinforcement Learning in parent selection mechanism and mutation : Minimizing makespan in permutation flow shop scheduling problems

Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1

Multiple evolutionary pressures shape identical consonant avoidance in the world's languages

Directed differential equation discovery using modified mutation and cross-over operators

Self-Replication, Spontaneous Mutations, and Exponential Genetic Drift in Neural Cellular Automata

AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction

T-Cell Receptor Optimization with Reinforcement Learning and Mutation Policies for Precesion Immunotherapy

Mutation Testing of Deep Reinforcement Learning Based on Real Faults