paper-with-me

홈 › Papers

3D-based RNA function prediction tools in rnaglib

2024-02-14 · Carlos Oliver, Vincent Mallet, Jérôme Waldispühl

Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate modeling choices remains time-consuming and lacks standardization. In this chapter, we describe the use of rnaglib, to train supervised and unsupervised machine learning-based function prediction models on datasets of RNA 3D structures.

📄 PDF Abstract BibTeX arXiv:2402.09330

Code (1)

cgoliver/rnaglib 공식 구현 pytorch

Tasks

Prediction

Similar Papers 제목 키워드 기반

RNAglib: A Python Package for RNA 2.5D Graphs

2021-09-09 · Vincent Mallet, Carlos Oliver, Jonathan Broadbent, William L. Hamilton 외

RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approac…

BIG-bench Machine Learning

A Comprehensive Benchmark for RNA 3D Structure-Function Modeling

2025-03-27 · Luis Wyss, Vincent Mallet, Wissam Karroucha, Karsten Borgwardt 외

The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, a lac…

BenchmarkingDeep LearningGraph Neural Network

AFDP: An Automated Function Description Prediction Approach to Improve Accuracy of Protein Function Predictions

2019-10-15

With the rapid growth in high-throughput biological sequencing technologies and subsequently the amount of produced omics data, it is essential to develop automated methods to annotate the functionality of unknown genes …

Protein Function Prediction

A Conformal Prediction Approach to Explore Functional Data

2013-02-26 · Jing Lei, Alessandro Rinaldo, Larry Wasserman

This paper applies conformal prediction techniques to compute simultaneous prediction bands and clustering trees for functional data. These tools can be used to detect outliers and clusters. Both our prediction bands and…

ClusteringConformal PredictionPrediction

Conformal Prediction Bands for Two-Dimensional Functional Time Series

2022-07-27 · Niccolò Ajroldi, Jacopo Diquigiovanni, Matteo Fontana, Simone Vantini

Time evolving surfaces can be modeled as two-dimensional Functional time series, exploiting the tools of Functional data analysis. Leveraging this approach, a forecasting framework for such complex data is developed. The…

Conformal PredictionPredictionTime SeriesTime Series Analysis+2