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Journal Article
Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer
Fabio Cumbo and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf177, https://doi.org/10.1093/bib/bbaf177
Published: 24 April 2025
... with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space...
Journal Article
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Navigating the Multiverse: A Hitchhiker’s Guide to Selecting Harmonisation Methods for Multimodal Biomedical Data
Murali Aadhitya Magateshvaren Saras and others
Biology Methods and Protocols, bpaf028, https://doi.org/10.1093/biomethods/bpaf028
Published: 17 April 2025
... is also presented along with examples and references. Conclusions This review provides a thorough taxonomy of methods for harmonising multimodal data and introduces a foundational 10-step guide for newcomers to implement a multimodal workflow. multimodal integration feature representation data...
Journal Article
DOMSCNet: a deep learning model for the classification of stomach cancer using multi-layer omics data
Kasmika Borah and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf115, https://doi.org/10.1093/bib/bbaf115
Published: 03 April 2025
... dataset is highly complex. In recent times, some computational methods have been developed for cancer omics data interpretation. However, various existing methods face challenges in accounting for diverse types of cancer omics data and struggle to effectively extract informative features...
Journal Article
MethPriorGCN: a deep learning tool for inferring DNA methylation prior knowledge and guiding personalized medicine
Jie Ni and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf131, https://doi.org/10.1093/bib/bbaf131
Published: 25 March 2025
.... To systematically mine reliable methylation prior knowledge from known DNA methylation-disease associations and develop robust computational methods for precision medicine applications, we propose MethPriorGCN. By integrating layer attention mechanisms and feature weighting mechanisms, MethPriorGCN not only...
Journal Article
Sparse Bernoulli mixture modeling with negative-unlabeled data: an approach to identify and characterize long COVID
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Tingyi Cao and others
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Biometrics
Biometrics, Volume 81, Issue 1, March 2025, ujaf021, https://doi.org/10.1093/biomtc/ujaf021
Published: 12 March 2025
...-unlabeled” as uninfected individuals must be PASC negative, but those with prior infection have unknown PASC status. Moreover, feature selection among many potentially informative characteristics can facilitate reaching a concise and easily interpretable PASC definition. Therefore, to characterize PASC...
Journal Article
A comparison of random forest variable selection methods for regression modeling of continuous outcomes
Nathaniel S O’Connell and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf096, https://doi.org/10.1093/bib/bbaf096
Published: 10 March 2025
...Nathaniel S O’Connell; Byron C Jaeger; Garrett S Bullock; Jaime Lynn Speiser random forest variable selection feature selection feature reduction regression Corresponding author. Division of Public Health Sciences, Wake Forest University School of Medicine, Medical Center Boulevard, Winston...
Journal Article
HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction
Yuguang Li and others
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf079, https://doi.org/10.1093/bib/bbaf079
Published: 04 March 2025
... evaluate HSSPPI on public benchmark datasets and the predicting results outperform the comparative models. This indicates the effectiveness of hierarchical protein modeling and also illustrates that HSSPPI has a strong feature extraction ability by considering spatial and sequential information...
Journal Article
Incremental value of multiparametric cardiac magnetic resonance imaging for non-invasive identification of significant acute cardiac allograft rejection: a prospective and biopsy-proven study
Pengyu Zhou and others
European Heart Journal - Cardiovascular Imaging, jeaf052, https://doi.org/10.1093/ehjci/jeaf052
Published: 11 February 2025
... examinations for identifying SR. Methods and results Heart transplantation (HTx) recipients with endomyocardial biopsy and healthy controls were prospectively recruited for CMR assessment. CMR feature tracking was performed to evaluate the left ventricular (LV) global strain in all three directions...
Journal Article
Neurophysiological profiles underlying action withholding and action discarding
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Roula Jamous and others
Cerebral Cortex, Volume 35, Issue 2, February 2025, bhaf026, https://doi.org/10.1093/cercor/bhaf026
Published: 10 February 2025
... management of feature bindings ( Takacs et al. 2020 ; Prochnow et al. 2022a ; Prochnow et al. 2022b ). This is well in line with conceptions according to which enhanced alpha power is associated with the inhibition of information processing, particularly the suppression of processing task-irrelevant...
Journal Article
QGRIME: A RIME optimizer with quantum rotation gate and Gaussian mutation for feature selection
Tian Bai and others
Journal of Computational Design and Engineering, Volume 12, Issue 2, February 2025, Pages 235–257, https://doi.org/10.1093/jcde/qwaf016
Published: 06 February 2025
...Tian Bai; Kaile Bu; Chentao Gao; Huiling Chen Correspondence: [email protected] Graphical Abstract Figure. Principle and feature selection effects of QGRIME. 04 07 2024...
Journal Article
Cardiac magnetic resonance feature tracking in Olympic athletes: a myocardial deformation analysis
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Sara Monosilio and others
European Journal of Preventive Cardiology, zwaf042, https://doi.org/10.1093/eurjpc/zwaf042
Published: 06 February 2025
...Sara Monosilio; Silvia Prosperi; Domenico Filomena; Erika Lemme; Giuseppe Di Gioia; Ruggiero Mango; Lucrezia Netti; Giovanni Tonti; Gianni Pedrizzetti; Gianfranco Gualdi; Maria Rosaria Squeo; Antonio Pelliccia; Viviana Maestrini CMR Feature tracking Strain Myocardial deformation Athletes...
Journal Article
Machine learning-based pH quantification from test strip images using multiple color spaces
Yuto Nakamura and Masahiro Nagao
Chemistry Letters, Volume 54, Issue 2, February 2025, upaf018, https://doi.org/10.1093/chemle/upaf018
Published: 04 February 2025
... web application. Graphical Abstract Graphical Abstract colorimetric analysis feature selection pH test strip Research on the application of machine learning to the field of chemistry has received a great deal of attention over the past decade. 1–5 The colorimetric method determines...
Journal Article
Tropical climate prediction method combining random forest and feature fusion
Guotao Liu
International Journal of Low-Carbon Technologies, Volume 20, 2025, Pages 154–166, https://doi.org/10.1093/ijlct/ctae281
Published: 25 January 2025
... pose significant threats to coastal populations, causing destruction and loss of life. Precisely forecasting the frequency and arrival dates is still a challenge. This research presents a technique for feature extraction and integration using a random forest (RF) model with a cascaded convolutional...
Journal Article
TargetCLP: clathrin proteins prediction combining transformed and evolutionary scale modeling-based multi-view features via weighted feature integration approach
Matee Ullah and others
Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbaf026, https://doi.org/10.1093/bib/bbaf026
Published: 23 January 2025
..., when designing machine learning-based predictors for clathrin proteins, for instance, TargetCLP in this work, PSSM, with a length equal to the provided protein sequence, cannot be employed directly to represent the clathrin protein’s feature vector. Therefore, in this study, we employed an image-based...
Journal Article
AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody–antigen interaction prediction
Kaiwen Zhang and others
Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbaf008, https://doi.org/10.1093/bib/bbaf008
Published: 20 January 2025
... performance in cross-species experiments highlights its potential for broad applications in biomedical research and therapeutic development. AntiBinder is designed to determine whether an antibody can bind to an antigen. Its architecture involves several key steps: extracting features from both the antibody...
Journal Article
scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data
Xiangfei Zhou and Hao Wu
Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbaf009, https://doi.org/10.1093/bib/bbaf009
Published: 20 January 2025
...Xiangfei Zhou; Hao Wu The scHiClassifier framework, depicted in Fig. 1 , comprises three key steps: data preparation, extraction of multiple feature sets, and construction of the fusion prediction model. In the first step, raw single-cell Hi-C data are preprocessed into contact matrices...
Journal Article
A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction
Baiming Zou and others
Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbae709, https://doi.org/10.1093/bib/bbae709
Published: 16 January 2025
... of each feature on the disease outcome. To this end, we can evaluate the role of each feature using rigorous statistical inference for machine learning models by adopting a PermFIT procedure [ 31 ], as described briefly below. Based on the PermFIT, we derive a powerful framework to identify important...
Journal Article
Unveiling patterns in spatial transcriptomics data: a novel approach utilizing graph attention autoencoder and multiscale deep subspace clustering network
Liqian Zhou and others
in
GigaScience
GigaScience, Volume 14, 2025, giae103, https://doi.org/10.1093/gigascience/giae103
Published: 13 January 2025
... methods can neither decipher complex structures in ST data nor entirely employ features embedded in different layers. Results This article introduces STMSGAL, a novel framework for analyzing ST data by incorporating graph attention autoencoder and multiscale deep subspace clustering. First, STMSGAL...
Journal Article
NCFDet: Enhanced point cloud features using the neural collapse phenomenon in multimodal fusion for 3D object detection
Yaming Xu and others
Journal of Computational Design and Engineering, Volume 12, Issue 1, January 2025, Pages 300–311, https://doi.org/10.1093/jcde/qwae115
Published: 31 December 2024
...-sensor autonomous driving and robotics systems, particularly in the context of navigating complex urban environments. The complementary nature of image and point cloud data allows for the detection of objects with greater accuracy and robustness when both image and point cloud features are employed...
Journal Article
STLBRF: an improved random forest algorithm based on standardized-threshold for feature screening of gene expression data
Huini Feng and others
Briefings in Functional Genomics, Volume 24, 2025, elae048, https://doi.org/10.1093/bfgp/elae048
Published: 30 December 2024
... is properly cited. For commercial re-use, please contact [email protected] Abstract When the traditional random forest (RF) algorithm is used to select feature elements in biostatistical data, a large amount of noise data and parameters can affect the importance of the selected feature elements...
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