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Recent Advances on Penalized Regression Models for Biological Data

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Article Oncology

BAHD1 serves as a critical regulator of breast cancer cell proliferation and invasion

Ze-Yu Yang et al.

Summary: The study identified the key gene BAHD1 associated with lymph node metastasis and prognosis in breast cancer through LASSO analysis, which plays an important role in cancer cell proliferation, migration, and invasion capacity. Moreover, the expression level of BAHD1 affects the expression of other important genes, which is crucial for the progression of breast cancer.

BREAST CANCER (2022)

Article Neuroimaging

Detection of functional and structural brain alterations in female schizophrenia using elastic net logistic regression

Ying Wu et al.

Summary: This study investigated patterns of brain functional and structural changes in female patients with schizophrenia using elastic net logistic regression analysis of resting-state functional magnetic resonance imaging data. The analysis revealed eight common regions between ALFF and gray matter analyses. Severity of symptoms was found to be positively associated with the ALFF in specific brain regions.

BRAIN IMAGING AND BEHAVIOR (2022)

Article Biochemistry & Molecular Biology

A Metabolomic Severity Score for Airflow Obstruction and Emphysema

Suneeta Godbole et al.

Summary: This study developed a metabolomic severity score for chronic obstructive pulmonary disease (COPD) using plasma metabolomics data. The score can better explain the variability in lung function and lung density, and it outperforms clinical covariates in predicting disease severity.

METABOLITES (2022)

Article Clinical Neurology

Temporal Grading Index of Functional Network Topology Predicts Pain Perception of Patients With Chronic Back Pain

Zhonghua Li et al.

Summary: This study used resting-state functional magnetic resonance imaging to generate dynamic functional networks for patients with chronic back pain (CBP) and healthy controls. The results showed spatiotemporal changes in functional network topology in patients with CBP, which could serve as a valuable biomarker for assessing pain sensation in the brain. A new feature index, called temporal grading index (TGI), was proposed to quantify the temporal deviation of network properties in CBP patients, and it showed outstanding performance in predicting pain intensity.

FRONTIERS IN NEUROLOGY (2022)

Article Biotechnology & Applied Microbiology

MLP-Based Regression Prediction Model For Compound Bioactivity

Yongfei Qin et al.

Summary: This study focuses on the estrogen receptor ER alpha, which plays a key role in the development of breast cancer and is considered an important target for treatment. The researchers developed a compound activity prediction model using statistical regression and neural network methods. The model successfully predicted the bioactivity values of new compounds, providing valuable insights for the development of anti-breast cancer drugs.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2022)

Article Biochemical Research Methods

Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications

Pei Wang et al.

Summary: This paper introduces a novel method for constructing gene differential co-expression networks (GDCNs) using the gray correlation coefficient (GCC). The GDCN-based approaches overcome the challenges of traditional methods and facilitate the inference of gene functions and the identification of informative genes.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2022)

Article Mathematics

A Robust Variable Selection Method for Sparse Online Regression via the Elastic Net Penalty

Wentao Wang et al.

Summary: This article presents a method called canal-adaptive elastic net for noise-resistant regularization and variable selection in noisy data streams with multicollinearity. Numerous simulation experiments have shown that canal-adaptive elastic net outperforms other methods in terms of prediction accuracy in data with multicollinearity and noise.

MATHEMATICS (2022)

Article Computer Science, Interdisciplinary Applications

Autonomous inference of complex network dynamics from incomplete and noisy data

Ting-Ting Gao et al.

Summary: The availability of empirical data on complex networked systems has increased in recent years, but a versatile computational toolbox for understanding a system's nodal and interaction dynamics remains elusive. This study develops a two-phase approach for inferring complex network dynamics, which is robust to incompleteness and noise. By applying this approach to various synthetic and real networks, the researchers are able to uncover the hidden microscopic mechanisms of a broad array of real networked systems, including the spread of diseases.

NATURE COMPUTATIONAL SCIENCE (2022)

Article Mathematical & Computational Biology

Adaptive group-regularized logistic elastic net regression

Magnus M. Munch et al.

Summary: In this study, a group-regularized (logistic) elastic net regression method is proposed, where external information on features is used to group penalties, leading to enhanced classification performance and feature selection.

BIOSTATISTICS (2021)

Article Psychology, Clinical

Machine learning enhances prediction of illness course: a longitudinal study in eating disorders

Ann F. Haynos et al.

Summary: This study compared machine learning (ML) with traditional regression for predicting eating disorder (ED) outcomes, finding that ML models had higher accuracy in predicting all outcomes over 2 years. Important predictors included baseline ED, psychiatric, and demographic characteristics.

PSYCHOLOGICAL MEDICINE (2021)

Article Biochemical Research Methods

Incorporating prior knowledge into regularized regression

Chubing Zeng et al.

Summary: The study introduces a new penalized regression approach that allows the integration of external meta-features a priori, showing through simulations that it outperforms standard LASSO regression in terms of parameter estimation and prediction performance when external data is informative. The method is demonstrated with applications to gene expression studies of bone density and breast cancer.

BIOINFORMATICS (2021)

Article Health Policy & Services

Identification of predictors and model for predicting prolonged length of stay in dengue patients

Md Shahid Ansari et al.

Summary: The study aimed to predict the hospital length of stay in dengue patients using logistic regression and random forest algorithms, showing a significant association between prolonged hospitalization and patient-specific variables. Logistic regression with elastic-net was found to be the best fit model with an AUC of 0.75.

HEALTH CARE MANAGEMENT SCIENCE (2021)

Article Automation & Control Systems

Adaptive LASSO logistic regression based on particle swarm optimization for Alzheimer's disease early diagnosis

Xinchun Cui et al.

Summary: The proposed PSO-ALLR algorithm effectively combines global search using PSO with local search using adaptive LASSO to achieve high classification accuracy in distinguishing AD and MCI from healthy controls. The method demonstrates promising results in accurately classifying AD vs. HC, MCI vs. HC, and cMCI vs. sMCI.

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS (2021)

Article Surgery

Evaluation and analysis of incidence and risk factors of lower extremity venous thrombosis after urologic surgeries: A prospective two-center cohort study using LASSO-logistic regression

Guyu Tang et al.

Summary: This study aimed to analyze the incidence and risk factors of lower extremity venous thrombosis after urologic surgery. Age, history of DVT, lymph node dissection were identified as factors associated with DVT occurrence. Using the LASSO logistic regression model provided reliable data on risk factors for DVT.

INTERNATIONAL JOURNAL OF SURGERY (2021)

Article Mathematics

The Higher-Order of Adaptive Lasso and Elastic Net Methods for Classification on High Dimensional Data

Autcha Araveeporn

Summary: The lasso and elastic net methods are commonly used techniques for parameter estimation and variable selection, with adaptive versions incorporating adaptive weights based on the power order of the estimator. This paper compares these methods in the context of high-dimensional data classification, with results indicating that the adaptive elastic net method outperforms on small dispersion compared to the adaptive lasso method.

MATHEMATICS (2021)

Article Health Care Sciences & Services

Etiology and Timing of Postoperative Rapid Response Team Activations

Jeremy P. Walco et al.

Summary: This retrospective cohort study evaluated the association between etiology and timing of rapid response team activations in postoperative patients, finding that respiratory triggers were associated with a significant increase in time to RRT activation. These findings may impact monitoring and interventions for clinically deteriorating patients.

JOURNAL OF MEDICAL SYSTEMS (2021)

Article Mathematics, Interdisciplinary Applications

Statistical Identification of Important Nodes in Biological Systems

Wang Pei

Summary: Biological systems can be modeled and described by biological networks, with important nodes identification having wide real-world applications. This paper reviews statistical identification methods of important nodes in biological systems from three aspects, and proposes that such identification can be seen as a mapping to the ranking score vector of nodes.

JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY (2021)

Article Biochemical Research Methods

Multidimensional analysis and detection of informative features in human brain white matter

Adam Richie-Halford et al.

Summary: This article introduces a method based on the sparse group lasso for selecting informative features in white matter for classification and regression tasks. The method demonstrates its performance in accurately distinguishing ALS patients from controls and predicting brain age.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Automation & Control Systems

Inferring Network Structure and Estimating Dynamical Process From Binary-State Data via Logistic Regression

Qi-Ming Liu et al.

Summary: This article presents a framework for inferring the structures and dynamics of complex networks based on time series data, even when the original dynamics are unknown. The method uses a Logistic regression with Sigmoid function to describe transition probabilities and employs mean-field approximation for maximum likelihood estimation. The framework has been validated on synthetic and empirical networks, showing high accuracy in revealing network structures and estimating dynamical processes.

IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS (2021)

Article Biochemistry & Molecular Biology

Computational Probing the Methylation Sites Related to EGFR Inhibitor-Responsive Genes

Rui Yuan et al.

Summary: This study revealed methylation sites associated with EGFR inhibitor sensitivity genes through the correlation between DNA methylation and drug sensitivity, providing new therapeutic targets for understanding anti-EGFR-inhibitor resistance in lung cancer.

BIOMOLECULES (2021)

Review Biochemical Research Methods

Network-based methods for predicting essential genes or proteins: a survey

Xingyi Li et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Article Statistics & Probability

A note on coding and standardization of categorical variables in (sparse) group lasso regression

Felicitas J. Detmer et al.

JOURNAL OF STATISTICAL PLANNING AND INFERENCE (2020)

Article Statistics & Probability

Adaptive Huber Regression

Qiang Sun et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2020)

Article Computer Science, Information Systems

Variational Bayesian weighted complex network reconstruction

Shuang Xu et al.

INFORMATION SCIENCES (2020)

Article Mathematics, Interdisciplinary Applications

Network structure reconstruction with symmetry constraint

Zihua Hang et al.

CHAOS SOLITONS & FRACTALS (2020)

Article Biochemical Research Methods

Structured Penalized Logistic Regression for Gene Selection in Gene Expression Data Analysis

Cheng Liu et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2019)

Article Biochemical Research Methods

Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families

Pei Wang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2019)

Article Biochemical Research Methods

Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Based on Conditional Mutual Information

Juntao Li et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

Windowed Granger causal inference strategy improves discovery of gene regulatory networks

Justin D. Finkle et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Geriatrics & Gerontology

Biological Brain Age Prediction Using Cortical Thickness Data: A Large Scale Cohort Study

Habtamu M. Aycheh et al.

FRONTIERS IN AGING NEUROSCIENCE (2018)

Review Mathematical & Computational Biology

Modeling and analysis of RNA-seq data: a review from a statistical perspective

Wei Vivian Li et al.

QUANTITATIVE BIOLOGY (2018)

Article Mathematics, Applied

A dynamic logistic regression for network link prediction

Zhou Jing et al.

SCIENCE CHINA-MATHEMATICS (2017)

Article Biochemistry & Molecular Biology

Gene set selection via LASSO penalized regression ( SLPR)

H. Robert Frost et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

Woosung Chung et al.

NATURE COMMUNICATIONS (2017)

Article Multidisciplinary Sciences

Transcriptomic basis for drought-resistance in Brassica napus L.

Pei Wang et al.

SCIENTIFIC REPORTS (2017)

Article Biochemical Research Methods

Tilting the lasso by knowledge-based post-processing

Kukatharmini Tharmaratnam et al.

BMC BIOINFORMATICS (2016)

Article Engineering, Biomedical

Graphical Features of Functional Genes in Human Protein Interaction Network

Pei Wang et al.

IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS (2016)

Article Statistics & Probability

Spline-Lasso in High-Dimensional Linear Regression

Jianhua Guo et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2016)

Article Statistics & Probability

Variable Selection With Prior Information for Generalized Linear Models via the Prior LASSO Method

Yuan Jiang et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2016)

Article Multidisciplinary Sciences

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Itay Tirosh et al.

SCIENCE (2016)

Article Mathematics, Applied

Adaptive bridge estimation for high-dimensional regression models

Zhihong Chen et al.

JOURNAL OF INEQUALITIES AND APPLICATIONS (2016)

Article Biochemistry & Molecular Biology

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

Giovanni Ciriello et al.

Article Statistics & Probability

High-Dimensional Variable Selection With Reciprocal L1-Regularization

Qifan Song et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2015)

Review Biochemistry & Molecular Biology

High-Throughput Sequencing Technologies

Jason A. Reuter et al.

MOLECULAR CELL (2015)

Review Genetics & Heredity

Methods of integrating data to uncover genotype-phenotype interactions

Marylyn D. Ritchie et al.

NATURE REVIEWS GENETICS (2015)

Article Physics, Multidisciplinary

Robust Reconstruction of Complex Networks from Sparse Data

Xiao Han et al.

PHYSICAL REVIEW LETTERS (2015)

Article Engineering, Mechanical

Functional characteristics of additional positive feedback in genetic circuits

Pei Wang et al.

NONLINEAR DYNAMICS (2015)

Article Biochemistry & Molecular Biology

Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies

Lin Hou et al.

HUMAN MOLECULAR GENETICS (2014)

Article Engineering, Biomedical

Identification and Evolution of Structurally Dominant Nodes in Protein-Protein Interaction Networks

Pei Wang et al.

IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS (2014)

Review Multidisciplinary Sciences

Challenges of Big Data analysis

Jianqing Fan et al.

NATIONAL SCIENCE REVIEW (2014)

Article Engineering, Biomedical

Application of L1/2 regularization logistic method in heart disease diagnosis

Bowen Zhang et al.

BIO-MEDICAL MATERIALS AND ENGINEERING (2014)

Article Mathematical & Computational Biology

Incorporating group correlations in genome-wide association studies using smoothed group Lasso

Jin Liu et al.

BIOSTATISTICS (2013)

Article Biochemical Research Methods

Sparse logistic regression with a L1/2 penalty for gene selection in cancer classification

Yong Liang et al.

BMC BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

Molecular pathway identification using biological network-regularized logistic models

Wen Zhang et al.

BMC GENOMICS (2013)

Article Pharmacology & Pharmacy

Multinomial Logistic Regression Ensembles

Kyewon Lee et al.

JOURNAL OF BIOPHARMACEUTICAL STATISTICS (2013)

Article Statistics & Probability

A Sparse-Group Lasso

Noah Simon et al.

JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS (2013)

Article Statistics & Probability

Efficient penalized estimating method in the partially varying-coefficient single-index model

Zhensheng Huang et al.

JOURNAL OF MULTIVARIATE ANALYSIS (2013)

Article Multidisciplinary Sciences

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

Christina Curtis et al.

NATURE (2012)

Review Statistics & Probability

A Selective Review of Group Selection in High-Dimensional Models

Jian Huang et al.

STATISTICAL SCIENCE (2012)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Statistics & Probability

A Constrained l1 Minimization Approach to Sparse Precision Matrix Estimation

Tony Cai et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2011)

Article Genetics & Heredity

Genome-wide association study identifies five new schizophrenia loci

Stephan Ripke et al.

NATURE GENETICS (2011)

Article Statistics & Probability

NEARLY UNBIASED VARIABLE SELECTION UNDER MINIMAX CONCAVE PENALTY

Cun-Hui Zhang

ANNALS OF STATISTICS (2010)

Article Computer Science, Interdisciplinary Applications

Regularization Paths for Generalized Linear Models via Coordinate Descent

Jerome Friedman et al.

JOURNAL OF STATISTICAL SOFTWARE (2010)

Article Computer Science, Artificial Intelligence

Data clustering: 50 years beyond K-means

Anil K. Jain

PATTERN RECOGNITION LETTERS (2010)

Article Computer Science, Information Systems

L (1/2) regularization

Xu ZongBen et al.

SCIENCE CHINA-INFORMATION SCIENCES (2010)

Article Statistics & Probability

ON THE ADAPTIVE ELASTIC-NET WITH A DIVERGING NUMBER OF PARAMETERS

Hui Zou et al.

ANNALS OF STATISTICS (2009)

Article Biochemical Research Methods

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

BIOINFORMATICS (2009)

Article Biology

A group bridge approach for variable selection

Jian Huang et al.

BIOMETRIKA (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Multidisciplinary Sciences

Human BAHD1 promotes heterochromatic gene silencing

Helene Bierne et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia et al.

SCIENCE (2009)

Article Biochemical Research Methods

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation

Nicholas J. Hudson et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Computer Science, Software Engineering

A coordinate gradient descent method for nonsmooth separable minimization

Paul Tseng et al.

MATHEMATICAL PROGRAMMING (2009)

Article Biochemical Research Methods

Network-constrained regularization and variable selection for analysis of genomic data

Caiyan Li et al.

BIOINFORMATICS (2008)

Article Statistics & Probability

The group lasso for logistic regression

Lukas Meier et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2008)

Article Biochemistry & Molecular Biology

Network-based global inference of human disease genes

Xuebing Wu et al.

MOLECULAR SYSTEMS BIOLOGY (2008)

Article Biochemical Research Methods

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Ali Mortazavi et al.

NATURE METHODS (2008)

Article Mathematical & Computational Biology

Multinomial goodness-of-fit tests for logistic regression models

Morten W. Fagerland et al.

STATISTICS IN MEDICINE (2008)

Article Mathematical & Computational Biology

Sparse inverse covariance estimation with the graphical lasso

Jerome Friedman et al.

BIOSTATISTICS (2008)

Article Mathematical & Computational Biology

Penalized logistic regression for detecting gene interactions

Mee Young Park et al.

BIOSTATISTICS (2008)

Article Statistics & Probability

PATHWISE COORDINATE OPTIMIZATION

Jerome Friedman et al.

ANNALS OF APPLIED STATISTICS (2007)

Article Multidisciplinary Sciences

Genome-wide association study identifies novel breast cancer susceptibility loci

Douglas F. Easton et al.

NATURE (2007)

Article Statistics & Probability

The adaptive lasso and its oracle properties

Hui Zou

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2006)

Article Biochemical Research Methods

Discovering disease-genes by topological features in human protein-protein interaction network

Jianzhen Xu et al.

BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target

S. Horvath et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Statistics & Probability

Model selection and estimation in regression with grouped variables

M Yuan et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2006)

Review Genetics & Heredity

Genome-wide association studies: Theoretical and practical concerns

WYS Wang et al.

NATURE REVIEWS GENETICS (2005)

Article Statistics & Probability

Regularization and variable selection via the elastic net

H Zou et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2005)

Article Statistics & Probability

Sparsity and smoothness via the fused lasso

R Tibshirani et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2005)

Article Statistics & Probability

Least angle regression

B Efron et al.

ANNALS OF STATISTICS (2004)

Article Mathematical & Computational Biology

Classification of gene microarrays by penalized logistic regression

J Zhu et al.

BIOSTATISTICS (2004)

Article Biochemical Research Methods

A simple and efficient algorithm for gene selection using sparse logistic regression

SK Shevade et al.

BIOINFORMATICS (2003)

Article Mathematical & Computational Biology

A mixed-effects multinomial logistic regression model

D Hedeker

STATISTICS IN MEDICINE (2003)

Article Statistics & Probability

Variable selection via nonconcave penalized likelihood and its oracle properties

JQ Fan et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2001)

Article Multidisciplinary Sciences

Lethality and centrality in protein networks

H Jeong et al.

NATURE (2001)