Journal Article
. 2000 Dec;290(5500).
doi: 10.1126/science.290.5500.2319.

A global geometric framework for nonlinear dimensionality reduction

J B Tenenbaum 1 V de Silva  J C Langford  
Affiliations
  • PMID: 11125149
  •     545 citations

Abstract

Scientists working with large volumes of high-dimensional data, such as global climate patterns, stellar spectra, or human gene distributions, regularly confront the problem of dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. The human brain confronts the same problem in everyday perception, extracting from its high-dimensional sensory inputs-30,000 auditory nerve fibers or 10(6) optic nerve fibers-a manageably small number of perceptually relevant features. Here we describe an approach to solving dimensionality reduction problems that uses easily measured local metric information to learn the underlying global geometry of a data set. Unlike classical techniques such as principal component analysis (PCA) and multidimensional scaling (MDS), our approach is capable of discovering the nonlinear degrees of freedom that underlie complex natural observations, such as human handwriting or images of a face under different viewing conditions. In contrast to previous algorithms for nonlinear dimensionality reduction, ours efficiently computes a globally optimal solution, and, for an important class of data manifolds, is guaranteed to converge asymptotically to the true structure.

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NMR Biomed, 2011 Oct 01; 25(4). PMID: 21960175    Free PMC article.
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Grid cells, place cells, and geodesic generalization for spatial reinforcement learning.
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PLoS Comput Biol, 2011 Nov 03; 7(10). PMID: 22046115    Free PMC article.
Use of Self-Organizing Maps for Balanced Scorecard analysis to monitor the performance of dialysis clinic chains.
Isabella Cattinelli, Elena Bolzoni, +8 authors, Emanuele Gatti.
Health Care Manag Sci, 2011 Nov 16; 15(1). PMID: 22083440
Generation of tactile maps for artificial skin.
Simon McGregor, Daniel Polani, Kerstin Dautenhahn.
PLoS One, 2011 Nov 22; 6(11). PMID: 22102863    Free PMC article.
GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics.
Karen Sargsyan, Jon Wright, Carmay Lim.
Nucleic Acids Res, 2011 Dec 06; 40(3). PMID: 22139913    Free PMC article.
Facial expression recognition based on local binary patterns and kernel discriminant isomap.
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Manifold learning for human population structure studies.
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PLoS One, 2012 Jan 25; 7(1). PMID: 22272259    Free PMC article.
Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data.
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BMC Bioinformatics, 2012 Feb 10; 13. PMID: 22316103    Free PMC article.
The Geometry of Visual Perception: Retinotopic and Non-retinotopic Representations in the Human Visual System.
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Proc IEEE Inst Electr Electron Eng, 2010 Jan 01; 98(3). PMID: 22334763    Free PMC article.
Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit.
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PLoS One, 2012 Mar 03; 7(2). PMID: 22384178    Free PMC article.
Using sketch-map coordinates to analyze and bias molecular dynamics simulations.
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Proc Natl Acad Sci U S A, 2012 Mar 20; 109(14). PMID: 22427357    Free PMC article.
Histology image analysis for carcinoma detection and grading.
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Comput Methods Programs Biomed, 2012 Mar 23; 107(3). PMID: 22436890    Free PMC article.
New statistical method to analyze three-dimensional landmark configurations obtained with cone-beam CT: basic features and clinical application for rapid maxillary expansion.
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Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation.
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Visual systems for interactive exploration and mining of large-scale neuroimaging data archives.
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Front Neuroinform, 2012 Apr 27; 6. PMID: 22536181    Free PMC article.
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration.
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BMC Bioinformatics, 2012 May 25; 13 Suppl 7. PMID: 22595000    Free PMC article.
A New Method for Pseudo-increasing Frame Rates of Echocardiography Images Using Manifold Learning.
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J Med Signals Sens, 2012 May 19; 1(2). PMID: 22606665    Free PMC article.
Characterizing global evolutions of complex systems via intermediate network representations.
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Sci Rep, 2012 May 29; 2. PMID: 22639731    Free PMC article.
Protein surface representation and analysis by dimension reduction.
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Proteome Sci, 2012 Jul 05; 10 Suppl 1. PMID: 22759567    Free PMC article.
Generalization through the recurrent interaction of episodic memories: a model of the hippocampal system.
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Psychol Rev, 2012 Jul 11; 119(3). PMID: 22775499    Free PMC article.
Interplay between path and speed in decision making by high-dimensional stochastic gene regulatory networks.
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PLoS One, 2012 Jul 21; 7(7). PMID: 22815725    Free PMC article.
Evaluation of hepatic tumor response to yttrium-90 radioembolization therapy using texture signatures generated from contrast-enhanced CT images.
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"Good enough solutions" and the genetics of complex diseases.
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Random forest-based similarity measures for multi-modal classification of Alzheimer's disease.
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Reverse engineering the euglenoid movement.
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Proc Natl Acad Sci U S A, 2012 Oct 11; 109(44). PMID: 23047705    Free PMC article.
Patterns of inspiratory phase-dependent activity in the in vitro respiratory network.
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Locally learning biomedical data using diffusion frames.
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Physiol Meas, 2012 Nov 16; 33(12). PMID: 23151442    Free PMC article.
Clustering gene expression data using a diffraction-inspired framework.
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Deliverable navigation for multicriteria step and shoot IMRT treatment planning.
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Phys Med Biol, 2012 Dec 12; 58(1). PMID: 23221364    Free PMC article.
The body-machine interface: a new perspective on an old theme.
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Automatically clustering large-scale miRNA sequences: methods and experiments.
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BMC Genomics, 2013 Jan 11; 13 Suppl 8. PMID: 23282099    Free PMC article.
CSF and brain structural imaging markers of the Alzheimer's pathological cascade.
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PLoS One, 2013 Jan 04; 7(12). PMID: 23284610    Free PMC article.
Multi-kernel graph embedding for detection, Gleason grading of prostate cancer via MRI/MRS.
Pallavi Tiwari, John Kurhanewicz, Anant Madabhushi.
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IEEE Trans Med Imaging, 2013 Jan 22; 32(3). PMID: 23335665    Free PMC article.
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PLoS One, 2013 Mar 05; 8(2). PMID: 23457633    Free PMC article.
Discriminating external and internal causes for heading changes in freely flying Drosophila.
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PLoS Comput Biol, 2013 Mar 08; 9(2). PMID: 23468601    Free PMC article.
Highly comparative time-series analysis: the empirical structure of time series and their methods.
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Visual to Parametric Interaction (V2PI).
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PLoS One, 2013 Apr 05; 8(3). PMID: 23555552    Free PMC article.
From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.
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Sci Rep, 2013 Apr 09; 3. PMID: 23563395    Free PMC article.
New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.
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Texture Representations Using Subspace Embeddings.
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A linear optimal transportation framework for quantifying and visualizing variations in sets of images.
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Int J Comput Vis, 2013 Jun 05; 101(2). PMID: 23729991    Free PMC article.
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.
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J Chem Theory Comput, 2013 Jun 12; 9(4). PMID: 23750122    Free PMC article.
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Evaluation of Dimensionality-reduction Methods from Peptide Folding-unfolding Simulations.
Mojie Duan, Jue Fan, +2 authors, Shuanghong Huo.
J Chem Theory Comput, 2013 Jun 19; 9(5). PMID: 23772182    Free PMC article.
Locally linear embedding (LLE) for MRI based Alzheimer's disease classification.
Xin Liu, Duygu Tosun, +2 authors, Alzheimer's Disease Neuroimaging Initiative.
Neuroimage, 2013 Jun 25; 83. PMID: 23792982    Free PMC article.
Survey of encoding and decoding of visual stimulus via FMRI: an image analysis perspective.
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Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding.
Carlo Vittorio Cannistraci, Gregorio Alanis-Lobato, Timothy Ravasi.
Bioinformatics, 2013 Jul 03; 29(13). PMID: 23812985    Free PMC article.
Augmenting weak semantic cognitive maps with an "abstractness" dimension.
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Comput Intell Neurosci, 2013 Jul 11; 2013. PMID: 23840200    Free PMC article.
EEG/MEG source reconstruction with spatial-temporal two-way regularized regression.
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Neuroinformatics, 2013 Jul 12; 11(4). PMID: 23842791
Empirical intrinsic geometry for nonlinear modeling and time series filtering.
Ronen Talmon, Ronald R Coifman.
Proc Natl Acad Sci U S A, 2013 Jul 13; 110(31). PMID: 23847205    Free PMC article.
Explicit shape descriptors: novel morphologic features for histopathology classification.
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Fast discriminative stochastic neighbor embedding analysis.
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Comput Math Methods Med, 2013 Jul 16; 2013. PMID: 23853667    Free PMC article.
WESD--Weighted Spectral Distance for measuring shape dissimilarity.
Ender Konukoglu, Ben Glocker, Antonio Criminisi, Kilian M Pohl.
IEEE Trans Pattern Anal Mach Intell, 2013 Jul 23; 35(9). PMID: 23868785    Free PMC article.
Seismic target classification using a wavelet packet manifold in unattended ground sensors systems.
Jingchang Huang, Qianwei Zhou, +3 authors, Xiaobing Yuan.
Sensors (Basel), 2013 Jul 25; 13(7). PMID: 23881125    Free PMC article.
Statistical Shape Model for Manifold Regularization: Gleason grading of prostate histology.
Rachel Sparks, Anant Madabhushi.
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Compressive Sensing on Manifolds Using a Nonparametric Mixture of Factor Analyzers: Algorithm and Performance Bounds.
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IEEE Trans Signal Process, 2010 Dec 01; 58(12). PMID: 23894225    Free PMC article.
Incremental learning of skill collections based on intrinsic motivation.
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Using manifold learning for atlas selection in multi-atlas segmentation.
Albert K Hoang Duc, Marc Modat, +5 authors, Alzheimer’s Disease Neuroimaging Initiative.
PLoS One, 2013 Aug 13; 8(8). PMID: 23936376    Free PMC article.
Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks.
Adam Stevens, Daniel Hanson, +3 authors, Peter Clayton.
BMC Genomics, 2013 Aug 15; 14. PMID: 23941278    Free PMC article.
A Robust and Efficient Doubly Regularized Metric Learning Approach.
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Decreased small-world functional network connectivity and clustering across resting state networks in schizophrenia: an fMRI classification tutorial.
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Front Hum Neurosci, 2013 Sep 14; 7. PMID: 24032010    Free PMC article.
Transfer Learning for Activity Recognition: A Survey.
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Efficient computation of k-Nearest Neighbour Graphs for large high-dimensional data sets on GPU clusters.
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PLoS One, 2013 Oct 03; 8(9). PMID: 24086314    Free PMC article.
Spectral multidimensional scaling.
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Proc Natl Acad Sci U S A, 2013 Oct 11; 110(45). PMID: 24108352    Free PMC article.
Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.
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Proc Natl Acad Sci U S A, 2013 Oct 23; 110(45). PMID: 24145435    Free PMC article.
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ScientificWorldJournal, 2013 Oct 29; 2013. PMID: 24163638    Free PMC article.
Dual-force ISOMAP: a new relevance feedback method for medical image retrieval.
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Vector Diffusion Maps and the Connection Laplacian.
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Sci Rep, 2014 Jan 17; 4. PMID: 24430561    Free PMC article.
Structure-based neuron retrieval across Drosophila brains.
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Neuroinformatics, 2014 Jan 22; 12(3). PMID: 24446234
Understanding health and disease with multidimensional single-cell methods.
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A spatial division clustering method and low dimensional feature extraction technique based indoor positioning system.
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Sensors (Basel), 2014 Jan 24; 14(1). PMID: 24451470    Free PMC article.
An algorithm for finding biologically significant features in microarray data based on a priori manifold learning.
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PLoS One, 2014 Mar 07; 9(3). PMID: 24595155    Free PMC article.
Individualized statistical learning from medical image databases: application to identification of brain lesions.
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Multiview discriminative geometry preserving projection for image classification.
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ScientificWorldJournal, 2014 Apr 17; 2014. PMID: 24737997    Free PMC article.
Millisecond dynamics of RNA polymerase II translocation at atomic resolution.
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Fast k-NNG construction with GPU-based quick multi-select.
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PLoS One, 2014 May 09; 9(5). PMID: 24809341    Free PMC article.
Visualizing energy landscapes with metric disconnectivity graphs.
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Supervised extensions of chemography approaches: case studies of chemical liabilities assessment.
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J Cheminform, 2014 May 29; 6. PMID: 24868246    Free PMC article.
Functional organization of glomerular maps in the mouse accessory olfactory bulb.
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Nat Neurosci, 2014 Jun 02; 17(7). PMID: 24880215    Free PMC article.
Network analysis identifies protein clusters of functional importance in juvenile idiopathic arthritis.
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Arthritis Res Ther, 2014 Jun 03; 16(3). PMID: 24886659    Free PMC article.
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Anatomical Parts-Based Regression Using Non-Negative Matrix Factorization.
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Principal components of hand kinematics and neurophysiological signals in motor cortex during reach to grasp movements.
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J Neurophysiol, 2014 Jul 06; 112(8). PMID: 24990564    Free PMC article.
An alternative to current psychiatric classifications: a psychological landscape hypothesis based on an integrative, dynamical and multidimensional approach.
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Philos Ethics Humanit Med, 2014 Jul 19; 9. PMID: 25033795    Free PMC article.
Manifold Learning by Preserving Distance Orders.
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Dimensionality of object representations in monkey inferotemporal cortex.
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Automatic computation of left ventricular volume changes over a cardiac cycle from echocardiography images by nonlinear dimensionality reduction.
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Features extraction of flotation froth images and BP neural network soft-sensor model of concentrate grade optimized by shuffled cuckoo searching algorithm.
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ScientificWorldJournal, 2014 Aug 19; 2014. PMID: 25133210    Free PMC article.
Mapping the stereotyped behaviour of freely moving fruit flies.
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Cancer progression modeling using static sample data.
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Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images.
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Recent developments in methods for identifying reaction coordinates.
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Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.
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An efficient approach for preprocessing data from a large-scale chemical sensor array.
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Interest communities and flow roles in directed networks: the Twitter network of the UK riots.
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Locally linear denoising on image manifolds.
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Big behavioral data: psychology, ethology and the foundations of neuroscience.
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Nat Neurosci, 2014 Oct 29; 17(11). PMID: 25349912
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Dynamic stability of sequential stimulus representations in adapting neuronal networks.
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Data smashing: uncovering lurking order in data.
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Shape mode analysis exposes movement patterns in biology: flagella and flatworms as case studies.
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Correlated spatio-temporal data collection in wireless sensor networks based on low rank matrix approximation and optimized node sampling.
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Ahmad Shalbaf, Hamid Behnam.
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Metro maps of plant disease dynamics--automated mining of differences using hyperspectral images.
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Highlighting nonlinear patterns in population genetics datasets.
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Scaling up graph-based semisupervised learning via prototype vector machines.
Kai Zhang, Liang Lan, +2 authors, Bahram Parvin.
IEEE Trans Neural Netw Learn Syst, 2015 Feb 27; 26(3). PMID: 25720002    Free PMC article.
Locating landmarks on high-dimensional free energy surfaces.
Ming Chen, Tang-Qing Yu, Mark E Tuckerman.
Proc Natl Acad Sci U S A, 2015 Mar 05; 112(11). PMID: 25737545    Free PMC article.
Perspective: a dynamics-based classification of ventricular arrhythmias.
James N Weiss, Alan Garfinkel, +4 authors, Zhilin Qu.
J Mol Cell Cardiol, 2015 Mar 15; 82. PMID: 25769672    Free PMC article.
Review.
Temporal ordering and registration of images in studies of developmental dynamics.
Carmeline J Dsilva, Bomyi Lim, +3 authors, Stanislav Y Shvartsman.
Development, 2015 Apr 03; 142(9). PMID: 25834019    Free PMC article.
Constitutive activation of oncogenic PDGFRα-mutant proteins occurring in GIST patients induces receptor mislocalisation and alters PDGFRα signalling characteristics.
Christelle Bahlawane, René Eulenfeld, +9 authors, Serge Haan.
Cell Commun Signal, 2015 Apr 17; 13. PMID: 25880691    Free PMC article.
Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data.
Kirsten E Diggins, P Brent Ferrell, Jonathan M Irish.
Methods, 2015 May 17; 82. PMID: 25979346    Free PMC article.
Highly Cited.
Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow.
Andreas Schlitzer, V Sivakamasundari, +13 authors, Florent Ginhoux.
Nat Immunol, 2015 Jun 10; 16(7). PMID: 26054720
Highly Cited.
Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis.
Ludovico Silvestri, Marco Paciscopi, +4 authors, Francesco S Pavone.
Front Neuroanat, 2015 Jun 16; 9. PMID: 26074783    Free PMC article.
Visual perception of procedural textures: identifying perceptual dimensions and predicting generation models.
Jun Liu, Junyu Dong, +2 authors, Mike Chantler.
PLoS One, 2015 Jun 25; 10(6). PMID: 26106895    Free PMC article.
Bearing Fault Diagnosis Based on Statistical Locally Linear Embedding.
Xiang Wang, Yuan Zheng, Zhenzhou Zhao, Jinping Wang.
Sensors (Basel), 2015 Jul 15; 15(7). PMID: 26153771    Free PMC article.
Novel Online Dimensionality Reduction Method with Improved Topology Representing and Radial Basis Function Networks.
Shengqiao Ni, Jiancheng Lv, Zhehao Cheng, Mao Li.
PLoS One, 2015 Jul 15; 10(7). PMID: 26161960    Free PMC article.
Content-based image retrieval of digitized histopathology in boosted spectrally embedded spaces.
Akshay Sridhar, Scott Doyle, Anant Madabhushi.
J Pathol Inform, 2015 Jul 15; 6. PMID: 26167385    Free PMC article.
A Review of Feature Selection and Feature Extraction Methods Applied on Microarray Data.
Zena M Hira, Duncan F Gillies.
Adv Bioinformatics, 2015 Jul 15; 2015. PMID: 26170834    Free PMC article.
Highly Cited. Review.
Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization.
Joshua I Glaser, Bradley M Zamft, George M Church, Konrad P Kording.
PLoS One, 2015 Jul 21; 10(7). PMID: 26192446    Free PMC article.
Topological data analysis of contagion maps for examining spreading processes on networks.
Dane Taylor, Florian Klimm, +4 authors, Peter J Mucha.
Nat Commun, 2015 Jul 22; 6. PMID: 26194875    Free PMC article.
Sampling from Determinantal Point Processes for Scalable Manifold Learning.
Christian Wachinger, Polina Golland.
Inf Process Med Imaging, 2015 Jul 30; 24. PMID: 26221713    Free PMC article.
Research on Taxiway Path Optimization Based on Conflict Detection.
Hang Zhou, Xinxin Jiang.
PLoS One, 2015 Aug 01; 10(7). PMID: 26226485    Free PMC article.
Manifold Based Optimization for Single-Cell 3D Genome Reconstruction.
Jonas Paulsen, Odin Gramstad, Philippe Collas.
PLoS Comput Biol, 2015 Aug 12; 11(8). PMID: 26262780    Free PMC article.
A simplicial complex-based approach to unmixing tumor progression data.
Theodore Roman, Amir Nayyeri, Brittany Terese Fasy, Russell Schwartz.
BMC Bioinformatics, 2015 Aug 13; 16. PMID: 26264682    Free PMC article.
Dynein-deficient flagella respond to increased viscosity with contrasting changes in power and recovery strokes.
Kate S Wilson, Olivia Gonzalez, Susan K Dutcher, Philip V Bayly.
Cytoskeleton (Hoboken), 2015 Sep 01; 72(9). PMID: 26314933    Free PMC article.
A novel sparse coding algorithm for classification of tumors based on gene expression data.
Morteza Kolali Khormuji, Mehrnoosh Bazrafkan.
Med Biol Eng Comput, 2015 Sep 05; 54(6). PMID: 26337064
A thesaurus for a neural population code.
Elad Ganmor, Ronen Segev, Elad Schneidman.
Elife, 2015 Sep 09; 4. PMID: 26347983    Free PMC article.
Joint modeling of cell and nuclear shape variation.
Gregory R Johnson, Taraz E Buck, +2 authors, Robert F Murphy.
Mol Biol Cell, 2015 Sep 12; 26(22). PMID: 26354424    Free PMC article.
Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation.
Hai Su, Fuyong Xing, +2 authors, Lin Yang.
IEEE/ACM Trans Comput Biol Bioinform, 2014 Jul 01; 11(4). PMID: 26356342    Free PMC article.
Multi-atlas learner fusion: An efficient segmentation approach for large-scale data.
Andrew J Asman, Yuankai Huo, Andrew J Plassard, Bennett A Landman.
Med Image Anal, 2015 Sep 14; 26(1). PMID: 26363845    Free PMC article.
Multiple Manifold Clustering Using Curvature Constrained Path.
Amir Babaeian, Alireza Bayestehtashk, Mojtaba Bandarabadi.
PLoS One, 2015 Sep 17; 10(9). PMID: 26375819    Free PMC article.
The oncogenic FIP1L1-PDGFRα fusion protein displays skewed signaling properties compared to its wild-type PDGFRα counterpart.
Serge Haan, Christelle Bahlawane, +9 authors, Monique Yvonne Wiesinger.
JAKSTAT, 2015 Sep 29; 4(1). PMID: 26413425    Free PMC article.
Mining protein interactomes to improve their reliability and support the advancement of network medicine.
Gregorio Alanis-Lobato.
Front Genet, 2015 Oct 07; 6. PMID: 26442112    Free PMC article.
Review.
An enhanced data visualization method for diesel engine malfunction classification using multi-sensor signals.
Yiqing Li, Yu Wang, Yanyang Zi, Mingquan Zhang.
Sensors (Basel), 2015 Oct 28; 15(10). PMID: 26506347    Free PMC article.
ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis.
Emma Pierson, Christopher Yau.
Genome Biol, 2015 Nov 04; 16. PMID: 26527291    Free PMC article.
Highly Cited.
Scalable High-Performance Image Registration Framework by Unsupervised Deep Feature Representations Learning.
Guorong Wu, Minjeong Kim, +2 authors, Dinggang Shen.
IEEE Trans Biomed Eng, 2015 Nov 10; 63(7). PMID: 26552069    Free PMC article.
Echocardiography without electrocardiogram using nonlinear dimensionality reduction methods.
Ahmad Shalbaf, Zahra AlizadehSani, Hamid Behnam.
J Med Ultrason (2001), 2015 Nov 19; 42(2). PMID: 26576567
Groupwise Image Registration Guided by a Dynamic Digraph of Images.
Zhenyu Tang, Yong Fan.
Neuroinformatics, 2015 Nov 21; 14(2). PMID: 26585712
The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes.
Yuan Xie, Tobias Bergström, +20 authors, Lene Uhrbom.
EBioMedicine, 2015 Dec 03; 2(10). PMID: 26629530    Free PMC article.
Highly Cited.
Striatal dynamics explain duration judgments.
Thiago S Gouvêa, Tiago Monteiro, +3 authors, Joseph J Paton.
Elife, 2015 Dec 08; 4. PMID: 26641377    Free PMC article.
Mapping Chemical Selection Pathways for Designing Multicomponent Alloys: an informatics framework for materials design.
Srikant Srinivasan, Scott R Broderick, +5 authors, Krishna Rajan.
Sci Rep, 2015 Dec 19; 5. PMID: 26681142    Free PMC article.
Dynamic MRI Using SmooThness Regularization on Manifolds (SToRM).
Sunrita Poddar, Mathews Jacob.
IEEE Trans Med Imaging, 2015 Dec 20; 35(4). PMID: 26685228    Free PMC article.
Modeling epidemics on adaptively evolving networks: A data-mining perspective.
Assimakis A Kattis, Alexander Holiday, Ana-Andreea Stoica, Ioannis G Kevrekidis.
Virulence, 2015 Dec 24; 7(2). PMID: 26695450    Free PMC article.
Locally Embedding Autoencoders: A Semi-Supervised Manifold Learning Approach of Document Representation.
Chao Wei, Senlin Luo, +3 authors, Limin Pan.
PLoS One, 2016 Jan 20; 11(1). PMID: 26784692    Free PMC article.
Medoidshift clustering applied to genomic bulk tumor data.
Theodore Roman, Lu Xie, Russell Schwartz.
BMC Genomics, 2016 Jan 29; 17 Suppl 1. PMID: 26817708    Free PMC article.
A continuous linear optimal transport approach for pattern analysis in image datasets.
Soheil Kolouri, Akif B Tosun, John A Ozolek, Gustavo K Rohde.
Pattern Recognit, 2016 Feb 10; 51. PMID: 26858466    Free PMC article.
Learning intervention-induced deformations for non-rigid MR-CT registration and electrode localization in epilepsy patients.
John A Onofrey, Lawrence H Staib, Xenophon Papademetris.
Neuroimage Clin, 2016 Feb 24; 10. PMID: 26900569    Free PMC article.
Cardiorespiratory Coordination after Training and Detraining. A Principal Component Analysis Approach.
Natàlia Balagué, Jacob González, +5 authors, Josep L Ventura.
Front Physiol, 2016 Feb 24; 7. PMID: 26903884    Free PMC article.
Inherent structure versus geometric metric for state space discretization.
Hanzhong Liu, Minghai Li, Jue Fan, Shuanghong Huo.
J Comput Chem, 2016 Feb 27; 37(14). PMID: 26915811    Free PMC article.
A hybrid manifold learning algorithm for the diagnosis and prognostication of Alzheimer's disease.
Peng Dai, Femida Gwadry-Sridhar, Michael Bauer, Michael Borrie.
AMIA Annu Symp Proc, 2015 Jan 01; 2015. PMID: 26958180    Free PMC article.
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.
Lin-Tai Da, Fátima Pardo-Avila, +5 authors, Xuhui Huang.
Nat Commun, 2016 Apr 20; 7. PMID: 27091704    Free PMC article.
Extensions to a manifold learning framework for time-series analysis on dynamic manifolds in bioelectric signals.
Burak Erem, Ramon Martinez Orellana, +7 authors, Dana H Brooks.
Phys Rev E, 2016 May 14; 93(4). PMID: 27176304    Free PMC article.
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.
Joshua D Welch, Alexander J Hartemink, Jan F Prins.
Genome Biol, 2016 May 25; 17(1). PMID: 27215581    Free PMC article.
Highly Cited.
Regularized Embedded Multiple Kernel Dimensionality Reduction for Mine Signal Processing.
Shuang Li, Bing Liu, Chen Zhang.
Comput Intell Neurosci, 2016 Jun 02; 2016. PMID: 27247562    Free PMC article.
Out-of-Sample Extrapolation utilizing Semi-Supervised Manifold Learning (OSE-SSL): Content Based Image Retrieval for Histopathology Images.
Rachel Sparks, Anant Madabhushi.
Sci Rep, 2016 Jun 07; 6. PMID: 27264985    Free PMC article.
Quantifying Individual Brain Connectivity with Functional Principal Component Analysis for Networks.
Alexander Petersen, Jianyang Zhao, Owen Carmichael, Hans-Georg Müller.
Brain Connect, 2016 Jun 09; 6(7). PMID: 27267074    Free PMC article.
Uncovering low-dimensional, miR-based signatures of acute myeloid and lymphoblastic leukemias with a machine-learning-driven network approach.
Julián Candia, Srujana Cherukuri, +4 authors, Wolfgang Losert.
Converg Sci Phys Oncol, 2016 Jun 09; 1(2). PMID: 27274862    Free PMC article.
Dense 3D Face Alignment from 2D Videos in Real-Time.
László A Jeni, Jeffrey F Cohn, Takeo Kanade.
IEEE Int Conf Autom Face Gesture Recognit Workshops, 2016 Jun 14; 1. PMID: 27293385    Free PMC article.
Prediction of high-dimensional states subject to respiratory motion: a manifold learning approach.
Wenyang Liu, Amit Sawant, Dan Ruan.
Phys Med Biol, 2016 Jun 15; 61(13). PMID: 27299958    Free PMC article.
A Novel Pre-Processing Technique for Original Feature Matrix of Electronic Nose Based on Supervised Locality Preserving Projections.
Pengfei Jia, Tailai Huang, +3 authors, Lidan Wang.
Sensors (Basel), 2016 Jul 05; 16(7). PMID: 27376295    Free PMC article.
Supervised Filter Learning for Representation Based Face Recognition.
Chao Bi, Lei Zhang, +4 authors, Baoxue Zhang.
PLoS One, 2016 Jul 16; 11(7). PMID: 27416030    Free PMC article.
Adaptive Dimensionality Reduction with Semi-Supervision (AdDReSS): Classifying Multi-Attribute Biomedical Data.
George Lee, David Edmundo Romo Bucheli, Anant Madabhushi.
PLoS One, 2016 Jul 16; 11(7). PMID: 27421116    Free PMC article.
Mass cytometry: blessed with the curse of dimensionality.
Evan W Newell, Yang Cheng.
Nat Immunol, 2016 Jul 21; 17(8). PMID: 27434000
Highly Cited. Review.
Efficient embedding of complex networks to hyperbolic space via their Laplacian.
Gregorio Alanis-Lobato, Pablo Mier, Miguel A Andrade-Navarro.
Sci Rep, 2016 Jul 23; 6. PMID: 27445157    Free PMC article.
A discriminative feature selection approach for shape analysis: Application to fetal brain cortical folding.
J Pontabry, F Rousseau, +2 authors, J-L Dietemann.
Med Image Anal, 2016 Aug 09; 35. PMID: 27498089    Free PMC article.
Accurate Estimation of the Intrinsic Dimension Using Graph Distances: Unraveling the Geometric Complexity of Datasets.
Daniele Granata, Vincenzo Carnevale.
Sci Rep, 2016 Aug 12; 6. PMID: 27510265    Free PMC article.
A preliminary review of influential works in data-driven discovery.
Mark Stalzer, Chris Mentzel.
Springerplus, 2016 Aug 20; 5(1). PMID: 27540499    Free PMC article.
Review.
Big data and deep data in scanning and electron microscopies: deriving functionality from multidimensional data sets.
Alex Belianinov, Rama Vasudevan, +10 authors, Sergei Kalinin.
Adv Struct Chem Imaging, 2015 Jan 01; 1. PMID: 27547705    Free PMC article.
Review.
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data.
David DeTomaso, Nir Yosef.
BMC Bioinformatics, 2016 Aug 25; 17(1). PMID: 27553427    Free PMC article.
Reinforcement Learning and Episodic Memory in Humans and Animals: An Integrative Framework.
Samuel J Gershman, Nathaniel D Daw.
Annu Rev Psychol, 2016 Sep 14; 68. PMID: 27618944    Free PMC article.
Highly Cited. Review.
Unsupervised Learning for Robust Respiratory Signal Estimation From X-Ray Fluoroscopy.
Peter Fischer, Thomas Pohl, +2 authors, Joachim Hornegger.
IEEE Trans Med Imaging, 2016 Sep 23; 36(4). PMID: 27654320    Free PMC article.
Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline.
Hao Chen, Mai Chan Lau, +3 authors, Jinmiao Chen.
PLoS Comput Biol, 2016 Sep 24; 12(9). PMID: 27662185    Free PMC article.
Highly Cited.
Role of the immune system in the peritoneal tumor spread of high grade serous ovarian cancer.
Katharina Auer, Anna Bachmayr-Heyda, +7 authors, Dietmar Pils.
Oncotarget, 2016 Sep 26; 7(38). PMID: 27665539    Free PMC article.
Identifying Significant Features in Cancer Methylation Data Using Gene Pathway Segmentation.
Zena M Hira, Duncan F Gillies.
Cancer Inform, 2016 Oct 01; 15. PMID: 27688706    Free PMC article.
Single-Cell Transcriptomics Bioinformatics and Computational Challenges.
Olivier B Poirion, Xun Zhu, Travers Ching, Lana Garmire.
Front Genet, 2016 Oct 07; 7. PMID: 27708664    Free PMC article.
Review.
Deep learning architecture for air quality predictions.
Xiang Li, Ling Peng, +2 authors, Tianhe Chi.
Environ Sci Pollut Res Int, 2016 Oct 14; 23(22). PMID: 27734318
The intrinsic geometry of the human brain connectome.
Allen Q Ye, Olusola A Ajilore, +8 authors, Alex D Leow.
Brain Inform, 2016 Oct 18; 2(4). PMID: 27747562    Free PMC article.
Situating the default-mode network along a principal gradient of macroscale cortical organization.
Daniel S Margulies, Satrajit S Ghosh, +9 authors, Jonathan Smallwood.
Proc Natl Acad Sci U S A, 2016 Nov 03; 113(44). PMID: 27791099    Free PMC article.
Highly Cited.
Public Health and Epidemiology Informatics.
A Flahault, A Bar-Hen, N Paragios.
Yearb Med Inform, 2016 Nov 11; (1). PMID: 27830257    Free PMC article.
node2vec: Scalable Feature Learning for Networks.
Aditya Grover, Jure Leskovec.
KDD, 2016 Nov 18; 2016. PMID: 27853626    Free PMC article.
Highly Cited.
Kernel Based Nonlinear Dimensionality Reduction and Classification for Genomic Microarray.
Xuehua Li, Lan Shu.
Sensors (Basel), 2008 Jul 15; 8(7). PMID: 27879930    Free PMC article.
Scale-Dependent Signal Identification in Low-Dimensional Subspace: Motor Imagery Task Classification.
Qingshan She, Haitao Gan, +3 authors, Yingchun Zhang.
Neural Plast, 2016 Nov 29; 2016. PMID: 27891256    Free PMC article.
Brain transcriptome atlases: a computational perspective.
Ahmed Mahfouz, Sjoerd M H Huisman, Boudewijn P F Lelieveldt, Marcel J T Reinders.
Brain Struct Funct, 2016 Dec 03; 222(4). PMID: 27909802    Free PMC article.
Review.
Manifold regularization for sparse unmixing of hyperspectral images.
Junmin Liu, Chunxia Zhang, +2 authors, Yuelin Gao.
Springerplus, 2016 Dec 10; 5(1). PMID: 27933263    Free PMC article.
Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex.
Benjamin R Cowley, Matthew A Smith, Adam Kohn, Byron M Yu.
PLoS Comput Biol, 2016 Dec 10; 12(12). PMID: 27935935    Free PMC article.
Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.
Anand Bhaskar, Adel Javanmard, Thomas A Courtade, David Tse.
Bioinformatics, 2016 Dec 28; 33(6). PMID: 28025204    Free PMC article.
Radiomics: a new application from established techniques.
Vishwa Parekh, Michael A Jacobs.
Expert Rev Precis Med Drug Dev, 2017 Jan 04; 1(2). PMID: 28042608    Free PMC article.
Highly Cited.
Parametrization of white matter manifold-like structures using principal surfaces.
Chen Yue, Vadim Zipunnikov, +4 authors, Brian Caffo.
J Am Stat Assoc, 2017 Jan 17; 111(515). PMID: 28090127    Free PMC article.
Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.
Jiaoyun Yang, Haipeng Wang, +2 authors, Gil Alterovitz.
BMC Bioinformatics, 2017 Jan 21; 18(1). PMID: 28103789    Free PMC article.
Principal Graph and Structure Learning Based on Reversed Graph Embedding.
Qi Mao, Li Wang, Ivor W Tsang, Yijun Sun.
IEEE Trans Pattern Anal Mach Intell, 2017 Jan 24; 39(11). PMID: 28114001    Free PMC article.
Text Authorship Identified Using the Dynamics of Word Co-Occurrence Networks.
Camilo Akimushkin, Diego Raphael Amancio, Osvaldo Novais Oliveira.
PLoS One, 2017 Jan 27; 12(1). PMID: 28125703    Free PMC article.
Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.
Jacqueline M Tabler, Maggie M Rigney, +11 authors, John B Wallingford.
Elife, 2017 Feb 09; 6. PMID: 28177282    Free PMC article.
A Systematic Relationship Between Functional Connectivity and Intracortical Myelin in the Human Cerebral Cortex.
Julia M Huntenburg, Pierre-Louis Bazin, +3 authors, Daniel S Margulies.
Cereb Cortex, 2017 Feb 12; 27(2). PMID: 28184415    Free PMC article.
Highly Cited.
Some Results on Mean Square Error for Factor Score Prediction.
Wim P Krijnen.
Psychometrika, 2006 Jun 01; 71(2). PMID: 28197953
Mapping and classifying molecules from a high-throughput structural database.
Sandip De, Felix Musil, +2 authors, Michele Ceriotti.
J Cheminform, 2017 Feb 17; 9. PMID: 28203290    Free PMC article.
Shape analysis of the cingulum, uncinate and arcuate fasciculi in patients with bipolar disorder.
Zhong Yi Sun, Josselin Houenou, +17 authors, Jean-François Mangin.
J Psychiatry Neurosci, 2017 Feb 25; 42(1). PMID: 28234596    Free PMC article.
Prediction and classification of Alzheimer disease based on quantification of MRI deformation.
Xiaojing Long, Lifang Chen, +2 authors, Alzheimer’s Disease Neuroimaging Initiative.
PLoS One, 2017 Mar 07; 12(3). PMID: 28264071    Free PMC article.
Toward a severity index for ROP: An unsupervised approach.
Peng Tian, Esra Ataer-Cansizoglu, +6 authors, Deniz Erdogmus.
Annu Int Conf IEEE Eng Med Biol Soc, 2017 Mar 09; 2016. PMID: 28268567    Free PMC article.
On biometric systems: electrocardiogram Gaussianity and data synthesis.
Wael Louis, Shahad Abdulnour, Sahar Javaher Haghighi, Dimitrios Hatzinakos.
EURASIP J Bioinform Syst Biol, 2017 Mar 09; 2017. PMID: 28270847    Free PMC article.
Subgroup detection in genotype data using invariant coordinate selection.
Daniel Fischer, Mervi Honkatukia, +4 authors, Johanna Vilkki.
BMC Bioinformatics, 2017 Mar 18; 18(1). PMID: 28302061    Free PMC article.
Using Dimensionality Reduction Techniques for Refining Passive Indoor Positioning Systems Based on Radio Fingerprinting.
Pedro E Lopez-de-Teruel, Oscar Canovas, Felix J Garcia.
Sensors (Basel), 2017 Apr 20; 17(4). PMID: 28420133    Free PMC article.
A meta-analysis testing eusocial co-option theories in termite gut physiology and symbiosis.
Michael E Scharf, Yunpeng Cai, +3 authors, Drion G Boucias.
Commun Integr Biol, 2017 Apr 22; 10(2). PMID: 28428832    Free PMC article.
Gaze Behavior Consistency among Older and Younger Adults When Looking at Emotional Faces.
Laurence Chaby, Isabelle Hupont, +2 authors, Mohamed Chetouani.
Front Psychol, 2017 Apr 30; 8. PMID: 28450841    Free PMC article.
Closed-loop neuromodulation systems: next-generation treatments for psychiatric illness.
Meng-Chen Lo, Alik S Widge.
Int Rev Psychiatry, 2017 May 20; 29(2). PMID: 28523978    Free PMC article.
Review.
Characterizing Dynamic Walking Patterns and Detecting Falls with Wearable Sensors Using Gaussian Process Methods.
Taehwan Kim, Jeongho Park, +2 authors, Jooyoung Park.
Sensors (Basel), 2017 May 23; 17(5). PMID: 28531125    Free PMC article.
T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking.
Lin-Tai Da, Chao E, +3 authors, Jin Yu.
Nucleic Acids Res, 2017 Jun 03; 45(13). PMID: 28575393    Free PMC article.
COMBINING REGIONAL METRICS FOR DISEASE-RELATED BRAIN POPULATION ANALYSIS.
Dong Hye Ye, Jihun Hamm, Kilian M Pohl.
Proc IEEE Int Symp Biomed Imaging, 2012 May 01; 2012. PMID: 28593031    Free PMC article.
AUTO-ENCODING OF DISCRIMINATING MORPHOMETRY FROM CARDIAC MRI.
Dong Hye Ye, Benoit Desjardins, +2 authors, Kilian M Pohl.
Proc IEEE Int Symp Biomed Imaging, 2014 Apr 01; 2014. PMID: 28593032    Free PMC article.
Neural Manifolds for the Control of Movement.
Juan A Gallego, Matthew G Perich, Lee E Miller, Sara A Solla.
Neuron, 2017 Jun 09; 94(5). PMID: 28595054    Free PMC article.
Highly Cited. Review.
Human Blood Monocyte Subsets: A New Gating Strategy Defined Using Cell Surface Markers Identified by Mass Cytometry.
Graham D Thomas, Anouk A J Hamers, +6 authors, Catherine C Hedrick.
Arterioscler Thromb Vasc Biol, 2017 Jun 10; 37(8). PMID: 28596372    Free PMC article.
Highly Cited.
Semi-Supervised Pattern Classification: Application to Structural MRI of Alzheimer's Disease.
Dong Hye Ye, Kilian M Pohl, Christos Davatzikos.
Int Workshop Pattern Recognit Neuroimaging, 2011 May 01; 2011. PMID: 28603748    Free PMC article.
Morphological Classification: Application to Cardiac MRI of Tetralogy of Fallot.
Dong Hye Ye, Harold Litt, Christos Davatzikos, Kilian M Pohl.
Funct Imaging Model Heart, 2011 May 01; 6666. PMID: 28626838    Free PMC article.
Cardiorespiratory Coordination in Repeated Maximal Exercise.
Sergi Garcia-Retortillo, Casimiro Javierre, +2 authors, Natàlia Balagué.
Front Physiol, 2017 Jun 24; 8. PMID: 28638349    Free PMC article.
Block-Diagonal Constrained Low-Rank and Sparse Graph for Discriminant Analysis of Image Data.
Tan Guo, Xiaoheng Tan, +2 authors, Lu Deng.
Sensors (Basel), 2017 Jun 24; 17(7). PMID: 28640206    Free PMC article.
Task-dependent recurrent dynamics in visual cortex.
Satohiro Tajima, Kowa Koida, +3 authors, Hidehiko Komatsu.
Elife, 2017 Jul 25; 6. PMID: 28737487    Free PMC article.
Assessment of the water quality monitoring network of the Piabanha River experimental watersheds in Rio de Janeiro, Brazil, using autoassociative neural networks.
Mariana D Villas-Boas, Francisco Olivera, Jose Paulo S de Azevedo.
Environ Monit Assess, 2017 Aug 09; 189(9). PMID: 28785884
Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.
Jiayi Wu, Yong-Bei Ma, +5 authors, Youdong Mao.
PLoS One, 2017 Aug 09; 12(8). PMID: 28786986    Free PMC article.
Direct Learning Hidden Excited State Interaction Patterns from ab initio Dynamics and Its Implication as Alternative Molecular Mechanism Models.
Fang Liu, Likai Du, Dongju Zhang, Jun Gao.
Sci Rep, 2017 Aug 20; 7(1). PMID: 28821842    Free PMC article.
Alzheimer's Disease Early Diagnosis Using Manifold-Based Semi-Supervised Learning.
Moein Khajehnejad, Forough Habibollahi Saatlou, Hoda Mohammadzade.
Brain Sci, 2017 Aug 22; 7(8). PMID: 28825647    Free PMC article.
Reconstruction of normal forms by learning informed observation geometries from data.
Or Yair, Ronen Talmon, Ronald R Coifman, Ioannis G Kevrekidis.
Proc Natl Acad Sci U S A, 2017 Aug 24; 114(38). PMID: 28831006    Free PMC article.
Data-analysis strategies for image-based cell profiling.
Juan C Caicedo, Sam Cooper, +21 authors, Anne E Carpenter.
Nat Methods, 2017 Sep 01; 14(9). PMID: 28858338    Free PMC article.
Highly Cited.
Acoustical Emission Analysis by Unsupervised Graph Mining: A Novel Biomarker of Knee Health Status.
Sinan Hersek, Maziyar Baran Pouyan, +5 authors, Omer T Inan.
IEEE Trans Biomed Eng, 2017 Sep 01; 65(6). PMID: 28858782    Free PMC article.
Predicting multicellular function through multi-layer tissue networks.
Marinka Zitnik, Jure Leskovec.
Bioinformatics, 2017 Sep 09; 33(14). PMID: 28881986    Free PMC article.
Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space.
Lei Huang, Li Liao, Cathy H Wu.
PLoS One, 2017 Sep 09; 12(9). PMID: 28886027    Free PMC article.
Neural Activity Patterns in the Human Brain Reflect Tactile Stickiness Perception.
Junsuk Kim, Jiwon Yeon, +3 authors, Sung-Phil Kim.
Front Hum Neurosci, 2017 Sep 25; 11. PMID: 28936171    Free PMC article.
Noise reduction in intracranial pressure signal using causal shape manifolds.
Abhejit Rajagopal, Robert B Hamilton, Fabien Scalzo.
Biomed Signal Process Control, 2016 Jul 01; 28. PMID: 28936230    Free PMC article.
Estimating the intrinsic dimension of datasets by a minimal neighborhood information.
Elena Facco, Maria d'Errico, Alex Rodriguez, Alessandro Laio.
Sci Rep, 2017 Sep 25; 7(1). PMID: 28939866    Free PMC article.
The Hidden Flow Structure and Metric Space of Network Embedding Algorithms Based on Random Walks.
Weiwei Gu, Li Gong, Xiaodan Lou, Jiang Zhang.
Sci Rep, 2017 Oct 17; 7(1). PMID: 29030547    Free PMC article.
Automated deconvolution of structured mixtures from heterogeneous tumor genomic data.
Theodore Roman, Lu Xie, Russell Schwartz.
PLoS Comput Biol, 2017 Oct 24; 13(10). PMID: 29059177    Free PMC article.
Embedding graphs in Lorentzian spacetime.
James R Clough, Tim S Evans.
PLoS One, 2017 Nov 07; 12(11). PMID: 29107967    Free PMC article.
Fault Detection of Bearing Systems through EEMD and Optimization Algorithm.
Dong-Han Lee, Jong-Hyo Ahn, Bong-Hwan Koh.
Sensors (Basel), 2017 Nov 17; 17(11). PMID: 29143772    Free PMC article.
Machine learning meets complex networks via coalescent embedding in the hyperbolic space.
Alessandro Muscoloni, Josephine Maria Thomas, +2 authors, Carlo Vittorio Cannistraci.
Nat Commun, 2017 Nov 21; 8(1). PMID: 29151574    Free PMC article.
Integrated radiomic framework for breast cancer and tumor biology using advanced machine learning and multiparametric MRI.
Vishwa S Parekh, Michael A Jacobs.
NPJ Breast Cancer, 2017 Nov 21; 3. PMID: 29152563    Free PMC article.
Efficient Generation of Transcriptomic Profiles by Random Composite Measurements.
Brian Cleary, Le Cong, +2 authors, Aviv Regev.
Cell, 2017 Nov 21; 171(6). PMID: 29153835    Free PMC article.
Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information.
Ryo Yokota, Yuki Kaminaga, Tetsuya J Kobayashi.
Front Immunol, 2017 Dec 01; 8. PMID: 29187849    Free PMC article.
Similarity-based Regularized Latent Feature Model for Link Prediction in Bipartite Networks.
Wenjun Wang, Xue Chen, Pengfei Jiao, Di Jin.
Sci Rep, 2017 Dec 07; 7(1). PMID: 29208988    Free PMC article.
Elastic K-means using posterior probability.
Aihua Zheng, Bo Jiang, +2 authors, Chris Ding.
PLoS One, 2017 Dec 15; 12(12). PMID: 29240756    Free PMC article.
Embedding Learning with Events in Heterogeneous Information Networks.
Huan Gui, Jialu Liu, +4 authors, Jiawei Han.
IEEE Trans Knowl Data Eng, 2017 Dec 16; 29(11). PMID: 29242698    Free PMC article.
Detecting intermediate protein conformations using algebraic topology.
Nurit Haspel, Dong Luo, Eduardo González.
BMC Bioinformatics, 2017 Dec 16; 18(Suppl 15). PMID: 29244007    Free PMC article.
LEICA: Laplacian eigenmaps for group ICA decomposition of fMRI data.
Chihuang Liu, Joseph JaJa, Luiz Pessoa.
Neuroimage, 2017 Dec 17; 169. PMID: 29246846    Free PMC article.
Modelling neuroanatomical variation during childhood and adolescence with neighbourhood-preserving embedding.
Gareth Ball, Chris Adamson, Richard Beare, Marc L Seal.
Sci Rep, 2017 Dec 21; 7(1). PMID: 29259302    Free PMC article.
Energy Harvesting Hybrid Acoustic-Optical Underwater Wireless Sensor Networks Localization.
Nasir Saeed, Abdulkadir Celik, Tareq Y Al-Naffouri, Mohamed-Slim Alouini.
Sensors (Basel), 2017 Dec 27; 18(1). PMID: 29278405    Free PMC article.
High throughput automated analysis of big flow cytometry data.
Albina Rahim, Justin Meskas, +8 authors, Ryan R Brinkman.
Methods, 2017 Dec 31; 134-135. PMID: 29287915    Free PMC article.
Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer.
Gary Wilk, Rosemary Braun.
Nucleic Acids Res, 2018 Jan 03; 46(3). PMID: 29294105    Free PMC article.
Manifold Learning of COPD.
Felix J S Bragman, Jamie R McClelland, +2 authors, David J Hawkes.
Med Image Comput Comput Assist Interv, 2018 Jan 09; 10435. PMID: 29308455    Free PMC article.
ShinyGPA: An interactive visualization toolkit for investigating pleiotropic architecture using GWAS datasets.
Emma Kortemeier, Paula S Ramos, +3 authors, Dongjun Chung.
PLoS One, 2018 Jan 09; 13(1). PMID: 29309429    Free PMC article.
Uremic Solute-Aryl Hydrocarbon Receptor-Tissue Factor Axis Associates with Thrombosis after Vascular Injury in Humans.
Vijaya B Kolachalama, Moshe Shashar, +11 authors, Vipul C Chitalia.
J Am Soc Nephrol, 2018 Jan 19; 29(3). PMID: 29343519    Free PMC article.
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Computational discovery of extremal microstructure families.
Desai Chen, Mélina Skouras, Bo Zhu, Wojciech Matusik.
Sci Adv, 2018 Jan 30; 4(1). PMID: 29376124    Free PMC article.
Reconstructing spatial organizations of chromosomes through manifold learning.
Guangxiang Zhu, Wenxuan Deng, +6 authors, Jianyang Zeng.
Nucleic Acids Res, 2018 Feb 07; 46(8). PMID: 29408992    Free PMC article.
Transition Manifolds of Complex Metastable Systems: Theory and Data-Driven Computation of Effective Dynamics.
Andreas Bittracher, Péter Koltai, +3 authors, Christof Schütte.
J Nonlinear Sci, 2018 Mar 13; 28(2). PMID: 29527099    Free PMC article.
Spatio-spectral classification of hyperspectral images for brain cancer detection during surgical operations.
Himar Fabelo, Samuel Ortega, +19 authors, Roberto Sarmiento.
PLoS One, 2018 Mar 20; 13(3). PMID: 29554126    Free PMC article.
Resonance-Based Time-Frequency Manifold for Feature Extraction of Ship-Radiated Noise.
Jiaquan Yan, Haixin Sun, +2 authors, En Cheng.
Sensors (Basel), 2018 Mar 23; 18(4). PMID: 29565288    Free PMC article.
Transcriptomics and machine learning predict diagnosis and severity of growth hormone deficiency.
Philip G Murray, Adam Stevens, +3 authors, Peter E Clayton.
JCI Insight, 2018 Apr 06; 3(7). PMID: 29618660    Free PMC article.
The latent geometry of the human protein interaction network.
Gregorio Alanis-Lobato, Pablo Mier, Miguel Andrade-Navarro.
Bioinformatics, 2018 Apr 11; 34(16). PMID: 29635317    Free PMC article.
Towards a new approach to reveal dynamical organization of the brain using topological data analysis.
Manish Saggar, Olaf Sporns, +4 authors, Allan L Reiss.
Nat Commun, 2018 Apr 13; 9(1). PMID: 29643350    Free PMC article.
Advancing systems immunology through data-driven statistical analysis.
Linda E Fong, Andrés R Muñoz-Rojas, Kathryn Miller-Jensen.
Curr Opin Biotechnol, 2018 Apr 16; 52. PMID: 29656236    Free PMC article.
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Feature Genes Selection Using Supervised Locally Linear Embedding and Correlation Coefficient for Microarray Classification.
Jiucheng Xu, Huiyu Mu, Yun Wang, Fangzhou Huang.
Comput Math Methods Med, 2018 Apr 19; 2018. PMID: 29666661    Free PMC article.
Analysis of Big Data in Gait Biomechanics: Current Trends and Future Directions.
Angkoon Phinyomark, Giovanni Petri, +2 authors, Reed Ferber.
J Med Biol Eng, 2018 Apr 20; 38(2). PMID: 29670502    Free PMC article.
Dense 3D Face Alignment from 2D Video for Real-Time Use.
László A Jeni, Jeffrey F Cohn, Takeo Kanade.
Image Vis Comput, 2017 Feb 01; 58. PMID: 29731533    Free PMC article.
Voting Simulation based Agglomerative Hierarchical Method for Network Community Detection.
Jianjun Cheng, Xinhong Yin, +4 authors, Xiaoyun Chen.
Sci Rep, 2018 May 26; 8(1). PMID: 29795231    Free PMC article.
An Enhanced Visualization Method to Aid Behavioral Trajectory Pattern Recognition Infrastructure for Big Longitudinal Data.
Hua Fang, Zhaoyang Zhang.
IEEE Trans Big Data, 2018 Jun 12; 4(2). PMID: 29888298    Free PMC article.
High-veracity functional imaging in scanning probe microscopy via Graph-Bootstrapping.
Xin Li, Liam Collins, +3 authors, Sergei V Kalinin.
Nat Commun, 2018 Jun 23; 9(1). PMID: 29930246    Free PMC article.
Using Spectral Representation to Classify Proteins' Conformational States.
Seyed Majid Saberi Fathi, Jack A Tuszynski.
Int J Mol Sci, 2018 Jul 20; 19(7). PMID: 30021967    Free PMC article.
Thought Chart: tracking the thought with manifold learning during emotion regulation.
Mengqi Xing, Johnson GadElkarim, +5 authors, Alex Leow.
Brain Inform, 2018 Jul 20; 5(2). PMID: 30022317    Free PMC article.
GPseudoRank: a permutation sampler for single cell orderings.
Magdalena E Strauß, John E Reid, Lorenz Wernisch.
Bioinformatics, 2018 Jul 28; 35(4). PMID: 30052778    Free PMC article.
Single-cell RNA sequencing technologies and bioinformatics pipelines.
Byungjin Hwang, Ji Hyun Lee, Duhee Bang.
Exp Mol Med, 2018 Aug 10; 50(8). PMID: 30089861    Free PMC article.
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Towards an Efficient One-Class Classifier for Mobile Devices and Wearable Sensors on the Context of Personal Risk Detection.
Luis A Trejo, Ari Yair Barrera-Animas.
Sensors (Basel), 2018 Sep 12; 18(9). PMID: 30200188    Free PMC article.
Machine Learning for Drug-Target Interaction Prediction.
Ruolan Chen, Xiangrong Liu, +2 authors, Juan Liu.
Molecules, 2018 Sep 12; 23(9). PMID: 30200333    Free PMC article.
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AspEm: Embedding Learning by Aspects in Heterogeneous Information Networks.
Yu Shi, Huan Gui, +2 authors, Jiawei Han.
Proc SIAM Int Conf Data Min, 2018 Sep 18; 2018. PMID: 30221081    Free PMC article.
Machine-learning based lipid mediator serum concentration patterns allow identification of multiple sclerosis patients with high accuracy.
Jörn Lötsch, Susanne Schiffmann, +7 authors, Alfred Ultsch.
Sci Rep, 2018 Oct 07; 8(1). PMID: 30291263    Free PMC article.
NeuroCave: A web-based immersive visualization platform for exploring connectome datasets.
Johnson J G Keiriz, Liang Zhan, +2 authors, Angus G Forbes.
Netw Neurosci, 2018 Oct 09; 2(3). PMID: 30294703    Free PMC article.
Nondestructive Inspection of Reinforced Concrete Utility Poles with ISOMAP and Random Forest.
Saeed Ullah, Minjoong Jeong, Woosang Lee.
Sensors (Basel), 2018 Oct 18; 18(10). PMID: 30326580    Free PMC article.
Improving the Security and QoE in Mobile Devices through an Intelligent and Adaptive Continuous Authentication System.
José María Jorquera Valero, Pedro Miguel Sánchez Sánchez, +4 authors, Gregorio Martínez Pérez.
Sensors (Basel), 2018 Nov 08; 18(11). PMID: 30400377    Free PMC article.
Statistical Shape Analysis of Large Datasets Based on Diffeomorphic Iterative Centroids.
Claire Cury, Joan A Glaunès, +6 authors, Imagen Consortium.
Front Neurosci, 2018 Nov 30; 12. PMID: 30483045    Free PMC article.
Manifold learning and maximum likelihood estimation for hyperbolic network embedding.
Gregorio Alanis-Lobato, Pablo Mier, Miguel A Andrade-Navarro.
Appl Netw Sci, 2016 Jan 01; 1(1). PMID: 30533502    Free PMC article.
Informatics tools to assess the success of procedural harmonization in preclinical multicenter biomarker discovery study on post-traumatic epileptogenesis.
Robert Ciszek, Xavier Ekolle Ndode-Ekane, +16 authors, Asla Pitkänen.
Epilepsy Res, 2019 Jan 04; 150. PMID: 30605864    Free PMC article.
Mapping changes in housing in sub-Saharan Africa from 2000 to 2015.
Lucy S Tusting, Donal Bisanzio, +13 authors, Samir Bhatt.
Nature, 2019 Mar 29; 568(7752). PMID: 30918405    Free PMC article.
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Weighted Graph Regularized Sparse Brain Network Construction for MCI Identification.
Renping Yu, Lishan Qiao, +3 authors, Dinggang Shen.
Pattern Recognit, 2019 Oct 04; 90. PMID: 31579345    Free PMC article.
Real-time 3D reconstruction from single-photon lidar data using plug-and-play point cloud denoisers.
Julián Tachella, Yoann Altmann, +5 authors, Stephen McLaughlin.
Nat Commun, 2019 Nov 05; 10(1). PMID: 31676824    Free PMC article.
Cluster tendency assessment in neuronal spike data.
Sara Mahallati, James C Bezdek, Milos R Popovic, Taufik A Valiante.
PLoS One, 2019 Nov 13; 14(11). PMID: 31714913    Free PMC article.
Intrinsic dimension estimation for locally undersampled data.
Vittorio Erba, Marco Gherardi, Pietro Rotondo.
Sci Rep, 2019 Nov 22; 9(1). PMID: 31748557    Free PMC article.
A manifold-based approach to sparse global constraint satisfaction problems.
Ali Baharev, Arnold Neumaier, Hermann Schichl.
J Glob Optim, 2019 Dec 07; 75(4). PMID: 31806924    Free PMC article.
Category learning can alter perception and its neural correlates.
Fernanda Pérez-Gay Juárez, Tomy Sicotte, Christian Thériault, Stevan Harnad.
PLoS One, 2019 Dec 07; 14(12). PMID: 31810079    Free PMC article.
Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis.
Shiquan Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou.
Genome Biol, 2019 Dec 12; 20(1). PMID: 31823809    Free PMC article.
A Frequency-Based Approach for the Detection and Classification of Structural Changes Using t-SNE †.
David Agis, Francesc Pozo.
Sensors (Basel), 2019 Nov 27; 19(23). PMID: 31766460    Free PMC article.
Multi-cancer samples clustering via graph regularized low-rank representation method under sparse and symmetric constraints.
Juan Wang, Cong-Hai Lu, +2 authors, Xiang-Zhen Kong.
BMC Bioinformatics, 2020 Jan 01; 20(Suppl 22). PMID: 31888442    Free PMC article.
Low-rank graph optimization for multi-view dimensionality reduction.
Youcheng Qian, Xueyan Yin, +2 authors, Wei Gao.
PLoS One, 2019 Dec 19; 14(12). PMID: 31851696    Free PMC article.
Using Low-Dimensional Manifolds to Map Relationships Between Dynamic Brain Networks.
Mohsen Bahrami, Robert G Lyday, +3 authors, Paul J Laurienti.
Front Hum Neurosci, 2020 Jan 11; 13. PMID: 31920590    Free PMC article.
Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets.
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Front Neurorobot, 2020 Jan 31; 13. PMID: 31998109    Free PMC article.
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Convolutional-Neural Network-Based Image Crowd Counting: Review, Categorization, Analysis, and Performance Evaluation.
Naveed Ilyas, Ahsan Shahzad, Kiseon Kim.
Sensors (Basel), 2019 Dec 22; 20(1). PMID: 31861734    Free PMC article.
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Comparing Cyclicity Analysis With Pre-established Functional Connectivity Methods to Identify Individuals and Subject Groups Using Resting State fMRI.
Somayeh Shahsavarani, Ivan T Abraham, +2 authors, Fatima T Husain.
Front Comput Neurosci, 2020 Feb 11; 13. PMID: 32038211    Free PMC article.
Exploration of Cell Development Pathways through High-Dimensional Single Cell Analysis in Trajectory Space.
Denis Dermadi, Michael Bscheider, +4 authors, Eugene C Butcher.
iScience, 2020 Feb 15; 23(2). PMID: 32058956    Free PMC article.
Unsupervised feature extraction of anterior chamber OCT images for ordering and classification.
Pablo Amil, Laura González, +4 authors, Ulrich Parlitz.
Sci Rep, 2019 Feb 06; 9(1). PMID: 30718688    Free PMC article.
Early Detection of Tomato Spotted Wilt Virus by Hyperspectral Imaging and Outlier Removal Auxiliary Classifier Generative Adversarial Nets (OR-AC-GAN).
Dongyi Wang, Robert Vinson, +4 authors, Yang Tao.
Sci Rep, 2019 Mar 15; 9(1). PMID: 30867450    Free PMC article.
Combined Use of Three Machine Learning Modeling Methods to Develop a Ten-Gene Signature for the Diagnosis of Ventilator-Associated Pneumonia.
Yunfang Cai, Wen Zhang, +2 authors, Jun Fang.
Med Sci Monit, 2020 Feb 08; 26. PMID: 32031163    Free PMC article.
regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors.
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PLoS Genet, 2018 Dec 18; 14(12). PMID: 30557297    Free PMC article.
Discovering and deciphering relationships across disparate data modalities.
Joshua T Vogelstein, Eric W Bridgeford, +3 authors, Cencheng Shen.
Elife, 2019 Jan 16; 8. PMID: 30644820    Free PMC article.
Regional protein expression in human Alzheimer's brain correlates with disease severity.
Jingshu Xu, Stefano Patassini, +11 authors, Richard D Unwin.
Commun Biol, 2019 Feb 08; 2. PMID: 30729181    Free PMC article.
LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data.
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Pac Symp Biocomput, 2019 Mar 14; 24. PMID: 30864335    Free PMC article.
GNE: a deep learning framework for gene network inference by aggregating biological information.
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BMC Syst Biol, 2019 Apr 07; 13(Suppl 2). PMID: 30953525    Free PMC article.
Beyond bulk: a review of single cell transcriptomics methodologies and applications.
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Curr Opin Biotechnol, 2019 Apr 13; 58. PMID: 30978643    Free PMC article.
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Microstructural and functional gradients are increasingly dissociated in transmodal cortices.
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PLoS Biol, 2019 May 21; 17(5). PMID: 31107870    Free PMC article.
DCG++: A data-driven metric for geometric pattern recognition.
Jiahui Guan, Fushing Hsieh, Patrice Koehl.
PLoS One, 2019 Jun 07; 14(6). PMID: 31170208    Free PMC article.
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Lan Huong Nguyen, Susan Holmes.
PLoS Comput Biol, 2019 Jun 21; 15(6). PMID: 31220072    Free PMC article.
Intrinsic dimensionality of human behavioral activity data.
Luana Fragoso, Tuhin Paul, +3 authors, Nathaniel D Osgood.
PLoS One, 2019 Jun 28; 14(6). PMID: 31247031    Free PMC article.
A quantitative model of conserved macroscopic dynamics predicts future motor commands.
Connor Brennan, Alexander Proekt.
Elife, 2019 Jul 12; 8. PMID: 31294689    Free PMC article.
Network-based features for retinal fundus vessel structure analysis.
Pablo Amil, Cesar F Reyes-Manzano, +2 authors, Cristina Masoller.
PLoS One, 2019 Jul 26; 14(7). PMID: 31344132    Free PMC article.
Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients.
Petr V Nazarov, Anke K Wienecke-Baldacchino, +6 authors, Stephanie Kreis.
BMC Med Genomics, 2019 Sep 20; 12(1). PMID: 31533822    Free PMC article.
Mass cytometry-based single-cell analysis of human stem cell reprogramming uncovers differential regulation of specific pluripotency markers.
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J Biol Chem, 2019 Oct 02; 294(49). PMID: 31570522    Free PMC article.
Integrating Multiple Models Using Image-as-Documents Approach for Recognizing Fine-Grained Home Contexts.
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Sensors (Basel), 2020 Jan 30; 20(3). PMID: 31991724    Free PMC article.
Visualizing structure and transitions in high-dimensional biological data.
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Diffusion Mapping of Eosinophil-Activation State.
Justyna Piasecka, Catherine A Thornton, Paul Rees, Huw D Summers.
Cytometry A, 2019 Sep 01; 97(3). PMID: 31472007    Free PMC article.
A trainable clustering algorithm based on shortest paths from density peaks.
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Multiparametric radiomics methods for breast cancer tissue characterization using radiological imaging.
Vishwa S Parekh, Michael A Jacobs.
Breast Cancer Res Treat, 2020 Feb 06; 180(2). PMID: 32020435    Free PMC article.
Manifold construction based on local distance invariance.
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Filter-Membrane-Based Ultrafiltration Coupled with Surface-Enhanced Raman Spectroscopy for Potential Differentiation of Benign and Malignant Thyroid Tumors from Blood Plasma.
Xiaozhou Liang, Xuchao Miao, +5 authors, Zufang Huang.
Int J Nanomedicine, 2020 Apr 14; 15. PMID: 32280222    Free PMC article.
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Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry.
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A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches.
Aman Chandra Kaushik, Aamir Mehmood, Xiaofeng Dai, Dong-Qing Wei.
Sci Rep, 2020 Apr 24; 10(1). PMID: 32322011    Free PMC article.
Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection.
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Molecules, 2020 Mar 08; 25(5). PMID: 32143444    Free PMC article.
Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry.
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Mass Spectrom Rev, 2019 Oct 12; 39(3). PMID: 31602691    Free PMC article.
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GSOAP: a tool for visualization of gene set over-representation analysis.
Tomas Tokar, Chiara Pastrello, Igor Jurisica.
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Linear and Non-linear Dimensionality-Reduction Techniques on Full Hand Kinematics.
Alexandra A Portnova-Fahreeva, Fabio Rizzoglio, +3 authors, Eric Rombokas.
Front Bioeng Biotechnol, 2020 May 21; 8. PMID: 32432105    Free PMC article.
Precise coupling of the thalamic head-direction system to hippocampal ripples.
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Nat Commun, 2020 May 21; 11(1). PMID: 32433538    Free PMC article.
Measuring relative opinion from location-based social media: A case study of the 2016 U.S. presidential election.
Zhaoya Gong, Tengteng Cai, +2 authors, Mark Graham.
PLoS One, 2020 May 23; 15(5). PMID: 32442212    Free PMC article.
Projected t-SNE for batch correction.
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Dealing with the shortcomings of spatial normalization: multi-subject parcellation of fMRI datasets.
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Poincaré maps for analyzing complex hierarchies in single-cell data.
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Bioentity2vec: Attribute- and behavior-driven representation for predicting multi-type relationships between bioentities.
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Constructing knowledge graphs and their biomedical applications.
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A Geometric Clustering Tool (AGCT) to robustly unravel the inner cluster structures of time-series gene expressions.
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Similarity maps and pairwise predictions for transmission dynamics of COVID-19 with neural networks.
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Gaussian bandwidth selection for manifold learning and classification.
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Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding.
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Approximating dynamic proximity with a hybrid geometry energy-based kernel for diffusion maps.
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Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning.
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Front Genet, 2019 Apr 20; 10. PMID: 31001321    Free PMC article.
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Finding Meanings in Low Dimensional Structures: Stochastic Neighbor Embedding Applied to the Analysis of Indri indri Vocal Repertoire.
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A New Methodology for Evaluating the Structural Similarity between Different Phases Using a Dimensionality Reduction Technique.
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