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List of works by Anant Madabhushi

A Deep Convolutional Neural Network for segmenting and classifying epithelial and stromal regions in histopathological images.

scientific article published on 17 February 2016

A Domain Constrained Deformable (DoCD) Model for Co-registration of Pre- and Post-Radiated Prostate MRI.

scientific article

A Learning Based Fiducial-driven Registration Scheme for Evaluating Laser Ablation Changes in Neurological Disorders.

scientific article

A Radio-genomics Approach for Identifying High Risk Estrogen Receptor-positive Breast Cancers on DCE-MRI: Preliminary Results in Predicting OncotypeDX Risk Scores

scientific article

A Review of Deep Learning in Medical Imaging: Imaging Traits, Technology Trends, Case Studies With Progress Highlights, and Future Promises

scientific article published in 2021

A boosted Bayesian multiresolution classifier for prostate cancer detection from digitized needle biopsies.

scientific article

A deep learning architecture for image representation, visual interpretability and automated basal-cell carcinoma cancer detection

scientific article published on 01 January 2013

A deep learning based strategy for identifying and associating mitotic activity with gene expression derived risk categories in estrogen receptor positive breast cancers.

scientific article

A deep-learning classifier identifies patients with clinical heart failure using whole-slide images of H&E tissue.

scientific article

A high-throughput active contour scheme for segmentation of histopathological imagery.

scientific article

A magnetic resonance spectroscopy driven initialization scheme for active shape model based prostate segmentation.

scientific article published on 28 October 2010

A quantitative histomorphometric classifier (QuHbIC) identifies aggressive versus indolent p16-positive oropharyngeal squamous cell carcinoma.

scientific article

A resolution adaptive deep hierarchical (RADHicaL) learning scheme applied to nuclear segmentation of digital pathology images.

scientific article

Accurate and reproducible invasive breast cancer detection in whole-slide images: A Deep Learning approach for quantifying tumor extent

scientific article

Accurate prostate volume estimation using multifeature active shape models on T2-weighted MRI.

scientific article published in June 2011

Adaptive Dimensionality Reduction with Semi-Supervision (AdDReSS): Classifying Multi-Attribute Biomedical Data

scientific article

Adaptive energy selective active contour with shape priors for nuclear segmentation and gleason grading of prostate cancer

scientific article published on 01 January 2011

Aggregated distance metric learning (ADM) for image classification in presence of limited training data

scientific article published on 01 January 2011

An Image Analysis Resource for Cancer Research: PIIP-Pathology Image Informatics Platform for Visualization, Analysis, and Management

scientific article

An active learning based classification strategy for the minority class problem: application to histopathology annotation.

scientific article

An integrated region-, boundary-, shape-based active contour for multiple object overlap resolution in histological imagery

scientific article

An integrated segmentation and shape-based classification scheme for distinguishing adenocarcinomas from granulomas on lung CT.

scientific article published on 14 March 2017

An integrated texton and bag of words classifier for identifying anaplastic medulloblastomas

scientific article published in January 2011

Anisotropic smoothing regularization (AnSR) in Thirion's Demons registration evaluates brain MRI tissue changes post-laser ablation

scientific article

Assessment of algorithms for mitosis detection in breast cancer histopathology images

scientific article published on 29 November 2014

Association of computerized texture features on MRI with early treatment response following laser ablation for neuropathic cancer pain: preliminary findings.

scientific article published on 25 September 2015

AutoStitcher: An Automated Program for Efficient and Robust Reconstruction of Digitized Whole Histological Sections from Tissue Fragments.

scientific article published on 26 July 2016

Automated Tubule Nuclei Quantification and Correlation with Oncotype DX risk categories in ER+ Breast Cancer Whole Slide Images

scientific article

Automated computer-derived prostate volumes from MR imaging data: comparison with radiologist-derived MR imaging and pathologic specimen volumes

scientific article

Brief-exposure to preoperative bevacizumab reveals a TGF-β signature predictive of response in HER2-negative breast cancers

scientific article published on 18 August 2015

CADOnc(©): An Integrated Toolkit For Evaluating Radiation Therapy Related Changes In The Prostate Using Multiparametric MRI.

scientific article

Cascaded Multi-view Canonical Correlation (CaMCCo) for Early Diagnosis of Alzheimer's Disease via Fusion of Clinical, Imaging and Omic Features

scientific article

Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer ⬇️

scientific article published on October 30, 2012

Cell orientation entropy (COrE): predicting biochemical recurrence from prostate cancer tissue microarrays

scientific article published on 01 January 2013

Central gland and peripheral zone prostate tumors have significantly different quantitative imaging signatures on 3 tesla endorectal, in vivo T2‐weighted MR imagery ⬇️

scientific article published on February 15, 2012

Changes in CT Radiomic Features Associated with Lymphocyte Distribution Predict Overall Survival and Response to Immunotherapy in Non-Small Cell Lung Cancer

scientific article published on 12 November 2019

Class-specific weighting for Markov random field estimation: Application to medical image segmentation ⬇️

scientific article published on July 16, 2012

Co-Registration of ex vivo Surgical Histopathology and in vivo T2 weighted MRI of the Prostate via multi-scale spectral embedding representation.

scientific article published on 18 August 2017

Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe): A new radiomics descriptor.

scientific article

Co-occurrence of local anisotropic gradient orientations (CoLIAGe): distinguishing tumor confounders and molecular subtypes on MRI

scientific article published on 01 January 2014

Co-occurring gland angularity in localized subgraphs: predicting biochemical recurrence in intermediate-risk prostate cancer patients

scientific article (publication date: 2014)

Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study

scientific article

Combination of Peri-Tumoral and Intra-Tumoral Radiomic Features on Bi-Parametric MRI Accurately Stratifies Prostate Cancer Risk: A Multi-Site Study

scientific article published on 06 August 2020

Combination of computer extracted shape and texture features enables discrimination of granulomas from adenocarcinoma on chest computed tomography

scientific article published on 18 April 2018

Combining low-, high-level and empirical domain knowledge for automated segmentation of ultrasonic breast lesions.

scientific article published on February 2003

Comparing MR image intensity standardization against tissue characterizability of magnetization transfer ratio imaging

scientific article published in September 2006

Computational imaging reveals shape differences between normal and malignant prostates on MRI.

scientific article published on February 2017

Computer Extracted Features from Initial H&E Tissue Biopsies Predict Disease Progression for Prostate Cancer Patients on Active Surveillance

scientific article published on 21 September 2020

Computer-Extracted Texture Features to Distinguish Cerebral Radionecrosis from Recurrent Brain Tumors on Multiparametric MRI: A Feasibility Study

scientific article published on 15 September 2016

Computer-aided prognosis: predicting patient and disease outcome via quantitative fusion of multi-scale, multi-modal data

scientific article

Computer-extracted Features Can Distinguish Noncancerous Confounding Disease from Prostatic Adenocarcinoma at Multiparametric MR Imaging.

scientific article

Computerized image analysis for identifying triple-negative breast cancers and differentiating them from other molecular subtypes of breast cancer on dynamic contrast-enhanced MR images: a feasibility study

scientific article

Computerized image-based detection and grading of lymphocytic infiltration in HER2+ breast cancer histopathology

scientific article

Concurrent segmentation of the prostate on MRI and CT via linked statistical shape models for radiotherapy planning.

scientific article published in April 2012

Connecting Markov random fields and active contour models: application to gland segmentation and classification.

scientific article published on 28 March 2017

Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data ⬇️

scientific article published on February 8, 2012

Convolutional neural network initialized active contour model with adaptive ellipse fitting for nuclear segmentation on breast histopathological images

scientific article published on 01 January 2019

Deep computational image analysis of immune cell niches reveals treatment-specific outcome associations in lung cancer

scientific article published in 2023

Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases

scientific article published on 26 July 2016

Deep learning reveals lung shape differences on baseline chest CT between mild and severe COVID-19: A multi-site retrospective study

scientific article published in 2024

Detection of prostate cancer on histopathology using color fractals and Probabilistic Pairwise Markov models

scientific article published in January 2011

Determining histology-MRI slice correspondences for defining MRI-based disease signatures of prostate cancer

scientific article published on 21 January 2011

Digital imaging in pathology: whole-slide imaging and beyond.

scientific article

Dimensionality reduction-based fusion approaches for imaging and non-imaging biomedical data: concepts, workflow, and use-cases

scientific article

Discriminative Scale Learning (DiScrn): Applications to Prostate Cancer Detection from MRI and Needle Biopsies.

scientific article published on 28 September 2017

Disorder in Pixel-Level Edge Directions on T1WI Is Associated with the Degree of Radiation Necrosis in Primary and Metastatic Brain Tumors: Preliminary Findings

scientific article published on 07 February 2019

Distinguishing lesions from posterior acoustic shadowing in breast ultrasound via non-linear dimensionality reduction.

scientific article

Editorial Comment

Editorial: TBME Letters special section on multiscale biomedical signal and image modeling and analysis

scientific article published on 13 December 2011

Emerging Themes in Image Informatics and Molecular Analysis for Digital Pathology

scientific article

Enhanced Multi-Protocol Analysis via Intelligent Supervised Embedding (EMPrAvISE): Detecting Prostate Cancer on Multi-Parametric MRI.

scientific article

Erratum to: Intratumoral and peritumoral radiomics for the pretreatment prediction of pathological complete response to neoadjuvant chemotherapy based on breast DCE-MRI.

scientific article published on 10 July 2017

Erratum to: Radiomic features from the peritumoral brain parenchyma on treatment-naïve multi-parametric MR imaging predict long versus short-term survival in glioblastoma multiforme: Preliminary findings

scientific article published on 12 June 2017

Evaluating feature selection strategies for high dimensional, small sample size datasets.

scientific article published in January 2011

Evaluating stability of histomorphometric features across scanner and staining variations: prostate cancer diagnosis from whole slide images

scientific article

Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge

scientific article

Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology

scientific article published on 17 February 2010

Explicit shape descriptors: novel morphologic features for histopathology classification.

scientific article published on 24 June 2013

Feature Importance in Nonlinear Embeddings (FINE): Applications in Digital Pathology

scientific article published on 14 July 2015

Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model.

scientific article published in August 2015

Fully Automated Prostate Magnetic Resonance Imaging and Transrectal Ultrasound Fusion via a Probabilistic Registration Metric.

scientific article published on March 2013

Graph embedding to improve supervised classification and novel class detection: application to prostate cancer

scientific article published on 01 January 2005

Harnessing non-destructive 3D pathology

scientific article published in 2021

Hierarchical normalized cuts: unsupervised segmentation of vascular biomarkers from ovarian cancer tissue microarrays

scientific article published on 01 January 2009

High-Throughput Biomarker Segmentation on Ovarian Cancer Tissue Microarrays via Hierarchical Normalized Cuts ⬇️

scientific article published on December 13, 2011

HistoStitcher(©): an interactive program for accurate and rapid reconstruction of digitized whole histological sections from tissue fragments.

scientific article

Histopathological image analysis: a review

scientific article (publication date: 2009)

Identifying MRI markers associated with early response following laser ablation for neurological disorders: preliminary findings

scientific article published on 11 December 2014

Identifying MRI markers to evaluate early treatment related changes post laser ablation for cancer pain management.

scientific article

Identifying Quantitative In Vivo Multi-Parametric MRI Features For Treatment Related Changes after Laser Interstitial Thermal Therapy of Prostate Cancer.

scientific article

Identifying in vivo DCE MRI markers associated with microvessel architecture and gleason grades of prostate cancer

scientific article

Image analysis and machine learning in digital pathology: Challenges and opportunities

scientific article published on 04 July 2016

Image filtering via generalized scale.

scientific article published on 9 August 2007

Improving supervised classification accuracy using non-rigid multimodal image registration: detecting prostate cancer

Integrated diagnostics: a conceptual framework with examples.

scientific article

Integrating Structural and Functional Imaging for Computer Assisted Detection of Prostate Cancer on Multi-Protocol In Vivo 3 Tesla MRI

scientific article

Integration of architectural and cytologic driven image algorithms for prostate adenocarcinoma identification.

scientific article

Interplay between bias field correction, intensity standardization, and noise filtering for T2-weighted MRI.

scientific article published in January 2011

Interplay between intensity standardization and inhomogeneity correction in MR image processing

scientific article published in May 2005

Intratumoral and peritumoral radiomics for the pretreatment prediction of pathological complete response to neoadjuvant chemotherapy based on breast DCE-MRI.

scientific article

MULTI-MODAL DATA FUSION SCHEMES FOR INTEGRATED CLASSIFICATION OF IMAGING AND NON-IMAGING BIOMEDICAL DATA.

scientific article

Markov random field driven region-based active contour model (MaRACel): application to medical image segmentation

scientific article published on 01 January 2010

Mitosis detection in breast cancer pathology images by combining handcrafted and convolutional neural network features

scientific article published on 10 October 2014

Multi-Pass Adaptive Voting for Nuclei Detection in Histopathological Images

scientific article published on 03 October 2016

Multi-attribute non-initializing texture reconstruction based active shape model (MANTRA)

scientific article published on 01 January 2008

Multi-field-of-view framework for distinguishing tumor grade in ER+ breast cancer from entire histopathology slides

scientific article

Multi-kernel graph embedding for detection, Gleason grading of prostate cancer via MRI/MRS

scientific article published on 13 December 2012

Multiattribute probabilistic prostate elastic registration (MAPPER): application to fusion of ultrasound and magnetic resonance imaging

scientific article

Multifeature Landmark-Free Active Appearance Models: Application to Prostate MRI Segmentation ⬇️

scientific article published on May 30, 2012

Multimodal wavelet embedding representation for data combination (MaWERiC): integrating magnetic resonance imaging and spectroscopy for prostate cancer detection

scientific article

Multisite evaluation of radiomic feature reproducibility and discriminability for identifying peripheral zone prostate tumors on MRI

scientific article published on 01 April 2019

NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures

scientific article

New methods of MR image intensity standardization via generalized scale

scientific article published in September 2006

Novel PCA-VIP scheme for ranking MRI protocols and identifying computer-extracted MRI measurements associated with central gland and peripheral zone prostate tumors

scientific article published on 18 June 2014

Novel morphometric based classification via diffeomorphic based shape representation using manifold learning

scientific article published on 01 January 2010

Nuclear Shape and Architecture in Benign Fields Predict Biochemical Recurrence in Prostate Cancer Patients Following Radical Prostatectomy: Preliminary Findings.

scientific article

Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells

scientific article published on 04 January 2017

Optimization of complex cancer morphology detection using the SIVQ pattern recognition algorithm

scientific article published in January 2012

Out-of-Sample Extrapolation utilizing Semi-Supervised Manifold Learning (OSE-SSL): Content Based Image Retrieval for Histopathology Images

scientific article published on 06 June 2016

Patient-specific pharmacokinetic parameter estimation on dynamic contrast-enhanced MRI of prostate: Preliminary evaluation of a novel AIF-free estimation method ⬇️

scientific article

Predicting classifier performance with limited training data: applications to computer-aided diagnosis in breast and prostate cancer

scientific article

Prediction of recurrence in early stage non-small cell lung cancer using computer extracted nuclear features from digital H&E images.

scientific article published on 19 October 2017

Prostate shapes on pre-treatment MRI between prostate cancer patients who do and do not undergo biochemical recurrence are different: Preliminary Findings.

scientific article published on 20 November 2017

Prostatome: a combined anatomical and disease based MRI atlas of the prostate

scientific article

Quantifying Post- Laser Ablation Prostate Therapy Changes on MRI via a Domain-Specific Biomechanical Model: Preliminary Findings

scientific article

Quantitative Evaluation of Treatment Related Changes on Multi-Parametric MRI after Laser Interstitial Thermal Therapy of Prostate Cancer

scientific article

Quantitative evaluation of multi-parametric MR imaging marker changes post-laser interstitial ablation therapy (LITT) for epilepsy.

scientific article

Quantitative identification of magnetic resonance imaging features of prostate cancer response following laser ablation and radical prostatectomy

scientific article published on 27 October 2014

Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma

scientific article published on 20 February 2020

Radiomic Texture and Shape Descriptors of the Rectal Environment on Post-Chemoradiation T2-Weighted MRI are Associated with Pathologic Tumor Stage Regression in Rectal Cancers: A Retrospective, Multi-Institution Study

scientific article published on 24 July 2020

Radiomic features for prostate cancer detection on MRI differ between the transition and peripheral zones: Preliminary findings from a multi-institutional study

scientific article published on 19 December 2016

Radiomic features from the peritumoral brain parenchyma on treatment-naïve multi-parametric MR imaging predict long versus short-term survival in glioblastoma multiforme: Preliminary findings.

scientific article

Radiomics Analysis on FLT-PET/MRI for Characterization of Early Treatment Response in Renal Cell Carcinoma: A Proof-of-Concept Study

scientific article published on April 2016

Radiomics and radiogenomics in lung cancer: A review for the clinician

scientific article published on 8 November 2017

Radiomics based targeted radiotherapy planning (Rad-TRaP): a computational framework for prostate cancer treatment planning with MRI.

scientific article

Radiomics-based convolutional neural network for brain tumor segmentation on multiparametric magnetic resonance imaging

scientific article published on 01 April 2019

Reimagining T Staging Through Artificial Intelligence and Machine Learning Image Processing Approaches in Digital Pathology

scientific article published on 01 November 2020

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scientific article published on 31 August 2017

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scientific article published on 26 January 2017

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Selecting features with group-sparse nonnegative supervised canonical correlation analysis: multimodal prostate cancer prognosis

scientific article published on 01 January 2014

Selective invocation of shape priors for deformable segmentation and morphologic classification of prostate cancer tissue microarrays

scientific article

Semi supervised multi kernel (SeSMiK) graph embedding: identifying aggressive prostate cancer via magnetic resonance imaging and spectroscopy

scientific article published on 01 January 2010

Shape Features of the Lesion Habitat to Differentiate Brain Tumor Progression from Pseudoprogression on Routine Multiparametric MRI: A Multisite Study

scientific article

Single cell qPCR reveals that additional HAND2 and microRNA-1 facilitate the early reprogramming progress of seven-factor-induced human myocytes

scientific article published on 10 August 2017

Sparse Non-negative Matrix Factorization (SNMF) based color unmixing for breast histopathological image analysis.

scientific article published on 28 April 2015

Spatial Architecture and Arrangement of Tumor-Infiltrating Lymphocytes for Predicting Likelihood of Recurrence in Early-Stage Non-Small Cell Lung Cancer

scientific article published on 10 September 2018

Spatial interplay patterns of cancer nuclei and tumor-infiltrating lymphocytes (TILs) predict clinical benefit for immune checkpoint inhibitors

scientific article published on 01 June 2022

Spatially aware cell cluster(spACC1) graphs: predicting outcome in oropharyngeal pl6+ tumors

scientific article published on 01 January 2013

Spatially weighted mutual information (SWMI) for registration of digitally reconstructed ex vivo whole mount histology and in vivo prostate MRI ⬇️

scientific article published on January 1, 2011

Spatio-temporal texture (SpTeT) for distinguishing vulnerable from stable atherosclerotic plaque on dynamic contrast enhancement (DCE) MRI in a rabbit model

scientific article published on April 2014

Special Section Guest Editorial: Digital Pathology

scientific article published in April 2017

Spectral embedding based active contour (SEAC) for lesion segmentation on breast dynamic contrast enhanced magnetic resonance imaging.

scientific article published on March 2013

Spectral embedding based probabilistic boosting tree (ScEPTre): classifying high dimensional heterogeneous biomedical data

scientific article published on 01 January 2009

Stable and Discriminatory Radiomic Features from the Tumor and Its Habitat Associated with Progression-Free Survival in Glioblastoma: A Multi-Institutional Study

scientific article published in 2022

Stacked Sparse Autoencoder (SSAE) for Nuclei Detection on Breast Cancer Histopathology Images

scientific article published on 20 July 2015

Stain Normalization using Sparse AutoEncoders (StaNoSA): Application to digital pathology

scientific article published on 16 May 2016

Statistical 3D Prostate Imaging Atlas Construction via Anatomically Constrained Registration

scientific article published on March 2013

Supervised multi-view canonical correlation analysis (sMVCCA): integrating histologic and proteomic features for predicting recurrent prostate cancer.

scientific article

Supervised regularized canonical correlation analysis: Integrating histologic and proteomic data for predicting biochemical failures ⬇️

scientific article published on January 1, 2011

Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery

scientific article

Textural kinetics: a novel dynamic contrast-enhanced (DCE)-MRI feature for breast lesion classification.

scientific article

Towards improved cancer diagnosis and prognosis using analysis of gene expression data and computer aided imaging

scientific article

Training a cell-level classifier for detecting basal-cell carcinoma by combining human visual attention maps with low-level handcrafted features.

scientific article published on 11 March 2017

Tumor Habitat-derived Radiomic Features at Pretreatment MRI That Are Prognostic for Progression-free Survival in Glioblastoma Are Associated with Key Morphologic Attributes at Histopathologic Examination: A Feasibility Study

scientific article published on 11 November 2020

Variable importance in nonlinear kernels (VINK): classification of digitized histopathology

scientific article published on 01 January 2013

Weighted maximum posterior marginals for random fields using an ensemble of conditional densities from multiple Markov chain Monte Carlo simulations

scientific article published on 17 February 2011

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