01 Publications
01
90 publications
Complete list sourced from papers.bib. Curated highlights on Google Scholar and ORCID.
01 Year 2026
- The 2024 Brain Tumor Segmentation Challenge Meningioma Radiotherapy (BraTS-MEN-RT) dataset
LaBella, Dominic, Schumacher, Katherine, Mix, Michael, Leu, Kevin, McBurney-Lin, Shan, et al.
Scientific Data 2026
02 Year 2025
- The Federated Tumor Segmentation (FeTS) Challenge 2024: Efficient and Robust Aggregation Methods
Linardos, Akis, Pati, Sarthak, Baid, Ujjwal, Edwards, Brandon, Foley, Patrick, et al.
Machine Learning for Biomedical Imaging Vol. 3 2025 - IMG-69. FeTS 2.0: Federated learning sets benchmark in post-op GBM segmentation
LaBella, Dominic, Kassem, Hasan, Edwards, Brandon, Sheller, Micah, Pati, Sarthak, et al.
Neuro-Oncology Vol. 27 2025 - IMG-121. BraTS-Pathology 2024: Insights and Future Directions Informed by the AI-RANO \& RANO-RGP Effort to Assess Glioblastoma Heterogeneity
Thakur, Siddhesh, Malec, Sylwia, Pitarc, Carla, Linardos, Akis, Innani, Shubham, et al.
Neuro-Oncology Vol. 27 2025 - From screening to subtyping in a single glance
Pati, Sarthak
Patterns Vol. 6 2025 - Optimization of deep learning models for inference in low resource environments
Thakur, Siddhesh, Pati, Sarthak, Wu, Junwen, Panchumarthy, Ravi, Karkada, Deepthi, et al.
Computers in Biology and Medicine Vol. 196 2025 - BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis
Kofler, Florian, Rosier, Marcel, Astaraki, Mehdi, M{\"o
arXiv preprint arXiv:2507.09036 2025 - Towards fair decentralized benchmarking of healthcare AI algorithms with the Federated Tumor Segmentation (FeTS) challenge
Zenk, Marcel, Baid, Uday, Pati, Sarthak, others
Nature Communications Vol. 16 2025 - Informatics at the Frontier of Cancer Research
Noller, Kathleen, Botsis, Taxiarchis, Camara, Pablo G, Ciotti, Lauren, Cooper, Lee AD, et al.
Cancer Research 2025 - BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023
Fathi Kazerooni, Anahita, Khalili, Nastaran, Liu, Xinyang, Haldar, Debanjan, Jiang, Zhifan, et al.
Machine Learning for Biomedical Imaging Vol. 3 2025 - An Unsupervised Brain Extraction Quality Control Approach for Efficient Neuro-Oncology Studies
Sarthak Pati, Stefan Wagner, Siddhesh Thakur, Evan Calabrese, Russell Shinohara, Spyridon Bakas
Journal of Imaging Informatics in Medicine 2025 - BraTS orchestrator: Democratizing and Disseminating state-of-the-art brain tumor image analysis
Kofler, Florian, Rosier, Marcel, Astaraki, Mehdi, Baid, Ujjwal, M{\"o
arXiv preprint arXiv:2506.13807 2025 - Inclusive, Differentially Private Federated Learning for Clinical Data
Parampottupadam, Santhosh, Co{\c{s
arXiv preprint arXiv:2505.22108 2025 - Analysis of the MICCAI Brain Tumor Segmentation--Metastases (BraTS-METS) 2025 Lighthouse Challenge: Brain Metastasis Segmentation on Pre-and Post-treatment MRI
Maleki, Nazanin, Amiruddin, Raisa, Moawad, Ahmed W, Yordanov, Nikolay, Gkampenis, Athanasios, et al.
arXiv preprint arXiv:2504.12527 2025 - Towards Reproducible, Stable, and Robust Machine Learning Research in Clinical Environments
Pati, Sarthak
2025 - Adapting to evolving MRI data: A transfer learning approach for Alzheimer's disease prediction
Turrisi, Rosanna, Pati, Sarthak, Pioggia, Giovanni, Tartarisco, Gennaro, Alzheimer's Disease Neuroimaging Initiative, others
NeuroImage Vol. 307 2025 - Collaborative evaluation for performance assessment of medical imaging applications
Kassem, Hasan, Singh, Akshita, Aristizabal, Alejandro, Bakas, Spyridon, Sheller, Micah, et al.
2025 - Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge
LaBella, Dominic, Baid, Ujjwal, Khanna, Omaditya, McBurney-Lin, Shan, McLean, Ryan, et al.
Machine Learning for Biomedical Imaging Vol. 3 2025
03 Year 2024
- Machine learning-based prognostic subgrouping of glioblastoma: A multicenter study
Akbari, Hamed, Bakas, Spyridon, Sako, Chiharu, Fathi Kazerooni, Anahita, Villanueva-Meyer, Javier, et al.
Neuro-Oncology 2024 - Pan-Cancer Tumor Infiltrating Lymphocyte Detection based on Federated Learning
Baid, Ujjwal, Pati, Sarthak, Kurc, Tahsin M, Gupta, Rajarsi, Bremer, Erich, et al.
2024 - The image biomarker standardization initiative: standardized convolutional filters for reproducible radiomics and enhanced clinical insights
Whybra, Philip, Zwanenburg, Alex, Andrearczyk, Vincent, Schaer, Roger, Apte, Aditya P, et al.
Radiology Vol. 310 2024 - BraTS-Path Challenge: Assessing Heterogeneous Histopathologic Brain Tumor Sub-regions
Bakas, Spyridon, Thakur, Siddhesh P, Faghani, Shahriar, Moassefi, Mana, Baid, Ujjwal, et al.
arXiv preprint arXiv:2405.10871 2024 - Brain tumor segmentation (brats) challenge 2024: Meningioma radiotherapy planning automated segmentation
LaBella, Dominic, Schumacher, Katherine, Mix, Michael, Leu, Kevin, McBurney-Lin, Shan, et al.
arXiv preprint arXiv:2405.18383 2024 - Advancing volumetric breast density segmentation: a deep learning approach with digital breast tomosynthesis
Doiphode, Nehal, Ahluwalia, Vinayak S, Mankowski, Walter C, Cohen, Eric A, Pati, Sarthak, et al.
Vol. 13174 2024 - Generatect: Text-conditional generation of 3d chest ct volumes
Hamamci, Ibrahim Ethem, Er, Sezgin, Sekuboyina, Anjany, Simsar, Enis, Tezcan, Alperen, et al.
2024 - Privacy preservation for federated learning in health care
Pati, Sarthak, Kumar, Sourav, Varma, Amokh, Edwards, Brandon, Lu, Charles, et al.
Patterns Vol. 5 2024 - BraTS-PEDs: results of the multi-consortium international pediatric brain tumor segmentation challenge 2023
Kazerooni, Anahita Fathi, Khalili, Nastaran, Liu, Xinyang, Haldar, Debanjan, Jiang, Zhifan, et al.
arXiv preprint arXiv:2407.08855 2024 - Best practices to evaluate the impact of biomedical research software—metric collection beyond citations
Afiaz, Awan, Ivanov, Andrey A, Chamberlin, John, Hanauer, David, Savonen, Candace L, et al.
Bioinformatics Vol. 40 2024 - GaNDLF-Synth: A Framework to Democratize Generative AI for (Bio) Medical Imaging
Pati, Sarthak, Mazurek, Szymon, Bakas, Spyridon
arXiv preprint arXiv:2410.00173 2024 - Artificial Intelligence for Response Assessment in Neuro Oncology (AI-RANO), part 1: review of current advancements
Villanueva-Meyer, Javier E, Bakas, Spyridon, Tiwari, Pallavi, Lupo, Janine M, Calabrese, Evan, et al.
The Lancet Oncology Vol. 25 2024 - Artificial Intelligence for Response Assessment in Neuro Oncology (AI-RANO), part 2: recommendations for standardisation, validation, and good clinical practice
Bakas, Spyridon, Vollmuth, Philipp, Galldiks, Norbert, Booth, Thomas C, Aerts, Hugo JWL, et al.
The Lancet Oncology Vol. 25 2024 - The Brain Tumor Segmentation-Metastases (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI
Moawad, Ahmed W, Janas, Anastasia, Baid, Ujjwal, Ramakrishnan, Divya, Saluja, Rachit, et al.
ArXiv 2024 - TMIC-60. BRATS-PATH: ASSESSING HETEROGENEOUS HISTOPATHOLOGIC REGIONS IN GLIOBLASTOMA
Thakur, Siddhesh, Faghani, Shahriar, Moassefi, Mana, Baid, Ujjwal, Chung, Verena, et al.
Neuro-Oncology Vol. 26 2024 - Volumetric Breast Density Estimation From Three-Dimensional Reconstructed Digital Breast Tomosynthesis Images Using Deep Learning
Ahluwalia, Vinayak S, Doiphode, Nehal, Mankowski, Walter C, Cohen, Eric A, Pati, Sarthak, et al.
JCO Clinical Cancer Informatics Vol. 8 2024
04 Year 2023
- Robust image population based stain color normalization: How many reference slides are enough?
Agraz, Jose L, Grenko, Caleb M, Chen, Andrew A, Viaene, Angela N, Nasrallah, MacLean D, et al.
IEEE Open Journal of Engineering in Medicine and Biology Vol. 3 2023 - Why is the winner the best?
Eisenmann, Matthias, Reinke, Annika, Weru, Vivienn, Tizabi, Minu D, Isensee, Fabian, et al.
2023 - GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows
Pati, Sarthak, Thakur, Siddhesh P, Hamamc{\i
Communications Engineering Vol. 2 2023 - Generatect: Text-guided 3d chest ct generation
Hamamci, Ibrahim Ethem, Er, Sezgin, Simsar, Enis, Tezcan, Alperen, Simsek, Ayse Gulnihan, et al.
CoRR 2023 - GenerateCT: Text-Conditional Generation of 3D Chest CT Volumes
Ethem Hamamci, Ibrahim, Er, Sezgin, Sekuboyina, Anjany, Simsar, Enis, Tezcan, Alperen, et al.
arXiv e-prints 2023 - Dentex: An abnormal tooth detection with dental enumeration and diagnosis benchmark for panoramic x-rays
Hamamci, Ibrahim Ethem, Er, Sezgin, Simsar, Enis, Yuksel, Atif Emre, Gultekin, Sadullah, et al.
arXiv preprint arXiv:2305.19112 2023 - Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
Afiaz, Awan, Ivanov, Andrey A, Chamberlin, John, Hanauer, David, Savonen, Candace L, et al.
ArXiv 2023 - Federated benchmarking of medical artificial intelligence with MedPerf
Karargyris, Alexandros, Umeton, Renato, Sheller, Micah J, Aristizabal, Alejandro, George, Johnu, et al.
Nature machine intelligence Vol. 5 2023 - Federated learning enables big data for rare cancer boundary detection (vol 13, 7346, 2022)
Pati, Sarthak, Baid, Ujjwal, Edwards, Brandon, Sheller, Micah, Wang, Shih-Han, et al.
2023 - 3.11 Federated Learning and Reproducibility in Healthcare
Pati, Sarthak
Inverse Biophysical Modeling and Machine Learning in Personalized Oncology 2023 - The Image Biomarker Standardization Initiative: Standardized convolutional filters for quantitative radiomics Authors and affiliations
Whybra, Philip, Zwanenburg, Alex, Andrearczyk, Vincent, Schaer, Roger, Apte, Aditya P, et al.
2023 - Panoptica--instance-wise evaluation of 3D semantic and instance segmentation maps
Kofler, Florian, M{\"o
arXiv preprint arXiv:2312.02608 2023 - The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting
Kofler, Florian, Meissen, Felix, Steinbauer, Felix, Graf, Robert, Ehrlich, Stefan K, et al.
arXiv preprint arXiv:2305.08992 2023
05 Year 2022
- Federated Learning for the Classification of Tumor Infiltrating Lymphocytes
Baid, Ujjwal, Pati, Sarthak, Kurc, Tahsin, Gupta, Rajarsi, Bremer, Erich, et al.
arXiv preprint arXiv:2203.16622 2022 - Artificial-intelligence-driven volumetric breast density estimation with digital breast tomosynthesis in a racially diverse screening cohort.
Ahluwalia, Vinayak S, Mankowski, Walter, Pati, Sarthak, Bakas, Spyridon, Brooks, Ari D, et al.
2022 - MammoFL: Mammographic Breast Density Estimation using Federated Learning
Muthukrishnan, Ramya, Heyler, Angelina, Katti, Keshava, Pati, Sarthak, Mankowski, Walter, et al.
arXiv preprint arXiv:2206.05575 2022 - Deep-learning-enabled volumetric breast density estimation with digital breast tomosynthesis
Ahluwalia, Vinayak S, Mankowski, Walter, Pati, Sarthak, Bakas, Spyridon, Brooks, Ari, et al.
Cancer Research Vol. 82 2022 - Expert tumor annotations and radiomics for locally advanced breast cancer in DCE-MRI for ACRIN 6657/I-SPY1
Chitalia, Rhea, Pati, Sarthak, Bhalerao, Megh, Thakur, Siddhesh Pravin, Jahani, Nariman, et al.
Scientific data Vol. 9 2022 - The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, \& radiomics
Bakas, Spyridon, Sako, Chiharu, Akbari, Hamed, Bilello, Michel, Sotiras, Aristeidis, et al.
Scientific data Vol. 9 2022 - The Federated Tumor Segmentation (FeTS) tool: an open-source solution to further solid tumor research
Pati, Sarthak, Baid, Ujjwal, Edwards, Brandon, Sheller, Micah J, Foley, Patrick, Reina, G Anthony, et al.
Physics in Medicine \& Biology Vol. 67 2022 - OpenFL: The Open Federated Learning library
Foley, Patrick, Sheller, Micah J, Edwards, Brandon, Pati, Sarthak, Riviera, Walter, et al.
Physics in Medicine \& Biology Vol. 67 2022 - Biomedical image analysis competitions: The state of current participation practice
Eisenmann, Matthias, Reinke, Annika, Weru, Vivienn, Tizabi, Minu Dietlinde, Isensee, Fabian, et al.
arXiv preprint arXiv:2212.08568 2022 - Federated learning enables big data for rare cancer boundary detection
Pati, Sarthak, Baid, Ujjwal, Edwards, Brandon, Sheller, Micah, Wang, Shih-Han, et al.
Nature Communications Vol. 13 2022 - NIMG-25. OPTIMIZATION OF ARTIFICIAL INTELLIGENCE ALGORITHMS FOR LOW-RESOURCE/CLINICAL ENVIRONMENTS: FOCUS ON CLINICALLY-RELEVANT GLIOMA REGION DELINEATION
Baheti, Bhakti, Thakur, Siddhesh, Pati, Sarthak, Karkada, Deepthi, Panchumarthy, Ravi, et al.
Neuro-Oncology Vol. 24 2022 - Leveraging 2D deep learning ImageNet-trained models for native 3D medical image analysis
Baheti, Bhakti, Pati, Sarthak, Menze, Bjoern, Bakas, Spyridon
2022 - Summary of Best Papers Selected for the 2023 Edition of the IMIA Yearbook, Section Cancer Informatics (CI)
Pati, S, Baid, U, Edwards, B, Sheller, M, Wang, SH, et al.
IEEE/ACM Trans Comput Biol Bioinform Vol. 19 2022
06 Year 2021
- Accurate and Robust Alignment of Differently Stained Histologic Images Based on Greedy Diffeomorphic Registration
Venet, Ludovic, Pati, Sarthak, Feldman, Michael D., Nasrallah, MacLean P., Yushkevich, Paul, Bakas, Spyridon
Applied Sciences Vol. 11 2021 - The federated tumor segmentation (fets) challenge
Pati, Sarthak, Baid, Ujjwal, Zenk, Maximilian, Edwards, Brandon, Sheller, Micah, et al.
arXiv preprint arXiv:2105.05874 2021 - OpenFL: An open-source framework for Federated Learning
Reina, G Anthony, Gruzdev, Alexey, Foley, Patrick, Perepelkina, Olga, Sharma, Mansi, et al.
arXiv preprint arXiv:2105.06413 2021 - Federated Tumor Segmentation
Bakas, Spyridon, Sheller, Micah, Pati, Sarthak, Edwards, Brandon, Reina, G Anthony, et al.
zenodo.4573127 Vol. 4573127 2021 - LabelFusion: Medical Image label fusion of segmentations
Pati, Sarthak, Baid, Ujjwal, Bakas, Spyridon
Zenodo 2021 - The rsna-asnr-miccai brats 2021 benchmark on brain tumor segmentation and radiogenomic classification
Baid, Ujjwal, Ghodasara, Satyam, Mohan, Suyash, Bilello, Michel, Calabrese, Evan, et al.
arXiv preprint arXiv:2107.02314 2021 - Interactive machine learning-based multi-label segmentation of solid tumors and organs
Bounias, Dimitrios, Singh, Ashish, Bakas, Spyridon, Pati, Sarthak, Rathore, Saima, et al.
Applied Sciences Vol. 11 2021 - Estimating glioblastoma biophysical growth parameters using deep learning regression
Pati, Sarthak, Sharma, Vaibhav, Aslam, Heena, Thakur, Siddhesh P, Akbari, Hamed, et al.
2021 - The Federated Tumor Segmentation (FeTS) Initiative: The First Real-World Large-Scale Data-Private Collaboration Focusing On Neuro-Oncology
Baid, Ujjwal, Pati, Sarthak, Thakur, Siddhesh, Edwards, Brandon, Sheller, Micah, et al.
Neuro-Oncology Vol. 23 2021 - Classification of infection and ischemia in diabetic foot ulcers using vgg architectures
G{\"u
2021 - Optimization of deep learning based brain extraction in mri for low resource environments
Thakur, Siddhesh P, Pati, Sarthak, Panchumarthy, Ravi, Karkada, Deepthi, Wu, Junwen, et al.
2021 - Robust, primitive, and unsupervised quality estimation for segmentation ensembles
Kofler, Florian, Ezhov, Ivan, Fidon, Lucas, Pirkl, Carolin M, Paetzold, Johannes C, et al.
Frontiers in Neuroscience Vol. 15 2021
07 Year 2020
- The image biomarker standardization initiative: standardized quantitative radiomics for high-throughput image-based phenotyping
Zwanenburg, Alex, Valli{\`e
Radiology Vol. 295 2020 - Cancer imaging phenomics via CaPTk: multi-institutional prediction of progression-free survival and pattern of recurrence in glioblastoma
Fathi Kazerooni, Anahita, Akbari, Hamed, Shukla, Gaurav, Badve, Chaitra, Rudie, Jeffrey D, et al.
JCO clinical cancer informatics Vol. 4 2020 - ANHIR: automatic non-rigid histological image registration challenge
Borovec, Ji{\v{r
IEEE transactions on medical imaging Vol. 39 2020 - The cancer imaging phenomics toolkit (CaPTk): technical overview
Pati, Sarthak, Singh, Ashish, Rathore, Saima, Gastounioti, Aimilia, Bergman, Mark, et al.
2020 - Standardization in quantitative imaging: a multicenter comparison of radiomic features from different software packages on digital reference objects and patient data sets
McNitt-Gray, Michael, Napel, S, Jaggi, A, Mattonen, SA, Hadjiiski, L, et al.
Tomography Vol. 6 2020 - Brain extraction on MRI scans in presence of diffuse glioma: Multi-institutional performance evaluation of deep learning methods and robust modality-agnostic training
Thakur, Siddhesh, Doshi, Jimit, Pati, Sarthak, Rathore, Saima, Sako, Chiharu, et al.
Neuroimage Vol. 220 2020 - Federated learning in medicine: facilitating multi-institutional collaborations without sharing patient data
Sheller, Micah J, Edwards, Brandon, Reina, G Anthony, Martin, Jason, Pati, Sarthak, et al.
Scientific reports Vol. 10 2020 - Standardised convolutional filtering for radiomics
Depeursinge, Adrien, Andrearczyk, Vincent, Whybra, Philip, van Griethuysen, Joost, M{\"u
arXiv preprint arXiv:2006.05470 2020 - Multi-institutional noninvasive in vivo characterization of IDH, 1p/19q, and EGFRvIII in glioma using neuro-Cancer Imaging Phenomics Toolkit (neuro-CaPTk)
Rathore, Saima, Mohan, Suyash, Bakas, Spyridon, Sako, Chiharu, Badve, Chaitra, et al.
Neuro-oncology advances Vol. 2 2020 - TMOD-09. GLIOBLASTOMA BIOPHYSICAL GROWTH ESTIMATION USING DEEP LEARNING-BASED REGRESSION
Pati, Sarthak, Sharma, Vaibhav, Aslam, Heena, Thakur, Siddhesh, Akbari, Hamed, et al.
Neuro-Oncology Vol. 22 2020 - Reproducibility analysis of multi-institutional paired expert annotations and radiomic features of the Ivy Glioblastoma Atlas Project (Ivy GAP) dataset
Pati, Sarthak, Verma, Ruchika, Akbari, Hamed, Bilello, Michel, Hill, Virginia B, et al.
Medical physics Vol. 47 2020
08 Year 2019
- Skull-stripping of glioblastoma MRI scans using 3D deep learning
Thakur, Siddhesh P, Doshi, Jimit, Pati, Sarthak, Ha, Sung Min, Sako, Chiharu, et al.
2019
09 Year 2018
- Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome
Davatzikos, Christos, Rathore, Saima, Bakas, Spyridon, Pati, Sarthak, Bergman, Mark, et al.
Journal of medical imaging Vol. 5 2018 - Brain cancer imaging phenomics toolkit (brain-CaPTk): an interactive platform for quantitative analysis of glioblastoma
Rathore, Saima, Bakas, Spyridon, Pati, Sarthak, Akbari, Hamed, Kalarot, Ratheesh, et al.
2018
10 Year 2016
- GLISTRboost: combining multimodal MRI segmentation, registration, and biophysical tumor growth modeling with gradient boosting machines for glioma segmentation
Bakas, Spyridon, Zeng, Ke, Sotiras, Aristeidis, Rathore, Saima, Akbari, Hamed, et al.
2016 - Segmentation of gliomas in pre-operative and post-operative multimodal magnetic resonance imaging volumes based on a hybrid generative-discriminative framework
Zeng, Ke, Bakas, Spyridon, Sotiras, Aristeidis, Akbari, Hamed, Rozycki, Martin, et al.
2016
11 Year 2013
- Accurate pose estimation using single marker single camera calibration system
Pati, Sarthak, Erat, Okan, Wang, Lejing, Weidert, Simon, Euler, Ekkehard, et al.
Vol. 8671 2013
12 Year 2010
- Locomotion classification using EMG signal
Pati, Sarthak, Joshi, Deepak, Mishra, Ashutosh
2010