Search Results for author: Donald E. Brown

Found 26 papers, 13 papers with code

Automatic Report Generation for Histopathology images using pre-trained Vision Transformers

1 code implementation10 Nov 2023 Saurav Sengupta, Donald E. Brown

In this work, we show that using an existing pre-trained Vision Transformer in a two-step process of first using it to encode 4096x4096 sized patches of the Whole Slide Image (WSI) and then using it as the encoder and an LSTM decoder for report generation, we can build a fairly performant and portable report generation mechanism that takes into account the whole of the high resolution image, instead of just the patches.

Image Segmentation Semantic Segmentation +1

Label-efficient Contrastive Learning-based model for nuclei detection and classification in 3D Cardiovascular Immunofluorescent Images

no code implementations7 Sep 2023 Nazanin Moradinasab, Rebecca A. Deaton, Laura S. Shankman, Gary K. Owens, Donald E. Brown

Previous methods use Maximum Intensity Projection (MIP) to convert immunofluorescent images with multiple slices to 2D images, which can cause signals from different z-stacks to falsely appear associated with each other.

Contrastive Learning

Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid

no code implementations5 Oct 2022 Saurav Sengupta, Johanna Loomba, Suchetha Sharma, Donald E. Brown, Lorna Thorpe, Melissa A Haendel, Christopher G Chute, Stephanie Hong

Using our deep learning approach, we are able to predict if a patient is suffering from Long COVID from a temporally ordered list of diagnosis codes up to 45 days post the first COVID positive test or diagnosis for each patient, with an accuracy of 70. 48\%.

Weakly Supervised Deep Instance Nuclei Detection using Points Annotation in 3D Cardiovascular Immunofluorescent Images

no code implementations29 Jul 2022 Nazanin Moradinasab, Yash Sharma, Laura S. Shankman, Gary K. Owens, Donald E. Brown

In this study, we used a weakly supervised learning approach to train the HoVer-Net segmentation model using point annotations to detect nuclei in fluorescent images.

Weakly-supervised Learning

MaNi: Maximizing Mutual Information for Nuclei Cross-Domain Unsupervised Segmentation

1 code implementation29 Jun 2022 Yash Sharma, Sana Syed, Donald E. Brown

Nuclei vary substantially in structure and appearances across different cancer types, leading to a drop in performance of deep learning models when trained on one cancer type and tested on another.

Segmentation Unsupervised Domain Adaptation +1

Encoding Cardiopulmonary Exercise Testing Time Series as Images for Classification using Convolutional Neural Network

1 code implementation26 Apr 2022 Yash Sharma, Nick Coronato, Donald E. Brown

Exercise testing has been available for more than a half-century and is a remarkably versatile tool for diagnostic and prognostic information of patients for a range of diseases, especially cardiovascular and pulmonary.

Time Series Time Series Analysis

Toward a Knowledge Discovery Framework for Data Science Job Market in the United States

1 code implementation14 Jun 2021 Mojtaba Heidarysafa, Kamran Kowsari, Masoud Bashiri, Donald E. Brown

The growth of the data science field requires better tools to understand such a fast-paced growing domain.

HistoTransfer: Understanding Transfer Learning for Histopathology

no code implementations13 Jun 2021 Yash Sharma, Lubaina Ehsan, Sana Syed, Donald E. Brown

In this work, we compare the performance of features extracted from networks trained on ImageNet and histopathology data.

Multi-Task Learning

Cluster-to-Conquer: A Framework for End-to-End Multi-Instance Learning for Whole Slide Image Classification

1 code implementation19 Mar 2021 Yash Sharma, Aman Shrivastava, Lubaina Ehsan, Christopher A. Moskaluk, Sana Syed, Donald E. Brown

We regularized the clustering mechanism by introducing a KL-divergence loss between the attention weights of patches in a cluster and the uniform distribution.

Image Classification Multiple Instance Learning +1

Gender Detection on Social Networks using Ensemble Deep Learning

no code implementations13 Apr 2020 Kamran Kowsari, Mojtaba Heidarysafa, Tolu Odukoya, Philip Potter, Laura E. Barnes, Donald E. Brown

Analyzing the ever-increasing volume of posts on social media sites such as Facebook and Twitter requires improved information processing methods for profiling authorship.

Classification Document Classification +1

Self-Attentive Adversarial Stain Normalization

1 code implementation4 Sep 2019 Aman Shrivastava, Will Adorno, Yash Sharma, Lubaina Ehsan, S. Asad Ali, Sean R. Moore, Beatrice C. Amadi, Paul Kelly, Sana Syed, Donald E. Brown

We propose a Self-Attentive Adversarial Stain Normalization (SAASN) approach for the normalization of multiple stain appearances to a common domain.

Translation whole slide images

Analysis of Railway Accidents' Narratives Using Deep Learning

1 code implementation17 Oct 2018 Mojtaba Heidarysafa, Kamran Kowsari, Laura E. Barnes, Donald E. Brown

These reports contain a variety of fixed field entries including primary cause of the accidents (a coded variable with 389 values) as well as a narrative field which is a short text description of the accident.

Word Embeddings

PrivLogit: Efficient Privacy-preserving Logistic Regression by Tailoring Numerical Optimizers

no code implementations3 Nov 2016 Wei Xie, Yang Wang, Steven M. Boker, Donald E. Brown

Leveraging this new method, we propose two new secure protocols for conducting logistic regression in a privacy-preserving and distributed manner.

BIG-bench Machine Learning Privacy Preserving +1

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