Search Results for author: Arcot Sowmya

Found 19 papers, 4 papers with code

BioFusionNet: Deep Learning-Based Survival Risk Stratification in ER+ Breast Cancer Through Multifeature and Multimodal Data Fusion

1 code implementation16 Feb 2024 Raktim Kumar Mondol, Ewan K. A. Millar, Arcot Sowmya, Erik Meijering

A co-dual-cross-attention mechanism combines the histopathological features with genetic data, enabling the model to capture the interplay between them.

Automatic 3D Multi-modal Ultrasound Segmentation of Human Placenta using Fusion Strategies and Deep Learning

no code implementations17 Jan 2024 Sonit Singh, Gordon Stevenson, Brendan Mein, Alec Welsh, Arcot Sowmya

Methods: We propose an automatic three-dimensional multi-modal (B-mode and power Doppler) ultrasound segmentation of the human placenta using deep learning combined with different fusion strategies. We collected data containing Bmode and power Doppler ultrasound scans for 400 studies.

Image Segmentation Placenta Segmentation +2

Visual Question Answering in the Medical Domain

no code implementations20 Sep 2023 Louisa Canepa, Sonit Singh, Arcot Sowmya

Medical visual question answering (Med-VQA) is a machine learning task that aims to create a system that can answer natural language questions based on given medical images.

Contrastive Learning Medical Visual Question Answering +3

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

1 code implementation30 Aug 2023 Jianning Li, Zongwei Zhou, Jiancheng Yang, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Chongyu Qu, Tiezheng Zhang, Xiaoxi Chen, Wenxuan Li, Marek Wodzinski, Paul Friedrich, Kangxian Xie, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Viet Duc Vu, Afaque R. Memon, Christopher Schlachta, Sandrine de Ribaupierre, Rajnikant Patel, Roy Eagleson, Xiaojun Chen, Heinrich Mächler, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Küstner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Löffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Arcot Sowmya, Eduardo A. Garza-Villarreal, Thania Balducci, Diego Angeles-Valdez, Roberto Souza, Leticia Rittner, Richard Frayne, Yuanfeng Ji, Vincenzo Ferrari, Soumick Chatterjee, Florian Dubost, Stefanie Schreiber, Hendrik Mattern, Oliver Speck, Daniel Haehn, Christoph John, Andreas Nürnberger, João Pedrosa, Carlos Ferreira, Guilherme Aresta, António Cunha, Aurélio Campilho, Yannick Suter, Jose Garcia, Alain Lalande, Vicky Vandenbossche, Aline Van Oevelen, Kate Duquesne, Hamza Mekhzoum, Jef Vandemeulebroucke, Emmanuel Audenaert, Claudia Krebs, Timo Van Leeuwen, Evie Vereecke, Hauke Heidemeyer, Rainer Röhrig, Frank Hölzle, Vahid Badeli, Kathrin Krieger, Matthias Gunzer, Jianxu Chen, Timo van Meegdenburg, Amin Dada, Miriam Balzer, Jana Fragemann, Frederic Jonske, Moritz Rempe, Stanislav Malorodov, Fin H. Bahnsen, Constantin Seibold, Alexander Jaus, Zdravko Marinov, Paul F. Jaeger, Rainer Stiefelhagen, Ana Sofia Santos, Mariana Lindo, André Ferreira, Victor Alves, Michael Kamp, Amr Abourayya, Felix Nensa, Fabian Hörst, Alexander Brehmer, Lukas Heine, Yannik Hanusrichter, Martin Weßling, Marcel Dudda, Lars E. Podleska, Matthias A. Fink, Julius Keyl, Konstantinos Tserpes, Moon-Sung Kim, Shireen Elhabian, Hans Lamecker, Dženan Zukić, Beatriz Paniagua, Christian Wachinger, Martin Urschler, Luc Duong, Jakob Wasserthal, Peter F. Hoyer, Oliver Basu, Thomas Maal, Max J. H. Witjes, Gregor Schiele, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Ping Luo, Bjoern Menze, Mauricio Reyes, Thomas M. Deserno, Christos Davatzikos, Behrus Puladi, Pascal Fua, Alan L. Yuille, Jens Kleesiek, Jan Egger

For the medical domain, we present a large collection of anatomical shapes (e. g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems.

Anatomy Mixed Reality

hist2RNA: An efficient deep learning architecture to predict gene expression from breast cancer histopathology images

1 code implementation10 Apr 2023 Raktim Kumar Mondol, Ewan K. A. Millar, Peter H Graham, Lois Browne, Arcot Sowmya, Erik Meijering

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC).

whole slide images

Temporal Pattern Mining for Analysis of Longitudinal Clinical Data: Identifying Risk Factors for Alzheimer's Disease

no code implementations11 Sep 2022 Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya

This method uses temporal abstraction to convert the data into a more appropriate form for modelling, temporal pattern mining, to discover patterns in the complex, longitudinal data and machine learning models of survival analysis to select the discovered patterns.

Survival Analysis

Ensemble feature selection with clustering for analysis of high-dimensional, correlated clinical data in the search for Alzheimer's disease biomarkers

no code implementations6 Jul 2022 Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya

When feature selection is applied to these datasets to identify the most important features, the biases inherent in some multivariate feature selectors due to correlated features make it difficult for these methods to distinguish between the important and irrelevant features and the results of the feature selection process can be unstable.

Clustering feature selection

Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery

no code implementations5 Jul 2022 Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya

A fixed threshold, which is typically applied, offers no guarantee that the final set of selected features contains only relevant features.

feature selection

Multi-scale alignment and Spatial ROI Module for COVID-19 Diagnosis

no code implementations4 Jul 2022 Hongyan Xu, Dadong Wang, Arcot Sowmya

However, in CT and CXR images, the infected area occupies only a small part of the image.

COVID-19 Diagnosis

Organ localisation using supervised and semi supervised approaches combining reinforcement learning with imitation learning

no code implementations6 Dec 2021 Sankaran Iyer, Alan Blair, Laughlin Dawes, Daniel Moses, Christopher White, Arcot Sowmya

The results of experiments on localisation of the Spleen, Left and Right Kidneys in CT Images using supervised and semi supervised learning (SSL) demonstrate the ability to address data limitations with a much smaller data set and fewer annotations, compared to other state-of-the-art methods.

Imitation Learning Reinforcement Learning (RL)

Video Generative Adversarial Networks: A Review

no code implementations4 Nov 2020 Nuha Aldausari, Arcot Sowmya, Nadine Marcus, Gelareh Mohammadi

Then, a comprehensive review of video GANs models is provided under two main divisions according to the presence or non-presence of a condition.

Anomaly Detection

Brain tumour segmentation using cascaded 3D densely-connected U-net

no code implementations16 Sep 2020 Mina Ghaffari, Arcot Sowmya, Ruth Oliver

In this paper, we propose a deep-learning based method to segment a brain tumour into its subregions: whole tumour, tumour core and enhancing tumour.


Scalable Inference for Nonparametric Hawkes Process Using Pólya-Gamma Augmentation

no code implementations29 Oct 2019 Feng Zhou, Zhidong Li, Xuhui Fan, Yang Wang, Arcot Sowmya, Fang Chen

In this paper, we consider the sigmoid Gaussian Hawkes process model: the baseline intensity and triggering kernel of Hawkes process are both modeled as the sigmoid transformation of random trajectories drawn from Gaussian processes (GP).

Bayesian Inference Gaussian Processes +1

Efficient EM-Variational Inference for Hawkes Process

no code implementations29 May 2019 Feng Zhou, Zhidong Li, Xuhui Fan, Yang Wang, Arcot Sowmya, Fang Chen

In classical Hawkes process, the baseline intensity and triggering kernel are assumed to be a constant and parametric function respectively, which limits the model flexibility.

Variational Inference

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