Biomedical Commons^™

Domain Adaptive Federated Learning For Multi-Institution Molecular Mutation Prediction And Bias Identification, W. Farzana, M. A. Witherow, I. Longoria, M. S. Sadique, A. Temtam, K. M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Deep learning models have shown potential in medical image analysis tasks. However, training a generalized deep learning model requires huge amounts of patient data that is usually gathered from multiple institutions which may raise privacy concerns. Federated learning (FL) provides an alternative to sharing data across institutions. Nonetheless, FL is susceptible to a few challenges including inversion attacks on model weights, heterogenous data distributions, and bias. This study addresses heterogeneity and bias issues for multi-institution patient data by proposing domain adaptive FL modeling using several radiomics (volume, fractal, texture) features for O6-methylguanine-DNA methyltransferase (MGMT) classification across multiple institutions. The proposed …

Special Section Editorial: Artificial Intelligence For Medical Imaging In Clinical Practice, Claudia Mello-Thoms, Karen Drukker, Sian Taylor-Phillips, Khan Iftekharuddin, Marios Gavrielides

Electrical & Computer Engineering Faculty Publications

This editorial introduces the JMI Special Section on Artificial Intelligence for Medical Imaging in Clinical Practice.

Opioid Use Disorder Prediction Using Machine Learning Of Fmri Data, A. Temtam, Liangsuo Ma, F. Gerard Moeller, M. S. Sadique, K. M. Iftekharuddin, Khan M. Iftekharuddin (Ed.), Weijie Chen (Ed.)

Electrical & Computer Engineering Faculty Publications

According to the Centers for Disease Control and Prevention (CDC) more than 932,000 people in the US have died since 1999 from a drug overdose. Just about 75% of drug overdose deaths in 2020 involved Opioid, which suggests that the US is in an Opioid overdose epidemic. Identifying individuals likely to develop Opioid use disorder (OUD) can help public health in planning effective prevention, intervention, drug overdose and recovery policies. Further, a better understanding of prediction of overdose leading to the neurobiology of OUD may lead to new therapeutics. In recent years, very limited work has been done using statistical …

Transfer Learning Using Infrared And Optical Full Motion Video Data For Gender Classification, Alexander M. Glandon, Joe Zalameda, Khan M. Iftekharuddin, Gabor F. Fulop (Ed.), David Z. Ting (Ed.), Lucy L. Zheng (Ed.)

Electrical & Computer Engineering Faculty Publications

This work is a review and extension of our ongoing research in human recognition analysis using multimodality motion sensor data. We review our work on hand crafted feature engineering for motion capture skeleton (MoCap) data, from the Air Force Research Lab for human gender followed by depth scan based skeleton extraction using LIDAR data from the Army Night Vision Lab for person identification. We then build on these works to demonstrate a transfer learning sensor fusion approach for using the larger MoCap and smaller LIDAR data for gender classification.

Toward Real-Time, Robust Wearable Sensor Fall Detection Using Deep Learning Methods: A Feasibility Study, Haben Yhdego, Christopher Paolini, Michel Audette

Electrical & Computer Engineering Faculty Publications

Real-time fall detection using a wearable sensor remains a challenging problem due to high gait variability. Furthermore, finding the type of sensor to use and the optimal location of the sensors are also essential factors for real-time fall-detection systems. This work presents real-time fall-detection methods using deep learning models. Early detection of falls, followed by pneumatic protection, is one of the most effective means of ensuring the safety of the elderly. First, we developed and compared different data-segmentation techniques for sliding windows. Next, we implemented various techniques to balance the datasets because collecting fall datasets in the real-time setting has …

Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose …

Qu-Brats: Miccai Brats 2020 Challenge On Quantifying Uncertainty In Brain Tumor Segmentation - Analysis Of Ranking Scores And Benchmarking Results, Raghav Mehta, Angelos Filos, Ujjwal Baid, Chiharu Sako, Richard Mckinley, Michael Rebsamen, Katrin Dätwyler, Raphael Meier, Piotr Radojewski, Gowtham Krishnan Murugesan, Sahil Nalawade, Chandan Ganesh, Ben Wagner, Fang F. Yu, Baowei Fei, Ananth J. Madhuranthakam, Joseph A. Maldjian, Laura Daza, Catalina Gómez, Pablo Arbeláez, Chengliang Dai, Shuo Wang, Hadrien Reynaud, Yuan-Han Mo, Elsa Angelini, Yike Guo, Wenjia Bai, Subhashis Banerjee, Lin-Min Pei, Murat Ak, Sarahi Rosas-González, Ilyess Zemmoura, Clovis Tauber, Minh H. Vu, Tufve Nyholm, Tommy Löfstedt, Laura Mora Ballestar, Veronica Vilaplana, Hugh Mchugh, Gonzalo Maso Talou, Alan Wang, Jay Patel, Ken Chang, Katharina Hoebel, Mishka Gidwani, Nishanth Arun, Sharut Gupta, Mehak Aggarwal, Praveer Singh, Elizabeth R. Gerstner, Jayashree Kalpathy-Cramer, Nicholas Boutry, Alexis Huard, Lasitha Vidyaratne, Md. Monibor Rahman, Khan M. Iftekharuddin, Joseph Chazalon, Elodie Puybareau, Guillaume Tochon, Jun Ma, Mariano Cabezas, Xavier Llado, Arnau Oliver, Liliana Valencia, Sergi Valverde, Mehdi Amian, Mohammadreza Soltaninejad, Andriy Myronenko, Ali Hatamizadeh, Xue Feng, Quan Dou, Nicholas Tustison, Craig Meyer, Nisarg A. Shah, Sanjay Talbar, Marc-André Weber, Abhishek Mahajan, Andras Jakab, Roland Wiest, Hassan M. Fathallah-Shaykh, Arash Nazeri, Mikhail Milchenko1, Daniel Marcus, Aikaterini Kotrotsou, Rivka Colen, John Freymann, Justin Kirby, Christos Davatzikos, Bjoern Menze, Spyridon Bakas, Yarin Gal, Tal Arbel

Electrical & Computer Engineering Faculty Publications

Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder the translation of DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties, could enable clinical review of the most uncertain regions, thereby building trust and paving the way towards clinical translation. Recently, a number of uncertainty estimation methods have been introduced for DL medical image segmentation tasks. …

A Comparative Study Of Two Prediction Models For Brain Tumor Progression, Deqi Zhou, Loc Tran, Jihong Wang, Jiang Li, Karen O. Egiazarian (Ed.), Sos S. Agaian (Ed.), Atanas P. Gotchev (Ed.)

Electrical & Computer Engineering Faculty Publications

MR diffusion tensor imaging (DTI) technique together with traditional T1 or T2 weighted MRI scans supplies rich information sources for brain cancer diagnoses. These images form large-scale, high-dimensional data sets. Due to the fact that significant correlations exist among these images, we assume low-dimensional geometry data structures (manifolds) are embedded in the high-dimensional space. Those manifolds might be hidden from radiologists because it is challenging for human experts to interpret high-dimensional data. Identification of the manifold is a critical step for successfully analyzing multimodal MR images.

We have developed various manifold learning algorithms (Tran et al. 2011; Tran et al. …

An Integrated Computer-Aided Robotic System For Dental Implantation, Xiaoyan Sun, Yongki Yoon, Jiang Li, Frederic D. Mckenzie

Electrical & Computer Engineering Faculty Publications

This paper describes an integrated system for dental implantation including both preoperative planning utilizing computer-aided technology and automatic robot operation during the intra-operative stage. A novel two-step registration procedure was applied for transforming the preoperative plan to the operation of the robot, with the help of a Coordinate Measurement Machine (CMM). Experiments with a patient-specific phantom were carried out to evaluate the registration error for both position and orientation. After adopting several improvements, registration accuracy of the system was significantly improved. Sub-millimeter accuracy with the Target Registration Errors (TREs) of 0.38±0.16 mm (N=5) was achieved. The target orientation errors after …

Prediction Of Brain Tumor Progression Using A Machine Learning Technique, Yuzhong Shen, Debrup Banerjee, Jiang Li, Adam Chandler, Yufei Shen, Frederic D. Mckenzie, Jihong Wang, Nico Karssemeijer (Ed.), Ronald M. Summers (Ed.)

Electrical & Computer Engineering Faculty Publications

A machine learning technique is presented for assessing brain tumor progression by exploring six patients' complete MRI records scanned during their visits in the past two years. There are ten MRI series, including diffusion tensor image (DTI), for each visit. After registering all series to the corresponding DTI scan at the first visit, annotated normal and tumor regions were overlaid. Intensity value of each pixel inside the annotated regions were then extracted across all of the ten MRI series to compose a 10 dimensional vector. Each feature vector falls into one of three categories:normal, tumor, and normal but progressed to …

Hybrid Committee Classifier For A Computerized Colonic Polyp Detection System, Jiang Li, Jianhua Yao, Nicholas Petrick, Ronald M. Summers, Amy K. Hara, Joseph M. Reinhardt (Ed.), Josien P.W. Pluim (Ed.)

Electrical & Computer Engineering Faculty Publications

We present a hybrid committee classifier for computer-aided detection (CAD) of colonic polyps in CT colonography (CTC). The classifier involved an ensemble of support vector machines (SVM) and neural networks (NN) for classification, a progressive search algorithm for selecting a set of features used by the SVMs and a floating search algorithm for selecting features used by the NNs. A total of 102 quantitative features were calculated for each polyp candidate found by a prototype CAD system. 3 features were selected for each of 7 SVM classifiers which were then combined to form a committee of SVMs classifier. Similarly, features …