Life Sciences Commons^™

Machine Learning As A Tool For Early Detection: A Focus On Late-Stage Colorectal Cancer Across Socioeconomic Spectrums, Hadiza Galadima, Rexford Anson-Dwamena, Ashley Johnson, Ghalib Bello, Georges Adunlin, James Blando

Community & Environmental Health Faculty Publications

Purpose: To assess the efficacy of various machine learning (ML) algorithms in predicting late-stage colorectal cancer (CRC) diagnoses against the backdrop of socio-economic and regional healthcare disparities. Methods: An innovative theoretical framework was developed to integrate individual- and census tract-level social determinants of health (SDOH) with sociodemographic factors. A comparative analysis of the ML models was conducted using key performance metrics such as AUC-ROC to evaluate their predictive accuracy. Spatio-temporal analysis was used to identify disparities in late-stage CRC diagnosis probabilities. Results: Gradient boosting emerged as the superior model, with the top predictors for late-stage CRC diagnosis being anatomic site, …

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin

Dissertations

Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Deep Learning For Plant Bioinformatics: An Explainable Gradient-Based Approach For Disease Detection, Muhammad Shoaib, Babar Shah, Nasir Sayed, Farman Ali, Rafi Ullah, Irfan Hussain

All Works

Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a …

Self-Supervised Pretraining And Transfer Learning On Fmri Data With Transformers, Sean Paulsen

Dartmouth College Ph.D Dissertations

Transfer learning is a machine learning technique founded on the idea that knowledge acquired by a model during “pretraining” on a source task can be transferred to the learning of a target task. Successful transfer learning can result in improved performance, faster convergence, and reduced demand for data. This technique is particularly desirable for the task of brain decoding in the domain of functional magnetic resonance imaging (fMRI), wherein even the most modern machine learning methods can struggle to decode labelled features of brain images. This challenge is due to the highly complex underlying signal, physical and neurological differences between …

Utilizing Few-Shot Meta Learning Algorithms For Medical Image Segmentation, Nick Littlefield

Thinking Matters Symposium

Deep learning models can be difficult to train because they require large amounts of data, which we usually do not have or are too expensive to get or annotate. To overcome this problem, we can use few-shot meta-learning, which allows us to train deep learning models with little data. Using a few examples, meta-learning, or learning-to-learn, aims to use the experience learned during training to generalize to unknown tasks. Medical imaging is an industry where it is particularly useful, as there is limited publicly available data due to patient privacy concerns and annotating costs.

This project examines how meta-learning performs …

Wearable Sensor Gait Analysis For Fall Detection Using Deep Learning Methods, Haben Girmay Yhdego

Electrical & Computer Engineering Theses & Dissertations

World Health Organization (WHO) data show that around 684,000 people die from falls yearly, making it the second-highest mortality rate after traffic accidents [1]. Early detection of falls, followed by pneumatic protection, is one of the most effective means of ensuring the safety of the elderly. In light of the recent widespread adoption of wearable sensors, it has become increasingly critical that fall detection models are developed that can effectively process large and sequential sensor signal data. Several researchers have recently developed fall detection algorithms based on wearable sensor data. However, real-time fall detection remains challenging because of the wide …

An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali

All Works

Plants play a crucial role in supplying food globally. Various environmental factors lead to plant diseases which results in significant production losses. However, manual detection of plant diseases is a time-consuming and error-prone process. It can be an unreliable method of identifying and preventing the spread of plant diseases. Adopting advanced technologies such as Machine Learning (ML) and Deep Learning (DL) can help to overcome these challenges by enabling early identification of plant diseases. In this paper, the recent advancements in the use of ML and DL techniques for the identification of plant diseases are explored. The research focuses on …

Multimodal Neuron Classification Based On Morphology And Electrophysiology, Aqib Ahmad

Graduate Theses, Dissertations, and Problem Reports

Categorizing neurons into different types to understand neural circuits and ultimately brain function is a major challenge in neuroscience. While electrical properties are critical in defining a neuron, its morphology is equally important. Advancements in single-cell analysis methods have allowed neuroscientists to simultaneously capture multiple data modalities from a neuron. We propose a method to classify neurons using both morphological structure and electrophysiology. Current approaches are based on a limited analysis of morphological features. We propose to use a new graph neural network to learn representations that more comprehensively account for the complexity of the shape of neuronal structures. In …

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

Assessing Wood Failure In Plywood By Deep Learning/Semantic Segmentation, Ramon Ferreira Oliveira

Theses and Dissertations

The current method for estimating wood failure is highly subjective. Various techniques have been proposed to improve the current protocol, but none have succeeded. This research aims to use deep learning/semantic segmentation using SegNet architecture to estimate wood failure in four types of three-ply plywood from mechanical shear strength specimens. We trained and tested our approach on custom and commercial plywood with bio-based and phenol-formaldehyde adhesives. Shear specimens were prepared and tested. Photographs of 255 shear bonded areas were taken. Forty photographs were used to solicit visual estimates from five human evaluators, and the remaining photographs were used to train …

An Effective Deep Learning Approach For The Classification Of Bacteriosis In Peach Leave, Muneer Akbar, Mohib Ullah, Babar Shah, Rafi Ullah Khan, Tariq Hussain, Farman Ali, Fayadh Alenezi, Ikram Syed, Kyung Sup Kwak

All Works

Bacteriosis is one of the most prevalent and deadly infections that affect peach crops globally. Timely detection of Bacteriosis disease is essential for lowering pesticide use and preventing crop loss. It takes time and effort to distinguish and detect Bacteriosis or a short hole in a peach leaf. In this paper, we proposed a novel LightWeight (WLNet) Convolutional Neural Network (CNN) model based on Visual Geometry Group (VGG-19) for detecting and classifying images into Bacteriosis and healthy images. Profound knowledge of the proposed model is utilized to detect Bacteriosis in peach leaf images. First, a dataset is developed which consists …

Deep Learning-Based Segmentation And Classification Of Leaf Images For Detection Of Tomato Plant Disease, Muhammad Shoaib, Tariq Hussain, Babar Shah, Ihsan Ullah, Sayyed Mudassar Shah, Farman Ali, Sang Hyun Park

All Works

Plants contribute significantly to the global food supply. Various Plant diseases can result in production losses, which can be avoided by maintaining vigilance. However, manually monitoring plant diseases by agriculture experts and botanists is time-consuming, challenging and error-prone. To reduce the risk of disease severity, machine vision technology (i.e., artificial intelligence) can play a significant role. In the alternative method, the severity of the disease can be diminished through computer technologies and the cooperation of humans. These methods can also eliminate the disadvantages of manual observation. In this work, we proposed a solution to detect tomato plant disease using a …

Integrating Deep Learning And Hydrodynamic Modeling To Improve The Great Lakes Forecast, Pengfei Xue, Aditya Wagh, Gangfeng Ma, Yilin Wang, Yongchao Yang, Tao Liu, Chenfu Huang

Michigan Tech Publications

The Laurentian Great Lakes, one of the world’s largest surface freshwater systems, pose a modeling challenge in seasonal forecast and climate projection. While physics-based hydrodynamic modeling is a fundamental approach, improving the forecast accuracy remains critical. In recent years, machine learning (ML) has quickly emerged in geoscience applications, but its application to the Great Lakes hydrodynamic prediction is still in its early stages. This work is the first one to explore a deep learning approach to predicting spatiotemporal distributions of the lake surface temperature (LST) in the Great Lakes. Our study shows that the Long Short-Term Memory (LSTM) neural network, …

Contrastive Learning For Unsupervised Auditory Texture Models, Christina Trexler

Computer Science and Computer Engineering Undergraduate Honors Theses

Sounds with a high level of stationarity, also known as sound textures, have perceptually relevant features which can be captured by stimulus-computable models. This makes texture-like sounds, such as those made by rain, wind, and fire, an appealing test case for understanding the underlying mechanisms of auditory recognition. Previous auditory texture models typically measured statistics from auditory filter bank representations, and the statistics they used were somewhat ad-hoc, hand-engineered through a process of trial and error. Here, we investigate whether a better auditory texture representation can be obtained via contrastive learning, taking advantage of the stationarity of auditory textures to …

Development Of Deep Learning Neural Network For Ecological And Medical Images, Shaobo Liu

Dissertations

Deep learning in computer vision and image processing has attracted attentions from various fields including ecology and medical image. Ecologists are interested in finding an effective model structure to classify different species. Tradition deep learning model use a convolutional neural network, such as LeNet, AlexNet, VGG models, residual neural network, and inception models, are first used on classifying bee wing and butterfly datasets. However, insufficient data sample and unbalanced samples in each class have caused a poor accuracy. To make improvement the test accuracy, data augmentation and transfer learning are applied. Recently developed deep learning framework based on mathematical morphology …

Using Deep Learning For Children Brain Image Analysis, Rafael Toche Pizano

Computer Science and Computer Engineering Undergraduate Honors Theses

Analyzing the correlation between brain volumetric/morphometry features and cognition/behavior in children is important in the field of pediatrics as identifying such relationships can help identify children who may be at risk for illnesses. Understanding these relationships can not only help identify children who may be at risk of illnesses, but it can also help evaluate strategies that promote brain development in children. Currently, one way to do this is to use traditional statistical methods such as a correlation analysis, but such an approach does not make it easy to generalize and predict how brain volumetric/morphometry will impact cognition/behavior. One of …

Deep Learning For Multi-Tissue Cancer Classification Of Gene Expressions, Tarek Khorshed

Theses and Dissertations

We contribute in saving the lives of cancer patients through early detection and diagnosis, since one of the major challenges in cancer treatment is that patients are diagnosed at very late stages when appropriate medical interventions become less effective and full curative treatment is no longer achievable. Cancer classification using gene expressions is extremely challenging given the complexity and high dimensionality of the data. Current classification methods typically rely on samples collected from a single tissue type and perform a prerequisite of gene feature selection to avoid processing the full set of genes. These methods fall short in taking advantage …

A Multi-Resolution Graph Convolution Network For Contiguous Epitope Prediction, Lisa Oh

Dartmouth College Master’s Theses

Computational methods for predicting binding interfaces between antigens and antibodies (epitopes and paratopes) are faster and cheaper than traditional experimental structure determination methods. A sufficiently reliable computational predictor that could scale to large sets of available antibody sequence data could thus inform and expedite many biomedical pursuits, such as better understanding immune responses to vaccination and natural infection and developing better drugs and vaccines. However, current state-of-the-art predictors produce discontiguous predictions, e.g., predicting the epitope in many different spots on an antigen, even though in reality they typically comprise a single localized region. We seek to produce contiguous predicted epitopes, …

New Methods For Deep Learning Based Real-Valued Inter-Residue Distance Prediction, Jacob Barger

Theses

Background: Much of the recent success in protein structure prediction has been a result of accurate protein contact prediction--a binary classification problem. Dozens of methods, built from various types of machine learning and deep learning algorithms, have been published over the last two decades for predicting contacts. Recently, many groups, including Google DeepMind, have demonstrated that reformulating the problem as a multi-class classification problem is a more promising direction to pursue. As an alternative approach, we recently proposed real-valued distance predictions, formulating the problem as a regression problem. The nuances of protein 3D structures make this formulation appropriate, allowing predictions …

Deepfrag-K: A Fragment-Based Deep Learning Approach For Protein Fold Recognition, Wessam Elhefnawy, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

Background: One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment level to improve the accuracy of protein fold recognition. DeepFrag-k is composed of two stages: the first stage employs a multi-modal Deep Belief Network (DBN) to predict the potential structural fragments given a sequence, represented as a fragment vector, and then the second stage uses a deep convolutional neural network (CNN) to classify the fragment vector into the corresponding fold.

Results: Our results show that DeepFrag-k yields …

Computational Methods For Predicting Protein-Protein Interactions And Binding Sites, Yiwei Li

Electronic Thesis and Dissertation Repository

Proteins are essential to organisms and participate in virtually every process within cells. Quite often, they keep the cells functioning by interacting with other proteins. This process is called protein-protein interaction (PPI). The bonding amino acid residues during the process of protein-protein interactions are called PPI binding sites. Identifying PPIs and PPI binding sites are fundamental problems in system biology.

Experimental methods for solving these two problems are slow and expensive. Therefore, great efforts are being made towards increasing the performance of computational methods.

We present DELPHI, a deep learning based program for PPI site prediction and SPRINT, an algorithmic …

Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the “second secret of life.” The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of …

Wind Power Forecasting Methods Based On Deep Learning: A Survey, Xing Deng, Haijian Shao, Chunlong Hu, Dengbiao Jiang, Yingtao Jiang

Electrical & Computer Engineering Faculty Research

Accurate wind power forecasting in wind farm can effectively reduce the enormous impact on grid operation safety when high permeability intermittent power supply is connected to the power grid. Aiming to provide reference strategies for relevant researchers as well as practical applications, this paper attempts to provide the literature investigation and methods analysis of deep learning, enforcement learning and transfer learning in wind speed and wind power forecasting modeling. Usually, wind speed and wind power forecasting around a wind farm requires the calculation of the next moment of the definite state, which is usually achieved based on the state of …

Image And Video-Based Autism Spectrum Disorder Detection Via Deep Learning, Mindi Ruan

Graduate Theses, Dissertations, and Problem Reports

People with Autism Spectrum Disorder (ASD) show atypical attention to social stimuli and aberrant gaze when viewing images of the physical world. However, it is unknown how they perceive the world from a first-person perspective. In this study, we used machine learning to classify photos taken in three different categories (people, indoors, and outdoors) as either having been taken by individuals with ASD or by peers without ASD. Our classifier effectively discriminated photos from all three categories but was particularly successful at classifying photos of people with >80% accuracy. Importantly, the visualization of our model revealed critical features that led …

Integration Of Random Forest Classifiers And Deep Convolutional Neural Networks For Classification And Biomolecular Modeling Of Cancer Driver Mutations, Steve Agajanian, Odeyemi Oluyemi, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to …

Model-Based Deep Autoencoders For Characterizing Discrete Data With Application To Genomic Data Analysis, Tian Tian

Dissertations

Deep learning techniques have achieved tremendous successes in a wide range of real applications in recent years. For dimension reduction, deep neural networks (DNNs) provide a natural choice to parameterize a non-linear transforming function that maps the original high dimensional data to a lower dimensional latent space. Autoencoder is a kind of DNNs used to learn efficient feature representation in an unsupervised manner. Deep autoencoder has been widely explored and applied to analysis of continuous data, while it is understudied for characterizing discrete data. This dissertation focuses on developing model-based deep autoencoders for modeling discrete data. A motivating example of …

Highly Accurate Fragment Library For Protein Fold Recognition, Wessam Elhefnawy

Computer Science Theses & Dissertations

Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease understanding. Fold recognition is a key step in the protein structure discovery process, especially when traditional computational methods fail to yield convincing structural homologies. In this work, we present a new protein fold recognition approach using machine learning and data mining methodologies.

First, we identify a protein structural fragment library (Frag-K) composed of a …

Discerning Novel Splice Junctions Derived From Rna-Seq Alignment: A Deep Learning Approach, Yi Zhang, Xinan Liu, James N. Macleod, Jinze Liu

Computer Science Faculty Publications

Background: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both possible and widely available. RNA-seq provides unprecedented resolution to identify gene structures and resolve the diversity of splicing variants. However, currently available ab initio aligners are vulnerable to spurious alignments due to random sequence matches and sample-reference genome discordance. As a consequence, a significant set of false positive exon junction predictions would be introduced, which will further confuse downstream analyses of splice variant discovery and abundance estimation.

Results: …

Deep Learning For Segmentation Of 3d Cryo-Em Images, Devin Reid Haslam

Computer Science Theses & Dissertations

Cryo-electron microscopy (cryo-EM) is an emerging biophysical technique for structural determination of protein complexes. However, accurate detection of secondary structures is still challenging when cryo-EM density maps are at medium resolutions (5-10 Å). Most existing methods are image processing methods that do not fully utilize available images in the cryo-EM database. In this paper, we present a deep learning approach to segment secondary structure elements as helices and β-sheets from medium- resolution density maps. The proposed 3D convolutional neural network is shown to detect secondary structure locations with an F1 score between 0.79 and 0.88 for six simulated test cases. …