Machine learning has been utilized in bio-imaging in recent years, however as it is relatively new and evolving, some researchers who wish to utilize machine learning tools have limited access because of a lack of programming knowledge. In electron microscopy (EM), immunogold labeling is commonly used to identify the target proteins, however the manual annotation of the gold particles in the images is a time-consuming and laborious process. Conventional image processing tools could provide semi-automated annotation, but those require that users make manual adjustments for every step of the analysis. To create a new high-throughput image analysis tool for immuno-EM, I developed a deep learning pipeline that was designed to deliver a completely automated annotation of immunogold particles in EM images. The program was made accessible for users without prior programming experience and was also expanded to be used on different types of immuno-EM images. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Living in the booming age of information, we have to rely on powerful information retrieval tools to seek the unique piece of desired knowledge from such a big data world, like using personalized search engine and recommendation systems. As one of the core components, ranking model can appear in almost everywhere as long as we need a relative order of desired/relevant entities. Based on the most general and intuitive assumption that entities without user actions (e.g., clicks, purchase, comments) are of less interest than those with user actions, the objective function of pairwise ranking models is formulated by measuring the contrast between positive (with actions) and negative (without actions) entities. This contrastive relationship is the core of pairwise ranking models. The construction of these positive-negative pairs has great influence on the model inference accuracy. Especially, it is challenging to explore the entity relationships in heterogeneous information network. In this thesis, we aim at advancing the development of the methodologies and principles of mining heterogeneous information network through learning entity relations from a pairwise learning to rank optimization perspective. More specifically we first show the connections of different relation learning objectives modified from different ranking metrics including both pairwise and list-wise objectives. We prove that most of popular ranking metrics can be optimized in the same lower bound. Secondly, we propose the class-imbalance problem imposed by entity relation comparison in ranking objectives, and prove that class-imbalance problem can lead to frequency 5 clustering and gradient vanishment problems. As a response, we indicate out that developing a fast adaptive sampling method is very essential to boost the pairwise ranking model. To model the entity dynamic dependency, we propose to unify the individual-level interaction and union-level interactions, and result in a multi-order attentive ranking model to improve the preference inference from multiple views.

The ubiquitous presence of automated decision-making systems that have a performance comparable to humans brought attention towards the necessity of interpretability for the generated predictions. Whether the goal is predicting the system’s behavior when the input changes, building user trust, or expert assistance in improving the machine learning methods, interpretability is paramount when the problem is not sufficiently validated in real applications, and when unacceptable results lead to significant consequences. While for humans, there are no standard interpretations for the decisions they make, the complexity of the systems with advanced information-processing capacities conceals the detailed explanations for individual predictions, encapsulating them under layers of abstractions and complex mathematical operations. Interpretability for deep learning classifiers becomes, thus, a challenging research topic where the ambiguity of the problem statement allows for multiple exploratory paths. Our work focuses on generating natural language interpretations for individual predictions of deep learning text classifiers. We propose a framework for extracting and identifying the phrases of the training corpus that influence the prediction confidence the most through unsupervised key phrase extraction and neural predictions. We assess the contribution margin that the added justification has when the deep learning model predicts the class probability of a text instance, by introducing and defining a contribution metric that allows one to quantify the fidelity of the explanation to the model. We assess both the performance impact of the proposed approach on the classification task as quantitative analysis and the quality of the generated justifications through extensive qualitative and error analysis. This methodology manages to capture the most influencing phrases of the training corpus as explanations that reveal the linguistic features used for individual test predictions, allowing humans to predict the behavior of the deep learning classifier.

<div><div><div><p>Determining the locations of nuclei in Zebrafish embryos is crucial for the study of the spatio-temporal behavior of these cells during the development process. With image seg- mentations, not only the location of the cell can be known, but also determine if each pixels is background or part of a nucleus. Traditional image processing techniques have been thor- oughly applied to this problem. These techniques suffer from bad generalization, many times relying on heuristic that apply to a specific type of image to reach a high accuracy when doing pixel by pixel segmentation. In previous work from our research lab, wavelet image segmentation was applied, but heuristics relied on expected nuclei size .</p><p>Machine learning techniques, and more specifically convolutional neural networks, have recently revolutionized image processing and computer vision in general. By relying on vast amounts of data and deep networks, problems in computer vision such as classification or semantic segmentation have reached new state of the art performance, and these techniques are continuously improving and pushing the boundaries of state of the art.</p><p>The lack of labeled data to as input to a machine learning model was the main bottleneck. To overcome this, this work utilized Amazon Turk platform. This platform allows users to create a task and give instructions to ‘Workers‘ , which agree to a price to complete each task. The data was preprocessed before being presented to the workers, and revised to make sure it was properly labeled.</p><p>Once labeled data was ready, the images and its corresponding segmented labels were used to train a U-Net model. In a nutshell, this models takes the input image, and at different scales, maps the image to a smaller vector. From this smaller vector, the model , again at different scales, constructs an image from this vector. During model training, the weights of the model are updated so that the image that is reconstructed minimizes the difference between the label image and the pixel segmentation.</p><p>We show that this method not only fits better the labeled ground truth image by the workers, but also generalizes well to other images of Zebrafish embryos. Once the model is trained, inference to obtain the segmented image is also orders of magnitude faster than previous techniques, including our previous wavelet segmentation method.</p></div></div></div>

With the rapid development of deep learning techniques, the application of Convolutional Neural Network (CNN) has benefited the task of target object recognition. Several state-of-the-art object detectors have achieved excellent performance on the precision for object recognition. When it comes to applying the detection results for the real world application of collaborative robots, the reliability and robustness of the target object detection stage is essential to support efficient task allocation. In this work, collaborative robots task allocation is based on the assumption that each individual robotic agent possesses specialized capabilities to be matched with detected targets representing tasks to be performed in the surrounding environment which impose specific requirements. The goal is to reach a specialized labor distribution among the individual robots based on best matching their specialized capabilities with the corresponding requirements imposed by the tasks. In order to further improve task recognition with convolutional neural networks in the context of robotic task allocation, this thesis proposes an innovative approach for progressively refining the target detection process by taking advantage of the fact that additional images can be collected by mobile cameras installed on robotic vehicles. The proposed methodology combines a CNN-based object detection module with a refinement module. For the detection module, a two-stage object detector, Mask RCNN, for which some adaptations on region proposal generation are introduced, and a one-stage object detector, YOLO, are experimentally investigated in the context considered. The generated recognition scores serve as input for the refinement module. In the latter, the current detection result is considered as the a priori evidence to enhance the next detection for the same target with the goal to iteratively improve the target recognition scores. Both the Bayesian method and the Dempster-Shafer theory are experimentally investigated to achieve the data fusion process involved in the refinement process. The experimental validation is conducted on indoor search-and-rescue (SAR) scenarios and the results presented in this work demonstrate the feasibility and reliability of the proposed progressive refinement framework, especially when the combination of adapted Mask RCNN and D-S theory data fusion is exploited.

<p>Through the computing advance and GPU (Graphics Processing Unit) availability for math calculation, the deep learning field becomes more popular and prevalent. Object detection with deep learning, which is the part of image processing, plays an important role in automatic vehicle drive and computer vision. Object detection includes object localization and object classification. Object localization involves that the computer looks through the image and gives the correct coordinates to localize the object. Object classification is that the computer classification targets into different categories. The traditional image object detection pipeline idea is from Fast/Faster R-CNN [32] [58]. The region proposal network generates the contained objects areas and put them into classifier. The first step is the object localization while the second step is the object classification. The time cost for this pipeline function is not efficient. Aiming to address this problem, You Only Look Once (YOLO) [4] network is born. YOLO is the single neural network end-to-end pipeline with the image processing speed being 45 frames per second in real time for network prediction. In this thesis, the convolution neural networks are introduced, including the state of art convolutional neural networks in recently years. YOLO implementation details are illustrated step by step. We adopt the YOLO network for our applications since the YOLO network has the faster convergence rate in training and provides high accuracy and it is the end to end architecture, which makes networks easy to optimize and train. </p>

Context: In recent years, households have been increasing energy consumption to very high levels, where it is no longer sustainable. There has been a dire need to find a way to use energy more sustainably due to the increase in the usage of energy consumption. One of the main causes of this unsustainable usage of energy consumption is that the user is not much acquainted with the energy consumed by the smart appliances (dishwasher, refrigerator, washing machine etc) in their households. By letting the household users know the energy usage consumed by the smart appliances. For the energy analytics companies, they must analyze the energy consumed by the smart appliances present in a house. To achieve this Kelly et. al. [7] have performed the task of energy disaggregation by using deep neural networks and producing good results. Zhang et. al. [7] has gone even a step further in improving the deep neural networks proposed by Kelly et. al., The task was performed by Non-intrusive load monitoring (NILM) technique. Objectives: The thesis aims to assess the performance of the deep neural networks which are proposed by Kelly et.al. [7], and Zhang et. al. [8]. We use deep neural networks for disaggregation of the dishwasher energy consumption, in the presence of vampire loads such as electric heaters, in a Swedish household setting. We also try to identify the training time of the proposed deep neural networks.  Methods: An intensive literature review is done to identify state-of-the-art deep neural network techniques used for energy disaggregation.  All the experiments are being performed on the dataset provided by the energy analytics company Eliq AB. The data is collected from 4 households in Sweden. All the households consist of vampire loads, an electrical heater, whose power consumption can be seen in the main power sensor. A separate smart plug is used to collect the dishwasher power consumption data. Each algorithm training is done on 2 houses with data provided by all the houses except two, which will be used for testing. The metrics used for analyzing the algorithms are Accuracy, Recall, Precision, Root mean square error (RMSE), and F1 measure. These software metrics would help us identify the best suitable algorithm for the disaggregation of dishwasher energy in our case.  Results: The results from our study have proved that Gated recurrent unit (GRU) performed best when compared to the other neural networks in our study like Simple recurrent neural network (SRN), Convolutional Neural Network (CNN), Long short-Term memory (LSTM) and Recurrent convolution neural network (RCNN). The Accuracy, RMSE and the F1 score of the GRU algorithm are higher when compared with the other algorithms. Also, if the user does not consider F1 score and RMSE as an evaluation metric and considers training time as his or her metric, then Simple recurrent neural network outperforms all the other neural nets with an average training time of 19.34 minutes.

OBJECTIVES: Cephalometric analysis is a tool used in orthodontics for craniofacial growth assessment. Magnitude and direction of mandibular growth pose challenges that may impede successful orthodontic treatment. Accurate growth prediction enables the practitioner to improve diagnostics and orthodontic treatment planning. Deep learning provides a novel method due to its ability to analyze massive quantities of data. We compared the growth prediction capabilities of a novel deep learning algorithm with an industry-standard method. METHODS: Using OrthoDx™, 17 mandibular landmarks were plotted on selected serial cephalograms of 101 growing subjects, obtained from the Forsyth Moorrees Twin Study. The Deep Learning Algorithm (DLA) was trained for a 2-year prediction with 81 subjects. X/Y coordinates of initial and final landmark positions were inputted into a multilayer perceptron that was trained to improve its growth prediction accuracy over several iterations. These parameters were then used on 20 test subjects and compared to the ground truth landmark locations to compute the accuracy. The 20 subjects’ growth was also predicted using Ricketts’s growth prediction (RGP) in Dolphin Imaging™ 11.9 and compared to the ground truth. Mean Absolute Error (MAE) of Ricketts and DLA were then compared to each other, and human landmark detection error used as a clinical reference mean (CRM). RESULTS: The 2-year mandibular growth prediction MAE was 4.21mm for DLA and 3.28mm for RGP. DLA’s error for skeletal landmarks was 2.11x larger than CRM, while RGP was 1.78x larger. For dental landmarks, DLA was 2.79x, and Ricketts was 1.73x larger than CRM. CONCLUSIONS: DLA is currently not on par with RGP for a 2-year growth prediction. However, an increase in data volume and increased training may improve DLA’s prediction accuracy. Regardless, significant future improvements to all growth prediction methods would more accurately assess growth from lateral cephalograms and improve orthodontic diagnoses and treatment plans.

To combat fake news, researchers mostly focused on detecting fake news and journalists built and maintained fact-checking sites (e.g., Snopes.com and Politifact.com). However, fake news dissemination has been greatly promoted by social media sites, and these fact-checking sites have not been fully utilized. To overcome these problems and complement existing methods against fake news, in this thesis, we propose a deep-learning based fact-checking URL recommender system to mitigate impact of fake news in social media sites such as Twitter and Facebook. In particular, our proposed framework consists of a multi-relational attentive module and a heterogeneous graph attention network to learn complex/semantic relationship between user-URL pairs, user-user pairs, and URL-URL pairs. Extensive experiments on a real-world dataset show that our proposed framework outperforms seven state-of-the-art recommendation models, achieving at least 3~5.3% improvement.

Preclinical research for developing new drugs is a long and expensive procedure. Experiments relying on image acquisition and analysis tend to be low throughput and use reporter systems that may influence the studied cells. With image-based assays focusing on extracting qualitative information from microscopic images of mammalian cells, more cost-efficient and high-throughput analyses are possible. Furthermore, studying cell morphology has proven to be a good indicator of cell phenotype. Using hand-crafted feature descriptors based on cell morphology, label-free quantification of cell apoptosis has been achieved. These hand-crafted descriptors are based on cell characteristics translated to quantifiable metrics, but risk being biased towards easily observable features and therefore miss subtle ones.         This project proposes an alternative approach by generating a latent representation of cell features using deep learning models and aims to find if they can compete with pre-defined hand-crafted representations in classifying live or dead cells. For this purpose, three deep learning models are implemented, one autoencoder and two variational-autoencoder. We develop a core architecture shared between the models based on a convolutional neural network using a latent space with 16 dimensions. We then train the models to recreate single-cell images of SKOV3 ovarian cancer cells. The latent representation was extracted at specific checkpoints during training and later used for training a logistic regression classifier. Finally, comparing classification accuracy between the hand-crafted feature representations and generated representation was made with novel cell images. The generated representations show a slight but consistent increase in classification accuracy, up to 4.9 percent points, even without capturing all morphological details in the recreation. Thus, we conclude that it is possible for generated representations to outperform hand-crafted feature descriptors in live or dead cell classification.