Epidemiological Prediction using Deep Learning

Department of Mathematical SciencesAccurate and real-time epidemic disease prediction plays a significant role in the health system and is of great importance for policy making, vaccine distribution and disease control. From the SIR model by Mckendrick and Kermack in the early 1900s, researchers have developed a various mathematical model to forecast the spread of disease. With all attempt, however, the epidemic prediction has always been an ongoing scientific issue due to the limitation that the current model lacks flexibility or shows poor performance. Owing to the temporal and spatial aspect of epidemiological data, the problem fits into the category of time-series forecasting. To capture both aspects of the data, this paper proposes a combination of recent Deep Leaning models and applies the model to ILI (influenza like illness) data in the United States. Specifically, the graph convolutional network (GCN) model is used to capture the geographical feature of the U.S. regions and the gated recurrent unit (GRU) model is used to capture the temporal dynamics of ILI. The result was compared with the Deep Learning model proposed by other researchers, demonstrating the proposed model outperforms the previous methods.clos

A continuous-time analysis of distributed stochastic gradient

We analyze the effect of synchronization on distributed stochastic gradient algorithms. By exploiting an analogy with dynamical models of biological quorum sensing -- where synchronization between agents is induced through communication with a common signal -- we quantify how synchronization can significantly reduce the magnitude of the noise felt by the individual distributed agents and by their spatial mean. This noise reduction is in turn associated with a reduction in the smoothing of the loss function imposed by the stochastic gradient approximation. Through simulations on model non-convex objectives, we demonstrate that coupling can stabilize higher noise levels and improve convergence. We provide a convergence analysis for strongly convex functions by deriving a bound on the expected deviation of the spatial mean of the agents from the global minimizer for an algorithm based on quorum sensing, the same algorithm with momentum, and the Elastic Averaging SGD (EASGD) algorithm. We discuss extensions to new algorithms which allow each agent to broadcast its current measure of success and shape the collective computation accordingly. We supplement our theoretical analysis with numerical experiments on convolutional neural networks trained on the CIFAR-10 dataset, where we note a surprising regularizing property of EASGD even when applied to the non-distributed case. This observation suggests alternative second-order in-time algorithms for non-distributed optimization that are competitive with momentum methods.Comment: 9/14/19 : Final version, accepted for publication in Neural Computation. 4/7/19 : Significant edits: addition of simulations, deep network results, and revisions throughout. 12/28/18: Initial submissio

Inverse and forward modeling tools for biophotonic data

Biophotonic data require specific treatments due to the difficulty of directly extracting information from them. Therefore, artificial intelligence tools including machine learning and deep learning brought into play. These tools can be grouped into inverse modeling, preprocessing and data modeling categories. In each of these three categories, one research question was investigated. First, the aim was to develop a method that can acquire the Raman-like spectra from coherent anti-Stokes Raman scattering (CARS) spectra without apriori knowledge. In general, CARS spectra suffer from the non-resonant background (NRB) contribution, and existing methods were commonly implemented to remove it. However, these methods were not able to completely remove the NRB and need additional preprocessing afterward. Therefore, deep learning via the long-short-term memory network was applied and outperformed these existing methods. Then, a denoising technique via deep learning was developed for reconstructing high-quality (HQ) multimodal images (MM) from low-quality (LQ) ones. Since the measurement of HQ MM images is time-consuming, which is impractical for clinical applications, we developed a network, namely incSRCNN, to directly predict HQ images using only LQ ones. This network shows better performance when compared with standard methods. Finally, we intended to improve the accuracy of the classification model in particular when LQ Raman data or Raman data with varying quality are obtained. Therefore, a novel method based on functional data analysis was implemented, which converts the Raman data into functions and then applies functional dimension reduction followed by a classification method. The results showed better performance for the functional approach in comparison with the classical method

Optimized Matrix Feature Analysis – Convolutional Neural Network (OMFA-CNN) Model for Potato Leaf Diseases Detection System

One of the most often grown crops is the potato. As a main food, potatoes are prioritised for cultivation worldwide. Because potatoes are such a rich source of vitamins and minerals, we can create a robust system for food security. However, a number of illnesses delay the growth of agriculture and harm potato output. Consequently, early disease identification can offer a better answer for effective crop production. In this research work aim is to classify and detect the potato leave (PL) diseases using OMFA-CNN deep learning model. An optimized matrix feature analysis-CNN deep learning model for PL disease detection is implemented. In the first phase, the PLs features are extracted from the potato leave images using K-means clustering image segmentation method. At the last phase, a new OMFA-CNN model are proposed using CNN to classify virus, and bacterial diseases of PLs, The PL disease dataset consists 2351 images gathered in real-time and from the Kaggle (PlantVillage) dataset. The implemented OMFA-CNN model attained 99.3 % precision and 99 % recall on potato disease detection. The implemented method is also compared with MASK RCNN,SVM and other models and attained significantly high precision and recall

Evaluating GAM-Like Neural Network Architectures for Interpretable Machine Learning

In many machine learning applications, interpretability is of the utmost importance. Artificial intelligence is proliferating, but before you entrust your finances, your well-being, or even your life to a machine, you’d really like to be sure that it knows what it’s doing. As a human, the best way to evaluate an algorithm is to pick it apart, understand how it works, and figure out how it arrives at the decisions it does. Unfortunately, as machine learning techniques become more powerful and more complicated, reverse-engineering is becoming more difficult. Engineers often choose to implement a model that is accurate rather than one that understandable. In this work, we demonstrate a novel technique that, in certain circumstances, can be both. This work introduces a novel neural network architecture that improves interpretability without sacrificing model accuracy. We test this architecture in a number of real-world classification datasets and demonstrate that it performs almost identically to state-of-the-art methods. We introduce Pandemic, a novel image classification benchmark, to demonstrate that our architecture has further applications in deep-learning models

Current overview and way forward for the use of machine learning in the field of petroleum gas hydrates

Gas hydrates represent one of the main flow assurance challenges in the oil and gas industry as they can lead to plugging of pipelines and process equipment. In this paper we present a literature study performed to evaluate the current state of the use of machine learning methods within the field of gas hydrates with specific focus on the oil chemistry. A common analysis technique for crude oils is Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) which could be a good approach to achieving a better understanding of the chemical composition of hydrates, and the use of machine learning in the field of FT-ICR MS was therefore also examined. Several machine learning methods were identified as promising, their use in the literature was reviewed and a text analysis study was performed to identify the main topics within the publications. The literature search revealed that the publications on the combination of FT-ICR MS, machine learning and gas hydrates is limited to one. Most of the work on gas hydrates is related to thermodynamics, while FT-ICR MS is mostly used for chemical analysis of oils. However, with the combination of FT-ICR MS and machine learning to evaluate samples related to gas hydrates, it could be possible to improve the understanding of the composition of hydrates and thereby identify hydrate active compounds responsible for the differences between oils forming plugging hydrates and oils forming transportable hydrates.Current overview and way forward for the use of machine learning in the field of petroleum gas hydratespublishedVersio

A Systematic Survey of Classification Algorithms for Cancer Detection

Cancer is a fatal disease induced by the occurrence of a count of inherited issues and also a count of pathological changes. Malignant cells are dangerous abnormal areas that could develop in any part of the human body, posing a life-threatening threat. To establish what treatment options are available, cancer, also referred as a tumor, should be detected early and precisely. The classification of images for cancer diagnosis is a complex mechanism that is influenced by a diverse of parameters. In recent years, artificial vision frameworks have focused attention on the classification of images as a key problem. Most people currently rely on hand-made features to demonstrate an image in a specific manner. Learning classifiers such as random forest and decision tree were used to determine a final judgment. When there are a vast number of images to consider, the difficulty occurs. Hence, in this paper, weanalyze, review, categorize, and discuss current breakthroughs in cancer detection utilizing machine learning techniques for image recognition and classification. We have reviewed the machine learning approaches like logistic regression (LR), Naïve Bayes (NB), K-nearest neighbors (KNN), decision tree (DT), and Support Vector Machines (SVM)

Image Features for Tuberculosis Classification in Digital Chest Radiographs

Tuberculosis (TB) is a respiratory disease which affects millions of people each year, accounting for the tenth leading cause of death worldwide, and is especially prevalent in underdeveloped regions where access to adequate medical care may be limited. Analysis of digital chest radiographs (CXRs) is a common and inexpensive method for the diagnosis of TB; however, a trained radiologist is required to interpret the results, and is subject to human error. Computer-Aided Detection (CAD) systems are a promising machine-learning based solution to automate the diagnosis of TB from CXR images. As the dimensionality of a high-resolution CXR image is very large, image features are used to describe the CXR image in a lower dimension while preserving the elements in the CXR necessary for the detection of TB. In this thesis, I present a set of image features using Pyramid Histogram of Oriented Gradients, Local Binary Patterns, and Principal Component Analysis which provides high classifier performance on two publicly available CXR datasets, and compare my results to current state-of-the-art research

Evaluation of machine learning algorithms for classification of primary biological aerosol using a new UV-LIF spectrometer

Atmos. Meas. Tech., 10, 695-708, 2017 http://www.atmos-meas-tech.net/10/695/2017/ doi:10.5194/amt-10-695-2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 3.0 License.Characterisation of bioaerosols has important implications within environment and public health sectors. Recent developments in ultraviolet light-induced fluorescence (UV-LIF) detectors such as the Wideband Integrated Bioaerosol Spectrometer (WIBS) and the newly introduced Multiparameter Bioaerosol Spectrometer (MBS) have allowed for the real-time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal spores and pollen. This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents, bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification. For unsupervised learning we tested hierarchical agglomerative clustering with various different linkages. For supervised learning, 11 methods were tested, including decision trees, ensemble methods (random forests, gradient boosting and AdaBoost), two implementations for support vector machines (libsvm and liblinear) and Gaussian methods (Gaussian naïve Bayesian, quadratic and linear discriminant analysis, the k-nearest neighbours algorithm and artificial neural networks). The methods were applied to two different data sets produced using the new MBS, which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. The first data set contained mixed PSLs and the second contained a variety of laboratory-generated aerosol. Clustering in general performs slightly worse than the supervised learning methods, correctly classifying, at best, only 67. 6 and 91. 1 % for the two data sets respectively. For supervised learning the gradient boosting algorithm was found to be the most effective, on average correctly classifying 82. 8 and 98. 27 % of the testing data, respectively, across the two data sets. A possible alternative to gradient boosting is neural networks. We do however note that this method requires much more user input than the other methods, and we suggest that further research should be conducted using this method, especially using parallelised hardware such as the GPU, which would allow for larger networks to be trained, which could possibly yield better results. We also saw that some methods, such as clustering, failed to utilise the additional shape information provided by the instrument, whilst for others, such as the decision trees, ensemble methods and neural networks, improved performance could be attained with the inclusion of such information.Peer reviewe