Machine Intelligence for Advanced Medical Data Analysis: Manifold Learning Approach

In the current work, linear and non-linear manifold learning techniques, specifically Principle Component Analysis (PCA) and Laplacian Eigenmaps, are studied in detail. Their applications in medical image and shape analysis are investigated. In the first contribution, a manifold learning-based multi-modal image registration technique is developed, which results in a unified intensity system through intensity transformation between the reference and sensed images. The transformation eliminates intensity variations in multi-modal medical scans and hence facilitates employing well-studied mono-modal registration techniques. The method can be used for registering multi-modal images with full and partial data. Next, a manifold learning-based scale invariant global shape descriptor is introduced. The proposed descriptor benefits from the capability of Laplacian Eigenmap in dealing with high dimensional data by introducing an exponential weighting scheme. It eliminates the limitations tied to the well-known cotangent weighting scheme, namely dependency on triangular mesh representation and high intra-class quality of 3D models. In the end, a novel descriptive model for diagnostic classification of pulmonary nodules is presented. The descriptive model benefits from structural differences between benign and malignant nodules for automatic and accurate prediction of a candidate nodule. It extracts concise and discriminative features automatically from the 3D surface structure of a nodule using spectral features studied in the previous work combined with a point cloud-based deep learning network. Extensive experiments have been conducted and have shown that the proposed algorithms based on manifold learning outperform several state-of-the-art methods. Advanced computational techniques with a combination of manifold learning and deep networks can play a vital role in effective healthcare delivery by providing a framework for several fundamental tasks in image and shape processing, namely, registration, classification, and detection of features of interest

Designing algorithms to aid discovery by chemical robots

Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery

Efficient Privacy-Aware Imagery Data Analysis

The widespread use of smartphones and camera-coupled Internet of Thing (IoT) devices triggers an explosive growth of imagery data. To extract and process the rich contents contained in imagery data, various image analysis techniques have been investigated and applied to a spectrum of application scenarios. In recent years, breakthroughs in deep learning have powered a new revolution for image analysis in terms of effectiveness with high resource consumption. Given the fact that most smartphones and IoT devices have limited computational capability and battery life, they are not ready for the processing of computational intensive analytics over imagery data collected by them, especially when deep learning is involved. To resolve the bottleneck of computation, storage, and energy for these resource constrained devices, offloading complex image analysis to public cloud computing platforms has become a promising trend in both academia and industry. However, an outstanding challenge with public cloud is on the protection of sensitive information contained in many imagery data, such as personal identities and financial data. Directly sending imagery data to the public cloud can cause serious privacy concerns and even legal issues. In this dissertation, I propose a comprehensive privacy-preserving imagery data analysis framework which can be integrated in different application scenarios to assist image analysis for resource-constrained devices with efficiency, accuracy, and privacy protection. I first identify security challenges in the utilization of public cloud for image analysis. Then, I design and develop a set of novel solutions to address these challenges. These solutions will be featured by strong privacy guarantee, lightweight computation, low accuracy loss compared with image analysis without privacy protection. To optimize the communication overhead and resource utilization of using cloud computing, I investigate edge computing, which is a promising technique to ameliorate the high communication overhead in cloud-assisted architectures. Furthermore, to boost the performance of my solutions under both cloud and edge deployment, I also provide a set of pluggable enhancement modules to be applied to meet different requirements for various tasks. By exploring the features of edge computing and cloud computing, I flexibly incorporate them as a comprehensive framework to provide privacy-preserving image analysis services

Extensible Structure-Informed Prediction of Formation Energy with Improved Accuracy and Usability employing Neural Networks

In the present paper, we introduce a new neural network-based tool for the prediction of formation energies of atomic structures based on elemental and structural features of Voronoi-tessellated materials. We provide a concise overview of the connection between the machine learning and the true material-property relationship, how to improve the generalization accuracy by reducing overfitting, and how new data can be incorporated into the model to tune it to a specific material system. The present work resulted in three final models optimized for (1) highest test accuracy on the Open Quantum Materials Database (OQMD), (2) performance in the discovery of new materials, and (3) performance at a low computational cost. On a test set of 21,800 compounds randomly selected from OQMD, they achieve a mean average error (MAE) of 28, 40, and 42 meV/atom, respectively. The second model provides better predictions on materials far from ones reported in OQMD, while the third reduces the computational cost by a factor of 8. We collect our results in a new open-source tool called SIPFENN (Structure-Informed Prediction of Formation Energy using Neural Networks). SIPFENN not only improves the accuracy beyond existing models but also ships in a ready-to-use form with pre-trained neural networks and a GUI interface. By virtue of this, it can be included in DFT calculations routines at nearly no cost