A common challenge in estimating parameters of probability density functions is the intractability of the normalizing constant. While in such cases maximum likelihood estimation may be implemented using numerical integration, the approach becomes computationally intensive. The score matching method of Hyv\"arinen [2005] avoids direct calculation of the normalizing constant and yields closed-form estimates for exponential families of continuous distributions over $\mathbb{R}^m$. Hyv\"arinen [2007] extended the approach to distributions supported on the non-negative orthant, $\mathbb{R}_+^m$. In this paper, we give a generalized form of score matching for non-negative data that improves estimation efficiency. As an example, we consider a general class of pairwise interaction models. Addressing an overlooked inexistence problem, we generalize the regularized score matching method of Lin et al. [2016] and improve its theoretical guarantees for non-negative Gaussian graphical models.

A central machine is interested in estimating the underlying structure of a sparse Gaussian Graphical Model (GGM) from datasets distributed across multiple local machines. The local machines can communicate with the central machine through a wireless multiple access channel. In this paper, we are interested in designing effective strategies where reliable learning is feasible under power and bandwidth limitations. Two approaches are proposed: Signs and Uncoded methods. In Signs method, the local machines quantize their data into binary vectors and an optimal channel coding scheme is used to reliably send the vectors to the central machine where the structure is learned from the received data. In Uncoded method, data symbols are scaled and transmitted through the channel. The central machine uses the received noisy symbols to recover the structure. Theoretical results show that both methods can recover the structure with high probability for large enough sample size. Experimental results indicate the superiority of Signs method over Uncoded method under several circumstances.

Data extracted from software repositories is used intensively in Software Engineering research, for example, to predict defects in source code. In our research in this area, with data from open source projects as well as an industrial partner, we noticed several shortcomings of conventional data mining approaches for classification problems: (1) Domain experts' acceptance is of critical importance, and domain experts can provide valuable input, but it is hard to use this feedback. (2) The evaluation of the model is not a simple matter of calculating AUC or accuracy. Instead, there are multiple objectives of varying importance, but their importance cannot be easily quantified. Furthermore, the performance of the model cannot be evaluated on a per-instance level in our case, because it shares aspects with the set cover problem. To overcome these problems, we take a holistic approach and develop a rule mining system that simplifies iterative feedback from domain experts and can easily incorporate the domain-specific evaluation needs. A central part of the system is a novel multi-objective anytime rule mining algorithm. The algorithm is based on the GRASP-PR meta-heuristic but extends it with ideas from several other approaches. We successfully applied the system in the industrial context. In the current article, we focus on the description of the algorithm and the concepts of the system. We provide an implementation of the system for reuse.

Machine learning (ML), artificial intelligence (AI) and other modern statistical methods are providing new opportunities to operationalize previously untapped and rapidly growing sources of data for patient benefit. Whilst there is a lot of promising research currently being undertaken, the literature as a whole lacks: transparency; clear reporting to facilitate replicability; exploration for potential ethical concerns; and, clear demonstrations of effectiveness. There are many reasons for why these issues exist, but one of the most important that we provide a preliminary solution for here is the current lack of ML/AI- specific best practice guidance. Although there is no consensus on what best practice looks in this field, we believe that interdisciplinary groups pursuing research and impact projects in the ML/AI for health domain would benefit from answering a series of questions based on the important issues that exist when undertaking work of this nature. Here we present 20 questions that span the entire project life cycle, from inception, data analysis, and model evaluation, to implementation, as a means to facilitate project planning and post-hoc (structured) independent evaluation. By beginning to answer these questions in different settings, we can start to understand what constitutes a good answer, and we expect that the resulting discussion will be central to developing an international consensus framework for transparent, replicable, ethical and effective research in artificial intelligence (AI-TREE) for health.

There has been a surge of interest in using machine learning (ML) to automatically detect malware through their dynamic behaviors. These approaches have achieved significant improvement in detection rates and lower false positive rates at large scale compared with traditional malware analysis methods. ML in threat detection has demonstrated to be a good cop to guard platform security. However it is imperative to evaluate - is ML-powered security resilient enough? In this paper, we juxtapose the resiliency and trustworthiness of ML algorithms for security, via a case study of evaluating the resiliency of ransomware detection via the generative adversarial network (GAN). In this case study, we propose to use GAN to automatically produce dynamic features that exhibit generalized malicious behaviors that can reduce the efficacy of black-box ransomware classifiers. We examine the quality of the GAN-generated samples by comparing the statistical similarity of these samples to real ransomware and benign software. Further we investigate the latent subspace where the GAN-generated samples lie and explore reasons why such samples cause a certain class of ransomware classifiers to degrade in performance. Our focus is to emphasize necessary defense improvement in ML-based approaches for ransomware detection before deployment in the wild. Our results and discoveries should pose relevant questions for defenders such as how ML models can be made more resilient for robust enforcement of security objectives.

Abstract: Classification is an important supervised machine learning method, which is necessary and challenging issue for ecological research. It offers a way to classify a dataset into subsets that share common patterns. Notably, there are many classification algorithms to choose from, each making certain assumptions about the data and about how classification should be formed. In this paper, we applied eight machine learning classification algorithms such as Decision Trees, Random Forest, Artificial Neural Network, Support Vector Machine, Linear Discriminant Analysis, k-nearest neighbors, Logistic Regression and Naive Bayes on ecological data. The goal of this study is to compare different machine learning classification algorithms in ecological dataset. In this analysis we have checked the accuracy test among the algorithms. In our study we conclude that Linear Discriminant Analysis and k-nearest neighbors are the best methods among all other methods.

With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis using gene expression data continues to pose challenges due to the high dimensionality and complexity of the data. Here we present models of deep learning (DL) and apply them to gene expression data for the diagnosis and categorization of cancer. In this study, we have developed two DL models using messenger ribonucleic acid (mRNA) datasets available from the Genomic Data Commons repository. Our models achieved 98% accuracy in cancer detection, with false negative and false positive rates below 1.7%. In our results, we demonstrated that 18 out of 32 cancer-typing classifications achieved more than 90% accuracy. Due to the limitation of a small sample size (less than 50 observations), certain cancers could not achieve a higher accuracy in typing classification, but still achieved high accuracy for the cancer detection task. To validate our models, we compared them with traditional statistical models. The main advantage of our models over traditional cancer detection is the ability to use data from various cancer types to automatically form features to enhance the detection and diagnosis of a specific cancer type.

Deep neural network models used for medical image segmentation are large because they are trained with high-resolution three-dimensional (3D) images. Graphics processing units (GPUs) are widely used to accelerate the trainings. However, the memory on a GPU is not large enough to train the models. A popular approach to tackling this problem is patch-based method, which divides a large image into small patches and trains the models with these small patches. However, this method would degrade the segmentation quality if a target object spans multiple patches. In this paper, we propose a novel approach for 3D medical image segmentation that utilizes the data-swapping, which swaps out intermediate data from GPU memory to CPU memory to enlarge the effective GPU memory size, for training high-resolution 3D medical images without patching. We carefully tuned parameters in the data-swapping method to obtain the best training performance for 3D U-Net, a widely used deep neural network model for medical image segmentation. We applied our tuning to train 3D U-Net with full-size images of 192 x 192 x 192 voxels in brain tumor dataset. As a result, communication overhead, which is the most important issue, was reduced by 17.1%. Compared with the patch-based method for patches of 128 x 128 x 128 voxels, our training for full-size images achieved improvement on the mean Dice score by 4.48% and 5.32 % for detecting whole tumor sub-region and tumor core sub-region, respectively. The total training time was reduced from 164 hours to 47 hours, resulting in 3.53 times of acceleration.

We study multiple rule-based and machine learning (ML) models for sepsis detection. We report the first neural network detection and prediction results on three categories of sepsis. We have used the retrospective Medical Information Mart for Intensive Care (MIMIC)-III dataset, restricted to intensive care unit (ICU) patients. Features for prediction were created from only common vital sign measurements. We show significant improvement of AUC score using neural network based ensemble model compared to single ML and rule-based models. For the detection of sepsis, severe sepsis, and septic shock, our model achieves an AUC of 0.94, 0.91 and 0.89, respectively. Four hours before the onset, it predicts the same three categories with an AUC of 0.80, 0.81 and 0.84 respectively. Further, we ranked the features and found that using six vital signs consistently provides higher detection and prediction AUC for all the models tested. Our novel ensemble model achieves highest AUC in detecting and predicting sepsis, severe sepsis, and septic shock in the MIMIC-III ICU patients, and is amenable to deployment in hospital settings.

Medical data are valuable for improvement of health care, policy making and many other purposes. Vast amount of medical data are stored in different locations, on many different devices and in different data silos. Sharing medical data among different sources is a big challenge due to regulatory, operational and security reasons. One potential solution is federated machine learning ,which is a method that sends machine learning algorithms simultaneously to all data sources, train models in each source and aggregates the learned models. This strategy allows utilization of valuable data without moving them.One challenge in applying federated machine learning is the heterogeneity of data from different sources. To tackle this problem, we proposed an adaptive boosting method that increases the efficiency of federated machine learning. Using intensive care unit data from hospital, we showed that LoAdaBoost federated learning outperformed baseline method and increased communication efficiency at negligible additional cost.