Journal of Data Science

The last decade has seen a vast increase of the abundance of data, fuelling the need for data analytic tools that can keep up with the data size and complexity. This has changed the way we analyze data: moving from away from single data analysts working on their individual computers, to large clusters and distributed systems leveraged by dozens of data scientists. Technological advances have been addressing the scalability aspects, however, the resulting complexity necessitates that more people are involved in a data analysis than before. Collaboration and leveraging of other’s work becomes crucial in the modern, interconnected world of data science. In this article we propose and describe an open-source, web-based, collaborative visualization and data analysis platform RCloud. It de-couples the user from the location of the data analysis while preserving security, interactivity and visualization capabilities. Its collaborative features enable data scientists to explore, work together and share analyses in a seamless fashion. We describe the concepts and design decisions that enabled it to support large data science teams in the industry and academia.

Estimating healthcare expenditures is important for policymakers and clinicians. The expenditure of patients facing a life-threatening illness can often be segmented into four distinct phases: diagnosis, treatment, stable, and terminal phases. The diagnosis phase encompasses healthcare expenses incurred prior to the disease diagnosis, attributed to frequent healthcare visits and diagnostic tests. The second phase, following diagnosis, typically witnesses high expenditure due to various treatments, gradually tapering off over time and stabilizing into a stable phase, and eventually to a terminal phase. In this project, we introduce a pre-disease phase preceding the diagnosis phase, serving as a baseline for healthcare expenditure, and thus propose a five-phase to evaluate the healthcare expenditures. We use a piecewise linear model with three population-level change points and $4p$ subject-level parameters to capture expenditure trajectories and identify transitions between phases, where p is the number of covariates. To estimate the model’s coefficients, we apply generalized estimating equations, while a grid-search approach is used to estimate the change-point parameters by minimizing the residual sum of squares. In our analysis of expenditures for stages I–III pancreatic cancer patients using the SEER-Medicare database, we find that the diagnostic phase begins one month before diagnosis, followed by an initial treatment phase lasting three months. The stable phase continues until eight months before death, at which point the terminal phase begins, marked by a renewed increase in expenditures.

Large pretrained transformer models have revolutionized modern AI applications with their state-of-the-art performance in natural language processing (NLP). However, their substantial parameter count poses challenges for real-world deployment. To address this, researchers often reduce model size by pruning parameters based on their magnitude or sensitivity. Previous research has demonstrated the limitations of magnitude pruning, especially in the context of transfer learning for modern NLP tasks. In this paper, we introduce a new magnitude-based pruning algorithm called mixture Gaussian prior pruning (MGPP), which employs a mixture Gaussian prior for regularization. MGPP prunes non-expressive weights under the guidance of the mixture Gaussian prior, aiming to retain the model’s expressive capability. Extensive evaluations across various NLP tasks, including natural language understanding, question answering, and natural language generation, demonstrate the superiority of MGPP over existing pruning methods, particularly in high sparsity settings. Additionally, we provide a theoretical justification for the consistency of the sparse transformer, shedding light on the effectiveness of the proposed pruning method.

When computations such as statistical simulations need to be carried out on a high performance computing (HPC) cluster, typical questions arise among researchers or practitioners. How do I interact with a HPC cluster? Do I need to type a long host name and also a password on every single login or file transfer? Why does my locally working code not run anymore on the HPC cluster? How can I install the latest versions of software on a HPC cluster to match my local setup? How can I submit a job and monitor its progress? This tutorial provides answers to such questions with experiments on an example HPC cluster.

Connections between subpar dietary choices and negative health consequences are well established in the field of nutritional epidemiology. Consequently, in the United States, there is a standard practice of conducting regular surveys to evaluate dietary habits. One notable example is the National Health and Nutrition Examination Survey (NHANES) conducted every two years by the Center for Disease Control (CDC). Several scoring methods have been developed to assess the quality of diet in the overall population as well as different pertinent subgroups using dietary recall data collected in these surveys. The Healthy Eating Index (HEI) is one such metric, developed based on recommendations from the United States Department of Health and Human Services (HHS) and Department of Agriculture (USDA) and widely used by nutritionists. Presently, there is a scarcity of user-friendly statistical software tools implementing the scoring of these standard scoring metrics. Herein, we develop an R package heiscore to address this need. Our carefully designed package, with its many user-friendly features, increases the accessibility of the HEI scoring using three different methods outlined by the National Cancer Institute (NCI). Additionally, we provide functions to visualize multidimensional diet quality data via various graphing techniques, including bar charts and radar charts. Its utility is illustrated with many examples, including comparisons between different demographic groups.

Yang et al. (2004) developed the two-dimensional principal component analysis (2DPCA) for image representation and recognition, widely used in different fields, including face recognition, biometrics recognition, cancer diagnosis, tumor classification, and others. 2DPCA has been proven to perform better and computationally more efficiently than traditional principal component analysis (PCA). However, some theoretical properties of 2DPCA are still unknown, including determining the number of principal components (PCs) in the training set, which is the critical step in applying 2DPCA. Without rigorous criteria for determining the number of PCs hampers the generalization of the application of 2DPCA. Given this issue, we propose a new method based on parallel analysis to determine the number of PCs in 2DPCA with statistical justification. Several image classification experiments demonstrate that the proposed method compares favourably to other state-of-the-art approaches regarding recognition accuracy and storage requirement, with a low computational cost.

The ultrasonic testing has been considered a promising method for diagnosing and characterizing masonry walls. As ultrasonic waves tend to travel faster in denser materials, their use is common in evaluating the conditions of various materials. Presence of internal voids, e.g., would alter the wave path, and this distinct behavior could be employed to identify unknown conditions within the material, allowing for the assessment of its condition. Therefore, we applied mixed models and Gaussian processes to analyze the behavior of ultrasonic waves on masonry walls and identify relevant factors impacting their propagation. We observed that the average propagation time behavior differs depending on the material for both models. Additionally, the condition of the wall influences the propagation time. Gaussian process and mixed model performances are compared, and we conclude that these models can be useful in a classification model to automatically identify anomalies within masonry walls.

Attention mechanism has become an almost ubiquitous model architecture in deep learning. One of its distinctive features is to compute non-negative probabilistic distribution to re-weight input representations. This work reconsiders attention weights as bidirectional coefficients instead of probabilistic measures for potential benefits in interpretability and representational capacity. After analyzing the iteration process of attention scores through backwards gradient propagation, we proposed a novel activation function, TanhMax, which possesses several favorable properties to satisfy the requirements of bidirectional attention. We conduct a battery of experiments to validate our analyses and advantages of proposed method on both text and image datasets. The results show that bidirectional attention is effective in revealing input unit’s semantics, presenting more interpretable explanations and increasing the expressive power of attention-based model.

Analyzing the gene-environment interaction (GEI) is crucial for understanding the etiology of many complex traits. Among various types of study designs, case-control studies are popular for analyzing gene-environment interactions due to their efficiency in collecting covariate information. Extensive literature explores efficient estimation under various assumptions made about the relationship between genetic and environmental variables. In this paper, we comprehensively review the methods based on or related to the retrospective likelihood, including the methods based on the hypothetical population concept, which has been largely overlooked in GEI research in the past decade. Furthermore, we establish the methodological connection between these two groups of methods by deriving a new estimator from both the retrospective likelihood and the hypothetical population perspectives. The validity of the derivation is demonstrated through numerical studies.

Imbalanced datasets present a significant challenge for machine learning models, often leading to biased predictions. To address this issue, data augmentation techniques are widely used to generate new samples for the minority class. However, in this paper, we challenge the common assumption that data augmentation is necessary to improve predictions on imbalanced datasets. Instead, we argue that adjusting the classifier cutoffs without data augmentation can produce similar results to oversampling techniques. Our study provides theoretical and empirical evidence to support this claim. Our findings contribute to a better understanding of the strengths and limitations of different approaches to dealing with imbalanced data, and help researchers and practitioners make informed decisions about which methods to use for a given task.