Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data最新文献

Demographics, social determinants of health, and family history documented in the unstructured text within the electronic health records are increasingly being studied to understand how this information can be utilized with the structured data to improve healthcare outcomes. After the GPT models were released, many studies have applied GPT models to extract this information from the narrative clinical notes. Different from the existing work, our research focuses on investigating the zero-shot learning on extracting this information together by providing minimum information to the GPT model. We utilize de-identified real-world clinical notes annotated for demographics, various social determinants, and family history information. Given that the GPT model might provide text different from the text in the original data, we explore two sets of evaluation metrics, including the traditional NER evaluation metrics and semantic similarity evaluation metrics, to completely understand the performance. Our results show that the GPT-3.5 method achieved an average of 0.975 F1 on demographics extraction, 0.615 F1 on social determinants extraction, and 0.722 F1 on family history extraction. We believe these results can be further improved through model fine-tuning or few-shots learning. Through the case studies, we also identified the limitations of the GPT models, which need to be addressed in future research.

Effective disease surveillance systems require large-scale epidemiological data to improve health outcomes and quality of care for the general population. As data may be limited within a single site, multi-site data (e.g., from a number of local/regional health systems) need to be considered. Leveraging distributed data across multiple sites for epidemiological analysis poses significant challenges. Due to the sensitive nature of epidemiological data, it is imperative to design distributed solutions that provide strong privacy protections. Current privacy solutions often assume a central site, which is responsible for aggregating the distributed data and applying privacy protection before sharing the results (e.g., aggregation via secure primitives and differential privacy for sharing aggregate results). However, identifying such a central site may be difficult in practice and relying on a central site may introduce potential vulnerabilities (e.g., single point of failure). Furthermore, to support clinical interventions and inform policy decisions in a timely manner, epidemiological analysis need to reflect dynamic changes in the data. Yet, existing distributed privacy-protecting approaches were largely designed for static data (e.g., one-time data sharing) and cannot fulfill dynamic data requirements. In this work, we propose a privacy-protecting approach that supports the sharing of dynamic epidemiological analysis and provides strong privacy protection in a decentralized manner. We apply our solution in continuous survival analysis using the Kaplan-Meier estimation model while providing differential privacy protection. Our evaluations on a real dataset containing COVID-19 cases show that our method provides highly usable results.

Healthcare workers such as doctors and nurses are expected to be trustworthy and creditable sources of vaccine-related information. Their opinions toward the COVID-19 vaccines may influence the vaccine uptake among the general population. However, vaccine hesitancy is still an important issue even among the healthcare workers. Therefore, it is critical to understand their opinions to help reduce the level of vaccine hesitancy. There have been studies examining healthcare workers' viewpoints on COVID-19 vaccines using questionnaires. Reportedly, a considerably higher proportion of vaccine hesitancy is observed among nurses, compared to doctors. We intend to verify and study this phenomenon at a much larger scale and in fine grain using social media data, which has been effectively and efficiently leveraged by researchers to address real-world issues during the COVID-19 pandemic. More specifically, we use a keyword search to identify healthcare workers and further classify them into doctors and nurses from the profile descriptions of the corresponding Twitter users. Moreover, we apply a transformer-based language model to remove irrelevant tweets. Sentiment analysis and topic modeling are employed to analyze and compare the sentiment and thematic differences in the tweets posted by doctors and nurses. We find that doctors are overall more positive toward the COVID-19 vaccines. The focuses of doctors and nurses when they discuss vaccines in a negative way are in general different. Doctors are more concerned with the effectiveness of the vaccines over newer variants while nurses pay more attention to the potential side effects on children. Therefore, we suggest that more customized strategies should be deployed when communicating with different groups of healthcare workers.

Sharing data and computation among concurrent queries has been an active research topic in database systems. While work in this area developed algorithms and systems that are shown to be effective, there is a lack of logical foundation for query processing and optimization. In this paper, we present PsiDB, a system model for processing a large number of database queries in a batch. The key idea is to generate a single query expression that returns a global relation containing all the data needed for individual queries. For that, we propose the use of a type of relational operators called $\psi$-operators in combining the individual queries into the global expression. We tackle the algebraic optimization problem in PsiDB by developing equivalence rules to transform concurrent queries with the purpose of revealing query optimization opportunities. Centering around the $\psi$-operator, our rules not only cover many optimization techniques adopted in existing batch processing systems, but also revealed new optimization opportunities. Experiments conducted on an early prototype of PsiDB show a performance improvement of up to 36X over a mainstream commercial DBMS.

Support vector machine (SVM) is a popular classification method for the analysis of a wide range of data including big biomedical data. Many SVM methods with feature selection have been developed under the frequentist regularization or Bayesian shrinkage frameworks. On the other hand, the value of incorporating a priori known biological knowledge, such as those from functional genomics and functional proteomics, into statistical analysis of -omic data has been recognized in recent years. Such biological information is often represented by graphs. We propose a novel method that assigns Laplace priors to the regression coefficients and incorporates the underlying graph information via a hyper-prior for the shrinkage parameters in the Laplace priors. This enables smoothing of shrinkage parameters for connected variables in the graph and conditional independence between shrinkage parameters for disconnected variables. Extensive simulations demonstrate that our proposed methods achieve the best performance compared to the other existing SVM methods in terms of prediction accuracy. The proposed method are also illustrated in analysis of genomic data from cancer studies, demonstrating its advantage in generating biologically meaningful results and identifying potentially important features.

This paper presents a novel use case of Graph Convolutional Network (GCN) learning representations for predictive data mining, specifically from user/task data in the domain of high-performance computing (HPC). It outlines an approach based on a coalesced data set: logs from the Slurm workload manager, joined with user experience survey data from computational cluster users. We introduce a new method of constructing a heterogeneous unweighted HPC graph consisting of multiple typed nodes after revealing the manifold relations between the nodes. The GCN structure used here supports two tasks: i) determining whether a job will complete or fail and ii) predicting memory and CPU requirements by training the GCN semi-supervised classification model and regression models on the generated graph. The graph is partitioned into partitions using graph clustering. We conducted classification and regression experiments using the proposed framework on our HPC log dataset and evaluated predictions by our trained models against baselines using test_score, F1-score, precision, recall for classification, and R1 score for regression, showing that our framework achieves significant improvements.

A ubiquitous problem in aggregating data across different experimental and observational data sources is a lack of software infrastructure that enables flexible and extensible standardization of data and metadata. To address this challenge, we developed HDMF, a hierarchical data modeling framework for modern science data standards. With HDMF, we separate the process of data standardization into three main components: (1) data modeling and specification, (2) data I/O and storage, and (3) data interaction and data APIs. To enable standards to support the complex requirements and varying use cases throughout the data life cycle, HDMF provides object mapping infrastructure to insulate and integrate these various components. This approach supports the flexible development of data standards and extensions, optimized storage backends, and data APIs, while allowing the other components of the data standards ecosystem to remain stable. To meet the demands of modern, large-scale science data, HDMF provides advanced data I/O functionality for iterative data write, lazy data load, and parallel I/O. It also supports optimization of data storage via support for chunking, compression, linking, and modular data storage. We demonstrate the application of HDMF in practice to design NWB 2.0 [13], a modern data standard for collaborative science across the neurophysiology community.

Support vector machine (SVM) is a popular classification method for analysis of high dimensional data such as genomics data. Recently a number of linear SVM methods have been developed to achieve feature selection through either frequentist regularization or Bayesian shrinkage, but the linear assumption may not be plausible for many real applications. In addition, recent work has demonstrated that incorporating known biological knowledge, such as those from functional genomics, into the statistical analysis of genomic data offers great promise of improved predictive accuracy and feature selection. Such biological knowledge can often be represented by graphs. In this article, we propose a novel knowledge-guided nonlinear Bayesian SVM approach for analysis of high-dimensional data. Our model uses graph information that represents the relationship among the features to guide feature selection. To achieve knowledge-guided feature selection, we assign an Ising prior to the indicators representing inclusion/exclusion of the features in the model. An efficient MCMC algorithm is developed for posterior inference. The performance of our method is evaluated and compared with several penalized linear SVM and the standard kernel SVM method in terms of prediction and feature selection in extensive simulation studies. Also, analyses of genomic data from a cancer study show that our method yields a more accurate prediction model for patient survival and reveals biologically more meaningful results than the existing methods.

Geocoding, the process of translating addresses to geographic coordinates, is a relatively straight-forward and well-studied process, but limitations due to privacy concerns may restrict usage of geographic data. The impact of these limitations are further compounded by the scale of the data, and in turn, also limits viable geocoding strategies. For example, healthcare data is protected by patient privacy laws in addition to possible institutional regulations that restrict external transmission and sharing of data. This results in the implementation of "in-house" geocoding solutions where data is processed behind an organization's firewall; quality assurance for these implementations is problematic because sensitive data cannot be used to externally validate results. In this paper, we present our software framework called bench4gis which benchmarks privacy-aware geocoding solutions by leveraging open big data as surrogate data for quality assurance; the scale of open big data sets for address data can ensure that results are geographically meaningful for the locale of the implementing institution.

In health care settings, patients who are physically proximate to other patients (co-presence) for a meaningful amount of time may have differential health outcomes depending on who they are in contact with. How to best measure this co-presence, however is an open question and previous approaches have limitations that may make them inappropriate for complex health care settings. Here, we introduce a novel method which we term "consistent co-presence", that implicitly models the many complexities of patient scheduling and movement through a hospital by randomly perturbing the timing of patients' entry time into the health care system. This algorithm generates networks that can be employed in models of patient outcomes, such as 1-year mortality, and are preferred over previously established alternative algorithms from a model comparison perspective. These results indicate that consistent co-presence retains meaningful information about patient-patient interaction, which may affect outcomes relevant to health care practice. Furthermore, the generalizabiity of this approach allows it to be applied to a wide variety of complex systems.