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Geometric computation can be heavy duty for spatial queries, in particular for complex geometries such as polygons with many edges based on a vector-based representation. While many techniques have been provided for spatial partitioning and indexing, they are mainly built on minimal bounding boxes or other approximation methods, which will not mitigate the high cost of geometric computation. In this paper, we propose a novel vector-raster hybrid approach through rasterization, where pixel-centric rich information is preserved to help not only filtering out more candidates but also reducing geometry computation load. Based on the hybrid model, we develop an efficient rasterization based ray casting method for point-in-polygon queries and a circle buffering method for point-to-polygon distance calculation, which is a common operation for distance based queries. Our experiments demonstrate that the hybrid model can boost the performance of spatial queries on complex polygons by up to one order of magnitude.

Neural Machine Translation (NMT) models achieve state-of-the-art performance on many translation benchmarks. As an active research field in NMT, knowledge distillation is widely applied to enhance the model's performance by transferring teacher model's knowledge on each training sample. However, previous work rarely discusses the different impacts and connections among these samples, which serve as the medium for transferring teacher knowledge. In this paper, we design a novel protocol that can effectively analyze the different impacts of samples by comparing various samples' partitions. Based on above protocol, we conduct extensive experiments and find that the teacher's knowledge is not the more, the better. Knowledge over specific samples may even hurt the whole performance of knowledge distillation. Finally, to address these issues, we propose two simple yet effective strategies, i.e., batch-level and global-level selections, to pick suitable samples for distillation. We evaluate our approaches on two large-scale machine translation tasks, WMT'14 English->German and WMT'19 Chinese->English. Experimental results show that our approaches yield up to +1.28 and +0.89 BLEU points improvements over the Transformer baseline, respectively., Accepted as a long paper at ACL 2021. Code is available at https://github.com/LeslieOverfitting/selective_distillation

Digital imaging plays a critical role for image guided diagnosis and clinical trials, and the amount of image data is fast growing. There are two major requirements for image data management: scalability for massive scales and support of comprehensive queries. Traditional Picture Archiving and Communication Systems (PACS for short) are based on relational data management systems and suffer from limited scalability and query support. Therefore, new systems that support fast, scalable and comprehensive queries on image data are highly demanded. In this paper, we introduce two alternative approaches: DCMRL/XMLStore (RL/XML for short)-a parallel, hybrid relational and XML data management approach, and DCMDocStore (DOC for short)-a NoSQL document store approach. DCMRL/XMLStore manages DICOM images as binary large objects and metadata as relational tables and XML documents based on IBM DB2, which is parallelized through data partitioning. DCMDocStore manages DICOM metadata as JSON objects, and DICOM images as encoded attachments in MongoDB running on multiple nodes. We have delivered two open source systems DCMRL/XMLStore and DCMDocStore. Both systems support scalable data management and comprehensive queries. We also evaluated them with nearly one million DICOM images from National Biomedical Imaging Archive. The results show that, DCMDocStore demonstrates high data loading speed, high scalability and fault tolerance. DCMRL/XMLStore provides efficient queries, but comes with slower data loading. Traditional PACS systems have inherent limitations on flexible queries and scalability for massive amount of images.

Spatial cross-matching operation over geospatial polygonal datasets is a highly compute-intensive yet an essential task to a wide array of real-world applications. At the same time, modern computing systems are typically equipped with multiple processing units capable of task parallelization and optimization at various levels. This mandates for the exploration of novel strategies in the geospatial domain focusing on efficient utilization of computing resources, such as CPUs and GPUs. In this paper, we present a CPU-GPU hybrid platform to accelerate the cross-matching operation of geospatial datasets. We propose a pipeline of geospatial subtasks that are dynamically scheduled to be executed on either CPU or GPU. To accommodate geospatial datasets processing on GPU using pixelization approach, we convert the floating point-valued vertices into integer-valued vertices with an adaptive scaling factor as a function of the area of minimum bounding box. We present a comparative analysis of GPU enabled cross-matching algorithm implementation in CUDA and OpenACC accelerated C++. We test our implementations over Natural Earth Data and our results indicate that although CUDA based implementations provide better performance, OpenACC accelerated implementations are more portable and extendable while still providing considerable performance gain as compared to CPU. We also investigate the effects of input data size on the IO / computation ratio and note that a larger dataset compensates for IO overheads associated with GPU computations. Finally, we demonstrate that an efficient cross-matching comparison can be achieved with a cost-effective GPU.

The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org.

Generative adversarial networks (GANs) have been highly successful for generating realistic synthetic data. In healthcare, synthetic data generation can be helpful for producing annotated data and improving data-driven research without worries on data privacy. However, electronic health records (EHRs) are noisy, incomplete and complex, and existing work on EHR data is mainly devoted to generating discrete elements such as diagnosis codes and medications or frequent laboratory values. In this work, we propose SMOOTH-GAN, a novel approach for generating reliable EHR data such as laboratory values and medications given diagnosis codes. SMOOTH-GAN takes advantage of a conditional GAN architecture with WGAN-GP loss, and is able to learn transitions between disease stages with high flexibility over data customization. Our experiments demonstrate the model’s effectiveness in terms of both statistical similarity and accuracy on machine learning based prediction. To further demonstrate the usage of our model, we apply counterfactual reasoning and generate data with occurrence of multiple diseases, which can provide unique datasets for artificial intelligence driven healthcare research.

Background In recent years, both suicide and overdose rates have been increasing. Many individuals who struggle with opioid use disorder are prone to suicidal ideation; this may often result in overdose. However, these fatal overdoses are difficult to classify as intentional or unintentional. Intentional overdose is difficult to detect, partially due to the lack of predictors and social stigmas that push individuals away from seeking help. These individuals may instead use web-based means to articulate their concerns. Objective This study aimed to extract posts of suicidality among opioid users on Reddit using machine learning methods. The performance of the models is derivative of the data purity, and the results will help us to better understand the rationale of these users, providing new insights into individuals who are part of the opioid epidemic. Methods Reddit posts between June 2017 and June 2018 were collected from r/suicidewatch, r/depression, a set of opioid-related subreddits, and a control subreddit set. We first classified suicidal versus nonsuicidal languages and then classified users with opioid usage versus those without opioid usage. Several traditional baselines and neural network (NN) text classifiers were trained using subreddit names as the labels and combinations of semantic inputs. We then attempted to extract out-of-sample data belonging to the intersection of suicide ideation and opioid abuse. Amazon Mechanical Turk was used to provide labels for the out-of-sample data. Results Classification results were at least 90% across all models for at least one combination of input; the best classifier was convolutional neural network, which obtained an F1 score of 96.6%. When predicting out-of-sample data for posts containing both suicidal ideation and signs of opioid addiction, NN classifiers produced more false positives and traditional methods produced more false negatives, which is less desirable for predicting suicidal sentiments. Conclusions Opioid abuse is linked to the risk of unintentional overdose and suicide risk. Social media platforms such as Reddit contain metadata that can aid machine learning and provide information at a personal level that cannot be obtained elsewhere. We demonstrate that it is possible to use NNs as a tool to predict an out-of-sample target with a model built from data sets labeled by characteristics we wish to distinguish in the out-of-sample target.

The recent technological advancement in digital pathology has enabled 3D tissue-based investigation of human diseases at extremely high resolutions. Discovering and verifying spatial patterns among massive 3D micro-anatomic biological objects such as blood vessels and cells derived from 3D pathology image volumes plays a pivotal role in understanding diseases. However, the exponential increase of available 3D data and the complex structures of biological objects make it extremely difficult to support spatial queries due to high I/O, communication and computational cost for 3D spatial queries. In this demonstration, we present our scalable in-memory based spatial query system iSPEED for large-scale 3D data with complex structures. Low latency is managed by storing in memory with progressive compression including successive levels of detail on object level. On the other hand, low computational cost is achieved by pre-generation of global spatial indexes in memory and additional on-demand generation of indexing at run-time. Furthermore, iSPEED applies structural indexing on complex structured objects in multiple query types to gain performance advantage. During query processing, the memory footprint of iSPEED is minimal due to its indexing structure and progressive decompression on-demand. We demonstrate iSPEED query capability with three representative queries: 3D spatial joins, nearest neighbor and spatial proximity estimation on multiple datasets using a web based RESTful interface. Users can furthermore explore the input data structure, manage and adjust query pipeline parameters on the interface. PVLDB Reference Format: Hoang Vo, Yanhui Liang, Jun Kong, and Fusheng Wang. iSPEED: a Scalable and Distributed In-Memory Based Spatial Query System for Large and Structurally Complex 3D Data.

Background With increased specialization of health care services and high levels of patient mobility, accessing health care services across multiple hospitals or clinics has become very common for diagnosis and treatment, particularly for patients with chronic diseases such as cancer. With informed knowledge of a patient’s history, physicians can make prompt clinical decisions for smarter, safer, and more efficient care. However, due to the privacy and high sensitivity of electronic health records (EHR), most EHR data sharing still happens through fax or mail due to the lack of systematic infrastructure support for secure, trustable health data sharing, which can also cause major delays in patient care. Objective Our goal was to develop a system that will facilitate secure, trustable management, sharing, and aggregation of EHR data. Our patient-centric system allows patients to manage their own health records across multiple hospitals. The system will ensure patient privacy protection and guarantee security with respect to the requirements for health care data management, including the access control policy specified by the patient. Methods We propose a permissioned blockchain-based system for EHR data sharing and integration. Each hospital will provide a blockchain node integrated with its own EHR system to form the blockchain network. A web-based interface will be used for patients and doctors to initiate EHR sharing transactions. We take a hybrid data management approach, where only management metadata will be stored on the chain. Actual EHR data, on the other hand, will be encrypted and stored off-chain in Health Insurance Portability and Accountability Act–compliant cloud-based storage. The system uses public key infrastructure–based asymmetric encryption and digital signatures to secure shared EHR data. Results In collaboration with Stony Brook University Hospital, we developed ACTION-EHR, a system for patient-centric, blockchain-based EHR data sharing and management for patient care, in particular radiation treatment for cancer. The prototype was built on Hyperledger Fabric, an open-source, permissioned blockchain framework. Data sharing transactions were implemented using chaincode and exposed as representational state transfer application programming interfaces used for the web portal for patients and users. The HL7 Fast Healthcare Interoperability Resources standard was adopted to represent shared EHR data, making it easy to interface with hospital EHR systems and integrate a patient’s EHR data. We tested the system in a distributed environment at Stony Brook University using deidentified patient data. Conclusions We studied and developed the critical technology components to enable patient-centric, blockchain-based EHR sharing to support cancer care. The prototype demonstrated the feasibility of our approach as well as some of the major challenges. The next step will be a pilot study with health care providers in both the United States and Switzerland. Our work provides an exemplar testbed to build next-generation EHR sharing infrastructures.

Health care is undergoing a big data revolution, with vast amounts of information supplied from numerous sources, leading to major paradigm shifts including precision medicine and AI-driven health care among others. Yet, there still exist significant barriers before such approaches could be adopted in practice, including data integration and interoperability, data sharing, security and privacy protection, scalability, and policy and regulatory issues. Blockchain provides a unique opportunity to tackle major challenges in health care and biomedical research, such as enabling data sharing and integration for patient-centered care, data provenance allowing verification authenticity of the data, and optimization of some of the health care processes among others. Nevertheless, technological constraints of current blockchain technologies necessitate further research before mass adoption of blockchain-based health care data management is possible. We analyze context-based requirements and capabilities of the available technology and propose a research agenda and new approaches towards achieving intelligent health care data management using blockchain.

Spatial cross-matching operation over geospatial polygonal datasets is important to a variety of GIS applications. However, it involves extensive computation cost associated with intersection and union of a geospatial polygon pair from large scale datasets. This mandates for exploration of parallel computing capabilities such as GPU to increase the efficiency of such operations. In this paper, we present a CPU-GPU hybrid platform to accelerate the cross-matching operation of geospatial datasets. The computing tasks are dynamically scheduled to be executed either on CPU or GPU. To accommodate geospatial datasets processing on GPU using pixelization approach, we convert the floating point-valued vertices into integer-valued vertices with an adaptive scaling factor as a function of area of minimum bounding box. We test our framework over Natural Earth Dataset and achieve 10x speedup on NVIDIA GeForce GTX750 GPU and 14x speedup on Tesla K80 GPU over 280,000 polygon pairs in one tile and 400 tiles in total. We also investigate the effects of input data size to the IO / computation ratio and note that the sufficiently large input data size is required to better utilize the computing power of GPU. Finally, with comparison between two GPUs, our results demonstrate that the efficient cross-matching comparison can be achieved with a cost-effective GPU.

Increased availability of large amounts of address data provides opportunities for data driven studies to improve decision making in business applications and support precision public health with high resolution geolocations. Geocoding large number of addresses is challenging due to high cost and often disclosure of sensitive data to vendors over the Web. Most geocoders take advantage of Web APIs which require sending private addresses over the Internet, which may not be an option for many applications with sensitive data including public health and geo-medicine. Meanwhile, the cost for geocoding massive number of addresses could be high and becomes a major hurdle for many users. To overcome these challenges, we developed an open source on-premise geocoding software EaserGeocoder, which uses a novel integrative geocoding model to achieve high accuracy through integrating multiple open data sources. EaserGeocoder takes advantage of machine learning based approaches to determine best answers from multiple data sources. EaserGeocoder can also be easily parallelized to achieve high scalability through parallelized search and distributed computing. EaserGeocoder is on a par with commercial geocoding systems, outperforms open source systems, and is available for free.

INTRODUCTION: The United States federally mandated reporting of venous thromboembolism (VTE), defined by Agency for Healthcare Research & Quality Patient Safety Indicator 12 (AHRQ PSI-12), is based on administrative data, the accuracy of which has not been consistently demonstrated. We used IDEAL-X, a novel information extraction software system, to identify VTE from electronic medical records and evaluated its accuracy. METHODS: Medical records for 13,248 patients admitted to an orthopedic specialty hospital from 2009 to 2014 were reviewed. Patient encounters were defined as a hospital admission where both surgery (of the spine, hip, or knee) and a radiology diagnostic study that could detect VTE was performed. Radiology reports were both manually reviewed by a physician and analyzed by IDEAL-X. RESULTS: Among 2083 radiology reports, IDEAL-X correctly identified 176/181 VTE events, achieving a sensitivity of 97.2% [95% confidence interval (CI), 93.7%–99.1%] and specificity of 99.3% (95% CI, 98.9%–99.7%) when compared with manual review. Among 422 surgical encounters with diagnostic radiographic studies for VTE, IDEAL-X correctly identified 41 of 42 VTE events, achieving a sensitivity of 97.6% (95% CI, 87.4%–99.6%) and specificity of 99.8% (95% CI, 98.7%–100.0%). The performance surpassed that of AHRQ PSI-12, which had a sensitivity of 92.9% (95% CI, 80.5%–98.4%) and specificity of 92.9% (95% CI, 89.8%–95.3%), though only the difference in specificity was statistically significant (P < 0.01). CONCLUSION: IDEAL-X, a novel information extraction software system, identified VTE from radiology reports with high accuracy, with specificity surpassing AHRQ PSI-12. IDEAL-X could potentially improve detection and surveillance of many medical conditions from free text of electronic medical records.

Recent advancements in systematic analysis of high resolution whole slide images have increase efficiency of diagnosis, prognosis and prediction of cancer and important diseases. Due to the enormous sizes and dimensions of whole slide images, the analysis requires extensive computing resources which are not commonly available. Images have to be tiled for processing due to computer memory limitations, which lead to inaccurate results due to the ignorance of boundary crossing objects. Thus, we propose a generic and highly scalable cloud-based image analysis framework for whole slide images. The framework enables parallelized integration of image analysis steps, such as segmentation and aggregation of micro-structures in a single pipeline, and generation of final objects manageable by databases. The core concept relies on the abstraction of objects in whole slide images as different classes of spatial geometries, which in turn can be handled as text based records in MapReduce. The framework applies an overlapping partitioning scheme on images, and provides parallelization of tiling and image segmentation based on MapReduce architecture. It further provides robust object normalization, graceful handling of boundary objects with an efficient spatial indexing based matching method to generate accurate results. Our experiments on Amazon EMR show that MaReIA is highly scalable, generic and extremely cost effective by benchmark tests.

Public transport, especially the bus transport, can reduce the private car usage and fuel consumption, and alleviate traffic congestion. However, when traveling in buses, the travelers not only care about the waiting time, but also care about the crowdedness in the bus itself. Excessively overcrowded bus may drive away the anxious travelers and make them reluctant to take buses. So accurate, real-time and reliable passenger demand prediction becomes necessary, which can help determine the bus headway and help reduce the waiting time of passengers. Based on a large database from a real bus system, this paper aims to present a passenger demand prediction system for mobile users. The system includes a server-side bus information data stream processing and mining program and a client-side mobile application for Android smartphones. The server program continuously monitors for each bus stop the number of passengers waiting at the bus stop, the number of passengers that will pass the bus stop, as well as the traffic conditions in the area around the stop. It delivers real time bus and traffic information to mobile users via restful web services. The client-side location-based mobile application consumes these services to help mobile users make informed transportation choices. For example the availability of buses might be a deterrent when they are too crowded. However, there are three major challenges for predicting the passenger demands on bus services: inhomogeneous, seasonal bursty periods and periodicities. To overcome the challenges, we propose three predictive models and further take a data stream ensemble framework to predict the number of passengers. We develop a prototype system with different types of Android based mobile phones and comprehensively experiment over a 22-week period. The evaluation results suggest that the proposed system achieves outstanding prediction accuracy among 86,411 passenger demands on bus services, more than 78% of them are accurately forecasted. Build a passenger demand prediction system for mobile users.Propose a method for detecting parking places.Present the design of knowledge base.Build a location-based mobile application for mobile users.

Support of high performance queries on large volumes of spatial data has become increasingly important in many application domains, including geospatial problems in numerous disciplines, location based services, and emerging medical imaging applications. There are two major challenges for managing massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. Our goal is to develop a general framework to support high performance spatial queries and analytics for spatial big data on MapReduce and CPU-GPU hybrid platforms. In this paper, we introduce Hadoop-GIS -- a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through skew-aware spatial partitioning, on-demand indexing, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. To accelerate compute-intensive geometric operations, GPU based geometric computation algorithms are integrated into MapReduce pipelines. Our experiments have demonstrated that Hadoop-GIS is highly efficient and scalable, and outperforms parallel spatial DBMS for compute-intensive spatial queries.

Recent advances in digital pathology make it possible to support 3D tissue-based investigation of human diseases at extremely high resolutions. Exploring spatial relationships and patterns among massive 3D micro-anatomic biological objects such as blood vessels and cells derived from 3D pathology image volumes plays a critical role in studying human diseases. In this paper, we present our work on building an effective and scalable in-memory based spatial query system iSPEED for large-scale 3D data with complex structures. To achieve low latency, iSPEED stores data in memory with effective progressive compression for each 3D object with successive levels of detail. To minimize search space and computation cost, iSPEED pre-generates global spatial indexes in memory and employs on-demand indexing at run-time. In particular, iSPEED exploits structural indexing for complex structured objects in distance based queries. iSPEED provides a 3D spatial query engine that can be invoked on-demand to run many instances in parallel implemented with, but not limited to, MapReduce. iSPEED builds in-memory indexes and decompresses data on-demand, which has minimal memory footprint. We evaluate iSPEED with two representative queries: 3D spatial joins and 3D spatial proximity estimation. Our experiments demonstrate that iSPEED significantly improves the performance over traditional non-memory based spatial query systems.

Difficulty on collecting annotated medical images leads to lack of enough supervision and makes discrimination tasks challenging. However, raw data, e.g., spatial context information from 3D CT images, even without annotation, may contain rich useful information. In this paper, we exploit spatial context information as a source of supervision to solve discrimination tasks for fine-grained body part recognition with conventional 3D CT and MR volumes. The proposed pipeline consists of two steps: 1) pre-train a convolutional network for an auxiliary task of 2D slices ordering in a self-supervised manner; 2) transfer and fine-tune the pre-trained network for fine-grained body part recognition. Without any use of human annotation in the first stage, the pre-trained network can still outperform CNN trained from scratch on CT as well as M-R data. Moreover, by comparing with pre-trained CNN from ImageNet, we discover that the distance between source and target tasks plays a crucial role in transfer learning. Our experiments demonstrate that our approach can achieve high accuracy with a slice location estimation error of only a few slices on CT and MR data. To the best of our knowledge, our work is the first attempt studying the problem of robust body part recognition at a continuous level.

Under the traditional phase shift control, dual active bridge DC-DC converter (DAB) has a transient bias on the inductance current when the phase shift ratio changes suddenly, which leads to increase in the current stress of switch tubes and even unidirectional saturation of the transformer. All those will affect the stable operation of the converter. This paper focuses on quantifying the transient DC bias model on the control of triple phase shift when phase shift ratios change, and then the strategy proposed by the paper can eliminate the DC bias within one switching period and reduce current stress and response time by adjusting the drive signal during the transient transition process. Finally, the proposed strategy is verified by simulation results from Matlab/Simulink software.

There is a lack of tools to ease the integration and ontology based semantic queries in biomedical databases, which are often annotated with ontology concepts. We aim to provide a middle layer between ontology repositories and semantically annotated databases to support semantic queries directly in the databases with expressive standard database query languages. We have developed a semantic query engine that provides semantic reasoning and query processing, and translates the queries into ontology repository operations on NCBO BioPortal. Semantic operators are implemented in the database as user defined functions extended to the database engine, thus semantic queries can be directly specified in standard database query languages such as SQL and XQuery. The system provides caching management to boosts query performance. The system is highly adaptable to support different ontologies through easy customizations. We have implemented the system DBOntoLink as an open source software, which supports major ontologies hosted at BioPortal. DBOntoLink supports a set of common ontology based semantic operations and have them fully integrated with a database management system IBM DB2. The system has been deployed and evaluated with an existing biomedical database for managing and querying image annotations and markups (AIM). Our performance study demonstrates the high expressiveness of semantic queries and the high efficiency of the queries.

Background The integration and visualization of multimodal datasets is a common challenge in biomedical informatics. Several recent studies of The Cancer Genome Atlas (TCGA) data have illustrated important relationships between morphology observed in whole-slide images, outcome, and genetic events. The pairing of genomics and rich clinical descriptions with whole-slide imaging provided by TCGA presents a unique opportunity to perform these correlative studies. However, better tools are needed to integrate the vast and disparate data types. Objective To build an integrated web-based platform supporting whole-slide pathology image visualization and data integration. Materials and methods All images and genomic data were directly obtained from the TCGA and National Cancer Institute (NCI) websites. Results The Cancer Digital Slide Archive (CDSA) produced is accessible to the public ( ) and currently hosts more than 20 000 whole-slide images from 22 cancer types. Discussion The capabilities of CDSA are demonstrated using TCGA datasets to integrate pathology imaging with associated clinical, genomic and MRI measurements in glioblastomas and can be extended to other tumor types. CDSA also allows URL-based sharing of whole-slide images, and has preliminary support for directly sharing regions of interest and other annotations. Images can also be selected on the basis of other metadata, such as mutational profile, patient age, and other relevant characteristics. Conclusions With the increasing availability of whole-slide scanners, analysis of digitized pathology images will become increasingly important in linking morphologic observations with genomic and clinical endpoints.

With increasing popularity of cloud-based data management, improving the performance of queries in the cloud is an urgent issue to solve. Summary of data distribution and statistical information has been commonly used in traditional databases to support query optimization, and histograms are of particular interest. Naturally, histograms could be used to support query optimization and efficient utilization of computing resources in the cloud. Histograms could provide helpful reference information for generating optimal query plans, and generate basic statistics useful for guaranteeing the load balance of query processing in the cloud. Since it is too expensive to construct an exact histogram on massive data, building an approximate histogram is a more feasible solution. This problem, however, is challenging to solve in the cloud environment because of the special data organization and processing mode in the cloud. In this paper, we present HEDC++, an extended histogram estimator for data in the cloud, which provides efficient approximation approaches for both equi-width and equi-depth histograms. We design the histogram estimate workflow based on an extended MapReduce framework, and propose novel sampling mechanisms to leverage the sampling efficiency and estimate accuracy. We experimentally validate our techniques on Hadoop and the results demonstrate that HEDC++ can provide promising histogram estimate for massive data in the cloud.

Microscopic image analysis of nuclei in pathology images generates tremendous amount of spatially derived data to support biomedical research and potential diagnosis. Such spatial data can be managed by traditional SQL based spatial databases and queried by SQL for spatial relationships. However, traditional spatial databases are designed for structured data with limited expressibility, which is difficult to support queries for complex visual patterns. Moreover, SQL based queries are not intuitive for biomedical researchers or pathologists. In this paper, we investigate the expressive power of visual query for spatial databases and propose an effective yet general Iterative Example-based Visual Query IEVQuery framework to query shapes and distributions. More specifically, we extract features from nuclei in pathology databases, such as shape polygon nuclei density distribution, and nuclei growth directions to build search indexes. The user employs visual interactions such as sketching to input queries for interesting patterns. Meanwhile, the user is allowed to iteratively create queries, which are based on previous search results, to finely tune the features more accurately to find preferred results. We build a system to enable users to specify sketch based queries interactively for 1 nuclei shapes, 2 nuclei densities, and 3 nuclei growth directions. To validate our methods, we take a pathology database [11] consisting of hundreds of millions of nuclei, and enable the user to search in the database to find most matching results through our system.

The traditional data processing methods working on single computer show less scalability and efficiency for performing ordered full-outer-joining, on merging large number of individual Genome-Wide Associations Studies (GWAS) data. Although the emerging of big data platforms such as Hadoop and Spark shed lights on this problem, the inefficiency of keeping data in total-sorted order as well as the workload imbalance problem limit their performance. In this study, we designed and compared three new methodologies based on MapReduce, HBase and Spark respectively, to merge hundreds of individuals VCF files on their Single Nucleotide Polymorphism (SNP) location into a single TPED file. Our methodologies overcame the limitations stated above and considerably improved the performance with good scalability on input size and computing resources.

Systematic analysis of high resolution whole slide images enables more effective diagnosis, prognosis and prediction of cancer and other important diseases. Due to the enormous sizes and dimensions of whole slide images, the analysis requires extensive computing resources which are not commonly available. Images have to be divided into smaller regions for processing due to computer memory limitations, which will lead to inaccurate results due to the ignorance of boundary crossing objects. In this paper, we propose a highly scalable and cost effective MapReduce based image analysis framework for whole slide image processing, and provide a cloud based implementation. The framework takes a grid-based overlapping partitioning scheme, and provides parallelization of image segmentation based on MapReduce. It provides graceful handling of boundary objects with a highly efficient spatial indexing based matching method, thus avoiding loss of accuracy due to partitioning. We demonstrate that the system achieves high scalability and is cost-effective --- our experiments demonstrate that it costs less than fifteen cents to analyze one image on average using Amazon Elastic MapReduce.

Background: Extracting structured data from narrated medical reports is challenged by the complexity of heterogeneous structures and vocabularies and often requires significant manual effort. Traditional machine-based approaches lack the capability to take user feedbacks for improving the extraction algorithm in real time. Objective: Our goal was to provide a generic information extraction framework that can support diverse clinical reports and enables a dynamic interaction between a human and a machine that produces highly accurate results. Methods: A clinical information extraction system IDEAL-X has been built on top of online machine learning. It processes one document at a time, and user interactions are recorded as feedbacks to update the learning model in real time. The updated model is used to predict values for extraction in subsequent documents. Once prediction accuracy reaches a user-acceptable threshold, the remaining documents may be batch processed. A customizable controlled vocabulary may be used to support extraction. Results: Three datasets were used for experiments based on report styles: 100 cardiac catheterization procedure reports, 100 coronary angiographic reports, and 100 integrated reports—each combines history and physical report, discharge summary, outpatient clinic notes, outpatient clinic letter, and inpatient discharge medication report. Data extraction was performed by 3 methods: online machine learning, controlled vocabularies, and a combination of these. The system delivers results with F1 scores greater than 95%. Conclusions: IDEAL-X adopts a unique online machine learning–based approach combined with controlled vocabularies to support data extraction for clinical reports. The system can quickly learn and improve, thus it is highly adaptable. [JMIR Med Inform 2017;5(2):e12]

Recent years have witnessed an explosion of geospatial data, especially in the form of Volunteered Geographic Information (VGI). As a prominent example, OpenStreetMap (OSM) creates a free editable map of the world from a large number of contributors. On the other hand, social media platforms such as Twitter or Instagram supply dynamic social feeds at population level. As much of such data is geo-tagged, there is a high potential on integrating social media with OSM to enrich OSM with semantic annotations, which will complement existing objective description oriented annotations to provide a broader range of annotations. In this paper, we propose a comprehensive framework on integrating social media data and VGI data to derive knowledge about geographical objects, specifically, top relevant annotations from tweets for objects in OSM. We first integrate geo-tagged tweets with OSM data with scalable spatial queries running on MapReduce. We propose a frequency based method for annotating boundary based geographic objects, and a probability based method for annotating point based geographic objects, with consideration of noise. We evaluate our methods using a large geo-tagged tweets corpus and representative geographic objects from OSM, which demonstrates promising results through ground-truth comparison and case studies. We are able to produce up to 80% correct names for geographical objects and discover implicitly relevant information, such as popular exhibitions of a museum, the nicknames or visitors' impression to a tourism attraction.

3D analytical pathology imaging examines high resolution 3D image volumes of human tissues to facilitate biomedical research and provide potential effective diagnostic assistance. Such approach - quantitative analysis of large- scale 3D pathology image volumes - generates tremendous amounts of spatially derived 3D micro-anatomic objects, such as 3D blood vessels and nuclei. Spatial exploration of such massive 3D spatial data requires effective and efficient querying methods. In this paper, we present a scalable and efficient 3D spatial query system for querying massive 3D spatial data based on MapReduce. The system provides an on-demand spatial querying engine which can be executed with as many instances as needed on MapReduce at runtime. Our system supports multiple types of spatial queries on MapReduce through 3D spatial data partitioning, customizable 3D spatial query engine, and implicit parallel spatial query execution. We utilize multi-level spatial indexing to achieve efficient query processing, including global partition indexing for data retrieval and on-demand local spatial indexing for spatial query processing. We evaluate our system with two representative queries: 3D spatial joins and 3D k-nearest neighbor query. Our experiments demonstrate that our system scales to large number of computing nodes, and efficiently handles data-intensive 3D spatial queries that are challenging in analytical pathology imaging.

Advances of sensor and radio frequency identification (RFID) technology provide significant new power for humans to sense, understand and manage the world. RFID provides fast data collection with precise identification of objects with unique IDs without line of sight, thus it can be used for identifying, locating, tracking and monitoring physical objects. Despite these benefits, RFID poses many challenges for data processing and management: (i) RFID observations have implicit meanings, which have to be transformed and aggregated into semantic data represented in their data models; and (ii) RFID data are temporal, streaming, and in high volume, and have to be processed on the fly. Thus, a general RFID data processing framework is needed to automate the transformation of physical RFID observations into the virtual counterparts in the virtual world linked to business applications. In this paper, we take an event-oriented approach to process RFID data, by devising RFID application logic into complex events. We then formalize the specification and semantics of RFID events and rules. We discover that RFID events are highly temporal constrained, and include non-spontaneous events, and develop an RFID event detection engine that can effectively process complex RFID events. The declarative event-based approach greatly simplifies the work of RFID data processing, and can significantly reduce the cost of RFID data integration.

By storing the successive versions of a document in an incremental fashion, XML repositories and data warehouses achieve: (i) the efficient preservation of critical information and (ii) the ability to support historical queries on the evolution of documents and their contents. In this paper, we present efficient techniques for managing multi-version document histories and supporting powerful temporal queries on such documents. Our approach consists of: (i) concisely representing the successive versions of a document as an XML document that implements a temporally-grouped data model and (ii) using XML query languages, such as XQuery, to express complex queries on the content of a particular version, and on the temporal evolution of the document elements and contents. We show that the data definition and manipulation framework of XML and XQuery can effectively support temporal models and historical queries without requiring extensions to the current standards; in fact, this approach is effective at representing and querying the histories of relational database tables, which are difficult to manage using SQL. These conclusions emerge through a number of interesting case studies presented in this paper that include W3C documents, the UCLA course catalog, and the CIA World Factbook.

Effective support for temporal applications by database systems represents an important technical objective that is difficult to achieve since it requires an integrated solution for several problems, including (i) expressive temporal representations and data models, (ii) powerful languages for temporal queries and snapshot queries, (iii) indexing, clustering and query optimization techniques for managing temporal information efficiently, and (iv) architectures that bring together the different pieces of enabling technology into a robust system. In this paper, we present the ArchIS system that achieves these objectives by supporting a temporally grouped data model on top of RDBMS. ArchIS' architecture uses (a) XML to support temporally grouped (virtual) representations of the database history, (b) XQuery to express powerful temporal queries on such views, (c) temporal clustering and indexing techniques for managing the actual historical data in a relational database, and (d) SQL/XML for executing the queries on the XML views as equivalent queries on the relational database. The performance studies presented in the paper show that ArchIS is quite effective at storing and retrieving under complex query conditions the transaction-time history of relational databases, and can also assure excellent storage efficiency by providing compression as an option. This approach achieves full-functionality transaction-time databases without requiring temporal extensions in XML or database standards, and provides critical support to emerging application areas such as RFID.

A large number of cell-oriented cancer investigations require an effective and reliable cell segmentation method on three dimensional (3D) fluorescence microscopic images for quantitative analysis of cell biological properties. In this paper, we present a fully automated cell segmentation method that can detect cells from 3D fluorescence microscopic images. Enlightened by fluorescence imaging techniques, we regulated the image gradient field by gradient vector flow (GVF) with interpolated and smoothed data volume, and grouped voxels based on gradient modes identified by tracking GVF field. Adaptive thresholding was then applied to voxels associated with the same gradient mode where voxel intensities were enhanced by a multiscale cell filter. We applied the method to a large volume of 3D fluorescence imaging data of human brain tumor cells with (1) small cell false detection and missing rates for individual cells; and (2) trivial over and under segmentation incidences for clustered cells. Additionally, the concordance of cell morphometry structure between automated and manual segmentation was encouraging. These results suggest a promising 3D cell segmentation method applicable to cancer studies.

There is much current interest in publishing and viewing databases as XML documents. The general benefits of this approach follow from the popularity of XML and the tool set available for visualizing and processing information encoded in this universal standard. In this paper, we explore the additional and unique benefits achieved by this approach on temporal database applications. We show that XML with XQuery can provide surprisingly effective solutions to the problem of supporting historical queries on past content of database relations and their evolution. Indeed, using XML, the histories of database relations can be naturally represented by temporally grouped data models. Thus, we identify mappings from relations to XML that are most conducive to modeling and querying database histories, and show that temporal queries that would be difficult to express in SQL can be easily expressed in standard XQuery. This approach is very general, insofar as it can be used to store the version history of arbitrary documents and, for relational databases, it also supports queries on the evolution of their schema. Then, we turn to the problem of supporting efficiently the storage and the querying of relational table histories. We present an experimental study of the pros and cons of using native XML databases, versus using traditional databases, where the XML-represented histories are supported as views on the historical tables.

The Extremely Large Databases (XLDB) series of conferences/ workshops have been held successfully six times in recent years. The First XLDB Conference at Asia (XLDB Asia) was held at Beijing, China on June 22-23, 2012. The conference attracted nearly 200 participants. XLDB takes a fresh format on the organization through invited talks, lightning talks and open discussions. Most invited speakers are also owners of real extremely large data from industries and scientific research, practitioners who are handling the real data, or DBMS researchers who are researching new solutions. Based on the enthusiastic embrace and positive feedbacks from participants, we believe the conference series will continue as a venue for the discussion on the management and analysis of extremely large data sets with increasing popularity.

The growth of spatial big data has been explosive thanks to cost-effective and ubiquitous positioning technologies, and the generation of data from multiple sources in multi-forms. Such emerging spatial data has high potential to create new insights and values for our life through spatial analytics. However, spatial data analytics faces two major challenges. First, spatial data is both data-and compute-intensive due to the massive amounts of data and the multi-dimensional nature, which requires high performance spatial computing infrastructure and methods. Second, spatial big data sources are often isolated, for example, OpenStreetMap, census data and Twitter tweets are independent data sources. This leads to incompleteness of information and sometimes limited data accuracy, thus limited values from the data. Integrating spatial big data analytics by consolidating multiple data sources provides significant potential for data quality improvement in terms of completeness and accuracy, and much increased values derived from the data. In this paper, we present our vision of a high performance integrated spatial big data analytics framework. We provide a scalable spatial query based data integration engine with MapReduce, and demonstrate integrated spatial data analytics through a few use cases in our preliminary work. We then present our future plan on integrated spatial big data analytics for improving public health research and applications.

Scalable spatial query processing relies on effective spatial data partitioning for query parallelization, data pruning, and load balancing. These are often challenged by the intrinsic characteristics of spatial data, such as high skew in data distribution and high complexity of irregular multi-dimensional objects. In this demo, we present SATO, a spatial data partitioning framework that can quickly analyze and partition spatial data with an optimal spatial partitioning strategy for scalable query processing. SATO works in following steps: 1) Sample, which samples a small fraction of input data for analysis, 2) Analyze, which quickly analyzes sampled data to find an optimal partition strategy, 3) Tear, which provides data skew aware partitioning and supports MapReduce based scalable partitioning, and 4) Optimize, which collects succinct partition statistics for potential query optimization. SATO also provides multiple level partitioning, which can be used to significantly improve window based queries in cloud based spatial query processing systems. SATO comes with a visualization component that provides heat maps and histograms for qualitative evaluation. SATO has been implemented within the Hadoop-GIS, a high performance spatial data warehousing system over MapReduce. SATO is also released as an independent software package to support various scalable spatial query processing systems. Our experiments have demonstrated that SATO can generate much balanced partitioning that can significantly improve spatial query performance with MapReduce comparing to traditional spatial partitioning approaches.

In this paper, we present a novel framework for microscopic image analysis of nuclei, data management, and high performance computation to support translational research involving nuclear morphometry features, molecular data, and clinical outcomes. Our image analysis pipeline consists of nuclei segmentation and feature computation facilitated by high performance computing with coordinated execution in multi-core CPUs and Graphical Processor Units (GPUs). All data derived from image analysis are managed in a spatial relational database supporting highly efficient scientific queries. We applied our image analysis workflow to 159 glioblastomas (GBM) from The Cancer Genome Atlas dataset. With integrative studies, we found statistics of four specific nuclear features were significantly associated with patient survival. Additionally, we correlated nuclear features with molecular data and found interesting results that support pathologic domain knowledge. We found that Proneural subtype GBMs had the smallest mean of nuclear Eccentricity and the largest mean of nuclear Extent, and MinorAxisLength. We also found gene expressions of stem cell marker MYC and cell proliferation maker MKI67 were correlated with nuclear features. To complement and inform pathologists of relevant diagnostic features, we queried the most representative nuclear instances from each patient population based on genetic and transcriptional classes. Our results demonstrate that specific nuclear features carry prognostic significance and associations with transcriptional and genetic classes, highlighting the potential of high throughput pathology image analysis as a complementary approach to human-based review and translational research.

The proliferation of GPS-enabled devices, and the rapid improvement of scientific instruments have resulted in massive amounts of spatial data in the last decade. Support of high performance spatial queries on large volumes data has become increasingly important in numerous fields, which requires a scalable and efficient spatial data warehousing solution as existing approaches exhibit scalability limitations and efficiency bottlenecks for large scale spatial applications. In this demonstration, we present Hadoop-GIS -- a scalable and high performance spatial query system over MapReduce. Hadoop-GIS provides an efficient spatial query engine to process spatial queries, data and space based partitioning, and query pipelines that parallelize queries implicitly on MapReduce. Hadoop-GIS also provides an expressive, SQL-like spatial query language for work-load specification. We will demonstrate how spatial queries are expressed in spatially extended SQL queries, and submitted through a command line/web interface for execution. Parallel to our system demonstration, we explain the system architecture and details on how queries are translated to MapReduce operators, optimized, and executed on Hadoop. In addition, we will showcase how the system can be used to support two representative real world use cases: large scale pathology analytical imaging, and geo-spatial data warehousing.

XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups.

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present Hadoop-GIS - a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive.

Support of high performance queries on large volumes of scientific spatial data is becoming increasingly important in many applications. This growth is driven by not only geospatial problems in numerous fields, but also emerging scientific applications that are increasingly data- and compute-intensive. For example, digital pathology imaging has become an emerging field during the past decade, where examination of high resolution images of human tissue specimens enables more effective diagnosis, prediction and treatment of diseases. Systematic analysis of large-scale pathology images generates tremendous amounts of spatially derived quantifications of micro-anatomic objects, such as nuclei, blood vessels, and tissue regions. Analytical pathology imaging provides high potential to support image based computer aided diagnosis. One major requirement for this is effective querying of such enormous amount of data with fast response, which is faced with two major challenges: the "big data" challenge and the high computation complexity. In this paper, we present our work towards building a high performance spatial query system for querying massive spatial data on MapReduce. Our framework takes an on demand index building approach for processing spatial queries and a partition-merge approach for building parallel spatial query pipelines, which fits nicely with the computing model of MapReduce. We demonstrate our framework on supporting multi-way spatial joins for algorithm evaluation and nearest neighbor queries for microanatomic objects. To reduce query response time, we propose cost based query optimization to mitigate the effect of data skew. Our experiments show that the framework can efficiently support complex analytical spatial queries on MapReduce.

Cloud-based data management systems are emerging as scalable, fault-tolerant, and efficient solutions to manage large volumes of data with cost effective infrastructures, and more and more data analysis applications are migrated to the cloud. As an attractive solution to provide a quick sketch of massive data before a long wait of the final accurate query result, online processing of aggregate queries in the cloud is of paramount importance. This problem is challenging to solve because of the large block based data organization and distributed processing mode in the cloud. In this paper, we present COLA, a system for Cloud Online Aggregation to provide progressive approximate answers for both single tables and joined multiple tables. We develop an online query processing algorithm for MapReduce to support incremental and continuous computing of aggregations on joins which minimizes the waiting time before an acceptable estimate is achieved. We formulate a statistical foundation that supports block-level sampling for single-table online aggregations and effective estimation of approximate results and confidence intervals of statistical significance. We also develop a two-phase stratified sampling method to support multi-table aggregations to improve the approximate query answers and speed up the convergence of confidence intervals. We implement COLA in Hadoop, and our experiments demonstrate that COLA can deliver reasonable precise online estimates within a time period two orders of magnitude shorter than that used to produce exact answers.

While current biomedical ontology repositories offer primitive query capabilities, it is difficult or cumbersome to support ontology based semantic queries directly in semantically annotated biomedical databases. The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems. To fully realize semantic query capabilities based on ontologies, we develop a system DBOntoLink to provide unified semantic query interfaces by extending database query languages. With DBOntoLink, semantic queries can be directly and naturally specified as extended functions of the database query languages without any programming needed. DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal. We demonstrate the use of DBOntoLink in a real world biomedical database with semantically annotated medical image annotations.

The prevalence of medical report standards and structured reporting systems reflects the increasing demand for representing and preserving medical and clinical data with controlled vocabularies in well structured format. Strictly formatted medical reports offer high human readability and facilitate further data processing, such as querying, statistical analysis, and reasoning to support decision making. However, many medical reports, such as pathology reports, nursing notes and physician's notes, are written in free-text narration. Manually extracting free text reports by filling predefined data fields is cumbersome and error-prone. Meanwhile, information extraction tools try to automate such process, for example, through machine learning based methods. Such methods often require large volumes of training datasets annotated manually by humans, which is expensive to obtain. Furthermore, they are also limited by their accuracy (both precision and recall).To facilitate the process of extracting information from narrative medical reports and transforming extracted data into standardized structured forms, we present in this paper a semi-automatic system, ASLForm, that interacts with users, analyzes free text input and generates normalized answers to populate forms in real-time. This system learns from users' feedback transparently and establishes decision models incrementally. It requires no additional configurations and training datasets. ASLForm is not constrained to any domain, and is adaptable to free text input in any format. These features of the system offer high usability and portability. Its design also enables easy integration with existing reporting systems.

With increasing popularity of cloud based data management, improving the performance of queries in the cloud is an urgent issue to solve. Summary of data distribution and statistical information has been commonly used in traditional database to support query optimization, and histograms are of particular interest. Naturally, histograms could be used to support query optimization and efficient utilization of computing resources in the cloud. Histograms could provide helpful reference information for generating optimal query plan, and generate basic statistics useful for guaranteeing the load balance of query processing in the cloud. Since it is too expensive to construct the exact histogram on massive data, building the approximate histogram is a more feasible solution. This problem, however, is challenging to solve in the cloud environment because of the special data organization and processing mode in the cloud. In this paper, we present HEDC, a Histogram Estimator for Data in the Cloud. We design a histogram estimate workflow based on an extended MapReduce framework, and propose novel sampling mechanisms to leverage the sampling efficiency and estimate accuracy. We experimentally validate our techniques on Hadoop and the results demonstrate that HEDC can provide promising histogram estimate for massive data in the cloud.

As an important application of spatial databases in pathology imaging analysis, cross-comparing the spatial boundaries of a huge amount of segmented micro-anatomic objects demands extremely data- and compute-intensive operations, requiring high throughput at an affordable cost. However, the performance of spatial database systems has not been satisfactory since their implementations of spatial operations cannot fully utilize the power of modern parallel hardware. In this paper, we provide a customized software solution that exploits GPUs and multi-core CPUs to accelerate spatial cross-comparison in a cost-effective way. Our solution consists of an efficient GPU algorithm and a pipelined system framework with task migration support. Extensive experiments with real-world data sets demonstrate the effectiveness of our solution, which improves the performance of spatial cross-comparison by over 18 times compared with a parallelized spatial database approach., VLDB2012

Analyzing and querying large volumes of spatially derived data from scientific experiments has posed major challenges in the past decade. For example, the systematic analysis of imaged pathology specimens result in rich spatially derived information with GIS characteristics at cellular and sub-cellular scales, with nearly a million derived markups and hundred million features per image. This provides critical information for evaluation of experimental results, support of biomedical studies and pathology image based diagnosis. However, the vast amount of spatially oriented morphological information poses major challenges for analytical medical imaging. The major challenges I attack include: i) How can we provide cost effective, scalable spatial query support for medical imaging GIS? ii) How can we provide fast response queries on analytical imaging data to support biomedical research and clinical diagnosis? and iii) How can we provide expressive queries to support spatial queries and spatial pattern discoveries for end users? In my thesis, I work towards developing a MapReduce based framework MIGIS to support expressive, cost effective and high performance spatial queries. The framework includes a real-time spatial query engine RESQUE consisting of a variety of optimized access methods, boundary and density aware spatial data partitioning, a declarative query language interface, a query translator which automates translation of the spatial queries into MapReduce programs and an execution engine which parallelizes and executes queries on Hadoop. Our preliminary experiments demonstrate that MIGIS is a cost effective architecture which achieves high performance spatial query execution. MIGIS is extensible and can be adapted to support similar complex spatial queries for large scale spatial data in other scientific domains.

High-resolution pathology images provide rich information about the morphological and functional characteristics of biological systems, and are transforming the field of pathology into a new era. To facilitate the use of digital pathology imaging for biomedical research and clinical diagnosis, it is essential to manage and query both whole slide images (WSI) and analytical results generated from images, such as annotations made by humans and computed features and classifications made by computer algorithms. There are unique requirements on modeling, managing and querying whole slide images, including compatibility with standards, scalability, support of image queries at multiple granularities, and support of integrated queries between images and derived results from the images. In this paper, we present our work on developing the Pathology Image Database System (PIDB), which is a standard oriented image database to support retrieval of images, tiles, regions and analytical results, image visualization and experiment management through a unified interface and architecture. The system is deployed for managing and querying whole slide images for In Silico brain tumor studies at Emory University. PIDB is generic and open source, and can be easily used to support other biomedical research projects. It has the potential to be integrated into a Picture Archiving and Communications System (PACS) with powerful query capabilities to support pathology imaging.

In this paper, we present a comprehensive framework to support classification of nuclei in digital microscopy images of diffuse gliomas. This system integrates multiple modules designed for convenient human annotations, standard-based data management, efficient data query and analysis. In our study, 2770 nuclei of six types are annotated by neuropathologists from 29 whole-slide images of glioma biopsies. After machine-based nuclei segmentation for whole-slide images, a set of features describing nuclear shape, texture and cytoplasmic staining is calculated to describe each nucleus. These features along with nuclear boundaries are represented by a standardized data model and saved in the spatial relational database in our framework. Features derived from nuclei classified by neuropathologists are retrieved from the database through efficient spatial queries and used to train distinct classifiers. The best average classification accuracy is 87.43% for 100 independent five-fold cross validations. This suggests that the derived nuclear and cytoplasmic features can achieve promising classification results for six nuclear classes commonly presented in gliomas. Our framework is generic, and can be easily adapted for other related applications.