The amount of home-based exercise prescribed by a physical therapist is difficult to monitor. However, the integration of wearable inertial measurement unit (IMU) devices can aid in monitoring home exercise by analyzing exercise biomechanics. The objective of this study is to evaluate machine learning models for classifying nine different upper extremity exercises, based upon kinematic data captured from an IMU-based device. Fifty participants performed one compound and eight isolation exercises with their right arm. Each exercise was performed ten times for a total of 4500 trials. Joint angles were calculated using IMUs that were placed on the hand, forearm, upper arm, and torso. Various machine learning models were developed with different algorithms and train-test splits. Random forest models with flattened kinematic data as a feature had the greatest accuracy (98.6%). Using triaxial joint range of motion as the feature set resulted in decreased accuracy (91.9%) with faster speeds. Accuracy did not decrease below 90% until training size was decreased to 5% from 50%. Accuracy decreased (88.7%) when splitting data by participant. Upper extremity exercises can be classified accurately using kinematic data from a wearable IMU device. A random forest classification model was developed that quickly and accurately classified exercises. Sampling frequency and lower training splits had a modest effect on performance. When the data were split by subject stratification, larger training sizes were required for acceptable algorithm performance. These findings set the basis for more objective and accurate measurements of home-based exercise using emerging healthcare technologies.

Mobile devices have the potential to continuously monitor health by collecting movement data including walking speed during natural walking. Natural walking is walking without artificial speed constraints present in both treadmill and nurse-assisted walking. Fitness trackers have become popular which record steps taken and distance, typically using a fixed stride length. While useful for everyday purposes, medical monitoring requires precise accuracy and testing on real patients with a scientifically valid measure. Walking speed is closely linked to morbidity in patients and widely used for medical assessment via measured walking. The 6-min walk test (6MWT) is a standard assessment for chronic obstructive pulmonary disease and congestive heart failure. Current generation smartphone hardware contains similar sensor chips as in medical devices and popular fitness devices. We developed a middleware software, MoveSense, which runs on standalone smartphones while providing comparable readings to medical accelerometers. We evaluate six machine learning methods to obtain gait speed during natural walking training models to predict natural walking speed and distance during a 6MWT with 28 pulmonary patients and ten subjects without pulmonary condition. We also compare our model's accuracy to popular fitness devices. Our universally trained support vector machine models produce 6MWT distance with 3.23% error during a controlled 6MWT and 11.2% during natural free walking. Furthermore, our model attains 7.9% error when tested on five subjects for distance estimation compared to the 50-400% error seen in fitness devices during natural walking.

The papers in this special section focus on the use of predictive modeling in the area of health informatics. These papers were presented at the fifth BCB conference that was held in September 2014 at Newport Beach, CA. Predictive modeling in health informatics is an emerging discipline, data analytics in the era of Digital Health. The BCB conference emphasizes research projects with new computer science and information science such as machine learning and entity classification.

BACKGROUND: Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on controlled vocabularies, in particular, Gene Ontology (GO). However, the annotation of genes is a labor-intensive process; and the vocabularies are generally incomplete, leaving some important biological domains inadequately covered. RESULTS: We propose a statistical method that uses the primary literature, i.e. free-text, as the source to perform overrepresentation analysis. The method is based on a statistical framework of mixture model and addresses the methodological flaws in several existing programs. We implemented this method within a literature mining system, BeeSpace, taking advantage of its analysis environment and added features that facilitate the interactive analysis of gene sets. Through experimentation with several datasets, we showed that our program can effectively summarize the important conceptual themes of large gene sets, even when traditional GO-based analysis does not yield informative results. CONCLUSIONS: We conclude that the current work will provide biologists with a tool that effectively complements the existing ones for overrepresentation analysis from genomic experiments. Our program, Genelist Analyzer, is freely available at: http://workerbee.igb.uiuc.edu:8080/BeeSpace/Search.jsp.

A common task in many text mining applications is to generate a multi-faceted overview of a topic in a text collection. Such an overview not only directly serves as an informative summary of the topic, but also provides a detailed view of navigation to different facets of the topic. Existing work has cast this problem as a categorization problem and requires training examples for each facet. This has three limitations: (1) All facets are predefined, which may not fit the need of a particular user. (2) Training examples for each facet are often unavailable. (3) Such an approach only works for a predefined type of topics. In this paper, we break these limitations and study a more realistic new setup of the problem, in which we would allow a user to flexibly describe each facet with keywords for an arbitrary topic and attempt to mine a multi-faceted overview in an unsupervised way. We attempt a probabilistic approach to solve this problem. Empirical experiments on different genres of text data show that our approach can effectively generate a multi-faceted overview for arbitrary topics; the generated overviews are comparable with those generated by supervised methods with training examples. They are also more informative than unstructured flat summaries. The method is quite general, thus can be applied to multiple text mining tasks in different application domains.

A research prototype is presented for semantic indexing and retrieval in Information Retrieval. The prototype is motivated by a desire to provide a more efficient and effective information retrieval system compared to the current state of the art. An overview of the Interspace architecture layers is discussed. An object model supporting semantic operations is developed. The model contains a rich set of classes and relationships of the data for the semantic indexing module. The basis of our semantic indexing is done by the creation of concept space. A concept space is an index of a collection that uses document statistics to capture the relationships between concepts. It is useful for boosting text search, by term suggestion of alternative terms semantically related to query terms. Over the years, we have developed generic technology for concept spaces computation on large collections across many subjects. Recent computations on discipline-scale collections have been made on high-end supercomputers. This paper describes our implementation and implications of the computation in a distributed computing environment. Experimental results using different collection sizes and number of processes are presented to show the feasibility of this approach. We also show that laboratory and community collections are already easily computable using a group of PCs in a lab via a message-passing model. We conclude that PC clusters will shortly be able to compute semantic indexes for any real collections.

Digital libraries of geo-spatial multimedia content are currently deficient in providing fuzzy, concept-based retrieval mechanisms to users. The main challenge is that indexing and thesaurus creation are extremely labor-intensive processes for text documents and especially for images. Recently, 800,000 declassified satellite photographs were made available by the United States Geological Survey. Additionally, millions of satellite and aerial photographs are archived in national and local map libraries. Such enormous collections make human indexing and thesaurus generation methods impossible to utilize. In this article we propose a scalable method to automatically generate visual thesauri of large collections of geo-spatial media using fuzzy, unsupervised machine-learning techniques.

The Net of the 21st Century will radically transform interaction with knowledge. Users will navigate in the Interspace, across logical spaces of semantic indexes, rather than in the Internet, across physical networks of computer servers. Correlation across indexed collections is the most important feature of this infrastructure. Over ten years of research, the author has developed scalable technology for generating the necessary semantic indexes. Construction of large scale models of the Interspace is feasible now under controlled laboratory conditions. Community repositories for entire scientific disciplines have been constructed using supercomputer simulations on millions of documents. A model Interspace is a set of community repositories, interconnected by concept switching networks to support information analysis across subject domains. CANIS has constructed several model testbeds with increasingly better infrastructure technology. We propose a PACI Interspace for the NSF flagship efforts of the HPDC community. The Interspace would provide concept switching for the users while the Grid would provide object switching for the sources.

The Internet provides an exceptional testbed for developing algorithms that can improve browsing and searching large information spaces. Browsing and searching tasks are susceptible to problems of information overload and vocabulary differences. Much of the current research is aimed at the development and refinement of algorithms to improve browsing and searching by addressing these problems. Our research was focused on discovering whether two of the algorithms our research group has developed, a Kohonen algorithm category map for browsing, and an automatically generated concept space algorithm for searching, can help improve browsing and/or searching the Internet. Our results indicate that a Kohonen self-organizing map (SOM)-based algorithm can successfully categorize a large and eclectic Internet information space (the Entertainment sub-category of Yahoo!) into manageable sub-spaces that users can successfully navigate to locate a homepage of interest to them. The SOM algorithm worked best with browsing tasks that were very broad, and in which subjects skipped around between categories. Subjects especially liked the visual and graphical aspects of the map. Subjects who tried to do a directed search, and those that wanted to use the more familiar mental models (alphabetic or hierarchical organization) for browsing, found that the map did not work well. The results from the concept space experiment were especially encouraging. There were no significant differences among the precision measures for the set of documents identified by subject-suggested terms, thesaurus-suggested terms, and the combination of subject- and thesaurus-suggested terms. The recall measures indicated that the combination of subject- and thesaurus-suggested terms exhibited significantly better recall than subject-suggested terms alone. Furthermore, analysis of the home pages indicated that there was limited overlap between the homepages retrieved by the subject-suggested and thesaurus-suggested terms. Since the retrieved homepages for the most part were different, this suggests that a user can enhance a keyword-based search by using an automatically generated concept space. Subjects especially liked the level of control that they could exert over the search, and the fact that the terms suggested by the thesaurus were “real” (i.e., originating in the homepages) and therefore guaranteed to have retrieval success. © 1998 John Wiley & Sons, Inc.

In this article, we report research on an algorithmic approach to alleviating search uncertainty in a large information space. Grounded on object filtering, automatic indexing, and co-occurrence analysis, we performed a large-scale experiment using a parallel supercomputer (SGI Power Challenge) to analyze 400,000+ abstracts in an INSPEC computer engineering collection. Two system-generated thesauri, one based on a combined object filtering and automatic indexing method, and the other based on automatic indexing only, were compared with the human-generated INSPEC subject thesaurus. Our user evaluation revealed that the system-generated thesauri were better than the INSPEC thesaurus in concept recall, but in concept precision the 3 thesauri were comparable. Our analysis also revealed that the terms suggested by the 3 thesauri were complementary and could be used to significantly increase “variety” in search terms and thereby reduce search uncertainty. © 1998 John Wiley & Sons, Inc.

No abstract available.

This research presents an algorithmic approach to addressing the vocabulary problem in scientific information retrieval and information sharing, using the molecular biology domain as an example. We first present a literature review of cognitive studies related to the vocabulary problem and vocabulary-based search aids (thesauri) and then discuss techniques for building robust and domain-specific thesauri to assist in cross-domain scientific information retrieval. Using a variation of the automatic thesaurus generation techniques, which we refer to as the concept space approach, we recently conducted an experiment in the molecular biology domain in which we created a C. elegans worm thesaurus of 7,657 worm-specific terms and a Drosophila fly thesaurus of 15,626 terms. About 30% of these terms overlapped, which created vocabulary paths from one subject domain to the other. Based on a cognitive study of term association involving four biologists, we found that a large percentage (59.6–85.6%) of the terms suggested by the subjects were identified in the conjoined fly-worm thesaurus. However, we found only a small percentage (8.4–18.1%) of the associations suggested by the subjects in the thesaurus. In a follow-up document retrieval study involving eight fly biologists, an actual worm database (Worm Community System), and the conjoined fly-worm thesaurus, subjects were able to find more relevant documents (an increase from about 9 documents to 20) and to improve the document recall level (from 32.41 to 65.28%) when using the thesaurus, although the precision level did not improve significantly. Implications of adopting the concept space approach for addressing the vocabulary problem in internet and digital libraries applications are also discussed.

Database federation enables biological researchers to utilize resources more effectively, creating an environment in which the researcher can query multiple data sources without spending time learning new query mechanisms or issuing redundant queries which need to be integrated. Several mechanisms exist to federate databases. The ENQUire system is a network database federation system which uses a World-Wide-Web (WWW) interface to connect the users to various databases. Generic queries entered via a query generator form are sent in parallel to multiple databases, and the results are presented to the user in a unified format. All forms building, query generation, and results translation is done on the fly, and individual database translation modules can be added dynamically. ENQUire is a flexible answer to the problems of database federation on the WWW.

This research presents preliminary results generated from the semantic retrieval research component of the Illinois Digital Library Initiative (DLI) project. Using a variation of the automatic thesaurus generation techniques, to which we refer to as the concept space approach, we aimed to create graphs of domain-specific concepts (terms) and their weighted co-occurrence relationships for all major engineering domains. Merging these concept spaces and providing traversal paths across different concept spaces could potentially help alleviate the vocabulary (difference) problem evident in large-scale information retrieval. In order to address the scalability issue related to large-scale information retrieval and analysis for the current Illinois DLI project, we conducted experiments using the concept space approach on parallel supercomputers. Our test collection included computer science and electrical engineering abstracts extracted from the INSPEC database. The concept space approach called for extensive textual and statistical analysis (a form of knowledge discovery) based on automatic indexing and co-occurrence analysis algorithms, both previously tested in the biology domain. Initial testing results using a 512-node CM-5 and a 16-processor SGI Power Challenge were promising.

This research reports an algorithmic approach to the automatic generation of thesauri for electronic community systems. The techniques used included term filtering, automatic indexing, and cluster analysis. The testbed for our research was the Worm Community System, which contains a comprehensive library of specialized community data and literature, currently in use by molecular biologists who study the nematode worm C. elegans. The resulting worm thesaurus included 2709 researchers' names, 798 gene names, 20 experimental methods, and 4302 subject descriptors. On average, each term had about 90 weighted neighboring terms indicating relevant concepts. The thesaurus was developed as an online search aide. We tested the worm thesaurus in an experiment with six worm researchers of varying degrees of expertise and background. The experiment showed that the thesaurus was an excellent “memory-jogging” device and that it supported learning and serendipitous browsing. Despite some occurrences of obvious noise, the system was useful in suggesting relevant concepts for the researchers' queries and it helped improve concept recall. With a simple browsing interface, an automatic thesaurus can become a useful tool for online search and can assist researchers in exploring and traversing a dynamic and complex electronic community system. © 1995 John Wiley & Sons, Inc.

A novel facility in hypermedia systems is proposed to provide search using queries. The search mechanism is shown to complement linking, making the creation of rich linked structures easier. A prototype hypermedia system that provides search is described, and user experiences to date and some future directions are discussed.>