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Register a new userAn Empirical Meta-analysis of the Life Sciences (Linked?) Open Data on the Web
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Added by
Maulik Kamdar
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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While the biomedical community has published several open data sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, query, and integrate heterogeneous data and knowledge from multiple sources. To tackle these challenges, the community has experimented with Semantic Web and linked data technologies to create the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we extract schemas from more than 80 publicly available biomedical linked data graphs into an LSLOD schema graph and conduct an empirical meta-analysis to evaluate the extent of semantic heterogeneity across the LSLOD cloud. We observe that several LSLOD sources exist as stand-alone data sources that are not inter-linked with other sources, use unpublished schemas with minimal reuse or mappings, and have elements that are not useful for data integration from a biomedical perspective. We envision that the LSLOD schema graph and the findings from this research will aid researchers who wish to query and integrate data and knowledge from multiple biomedical sources simultaneously on the Web.
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The Linked Open Data practice has led to a significant growth of structured data on the Web in the last decade. Such structured data describe real-world entities in a machine-readable way, and have created an unprecedented opportunity for research in the field of Natural Language Processing. However, there is a lack of studies on how such data can be used, for what kind of tasks, and to what extent they can be useful for these tasks. This work focuses on the e-commerce domain to explore methods of utilising such structured data to create language resources that may be used for product classification and linking. We process billions of structured data points in the form of RDF n-quads, to create multi-million words of product-related corpora that are later used in three different ways for creating of language resources: training word embedding models, continued pre-training of BERT-like language models, and training Machine Translation models that are used as a proxy to generate product-related keywords. Our evaluation on an extensive set of benchmarks shows word embeddings to be the most reliable and consistent method to improve the accuracy on both tasks (with up to 6.9 percentage points in macro-average F1 on some datasets). The other two methods however, are not as useful. Our analysis shows that this could be due to a number of reasons, including the biased domain representation in the structured data and lack of vocabulary coverage. We share our datasets and discuss how our lessons learned could be taken forward to inform future research in this direction.
With applications to many disciplines, the traveling salesman problem (TSP) is a classical computer science optimization problem with applications to industrial engineering, theoretical computer science, bioinformatics, and several other disciplines. In recent years, there have been a plethora of novel approaches for approximate solutions ranging from simplistic greedy to cooperative distributed algorithms derived from artificial intelligence. In this paper, we perform an evaluation and analysis of cornerstone algorithms for the Euclidean TSP. We evaluate greedy, 2-opt, and genetic algorithms. We use several datasets as input for the algorithms including a small dataset, a mediumsized dataset representing cities in the United States, and a synthetic dataset consisting of 200 cities to test algorithm scalability. We discover that the greedy and 2-opt algorithms efficiently calculate solutions for smaller datasets. Genetic algorithm has the best performance for optimality for medium to large datasets, but generally have longer runtime. Our implementations is public available.
Energy is a complex idea that cuts across scientific disciplines. For life science students, an approach to energy that incorporates chemical bonds and chemical reactions is better equipped to meet the needs of life sciences students than a traditional introductory physics approach that focuses primarily on mechanical energy. We present a curricular sequence, or thread, designed to build up students understanding of chemical energy in an introductory physics course for the life sciences. This thread is designed to connect ideas about energy from physics, biology, and chemistry. We describe the kinds of connections among energetic concepts that we intended to develop to build interdisciplinary coherence, and present some examples of curriculum materials and student data that illustrate our approach.
This article provides a thorough meta-analysis of the anomaly detection problem. To accomplish this we first identify approaches to benchmarking anomaly detection algorithms across the literature and produce a large corpus of anomaly detection benchmarks that vary in their construction across several dimensions we deem important to real-world applications: (a) point difficulty, (b) relative frequency of anomalies, (c) clusteredness of anomalies, and (d) relevance of features. We apply a representative set of anomaly detection algorithms to this corpus, yielding a very large collection of experimental results. We analyze these results to understand many phenomena observed in previous work. First we observe the effects of experimental design on experimental results. Second, results are evaluated with two metrics, ROC Area Under the Curve and Average Precision. We employ statistical hypothesis testing to demonstrate the value (or lack thereof) of our benchmarks. We then offer several approaches to summarizing our experimental results, drawing several conclusions about the impact of our methodology as well as the strengths and weaknesses of some algorithms. Last, we compare results against a trivial solution as an alternate means of normalizing the reported performance of algorithms. The intended contributions of this article are many; in addition to providing a large publicly-available corpus of anomaly detection benchmarks, we provide an ontology for describing anomaly detection contexts, a methodology for controlling various aspects of benchmark creation, guidelines for future experimental design and a discussion of the many potential pitfalls of trying to measure success in this field.
Pseudo-labeling (PL) and Data Augmentation-based Consistency Training (DACT) are two approaches widely used in Semi-Supervised Learning (SSL) methods. These methods exhibit great power in many machine learning tasks by utilizing unlabeled data for efficient training. But in a more realistic setting (termed as open-set SSL), where unlabeled dataset contains out-of-distribution (OOD) samples, the traditional SSL methods suffer severe performance degradation. Recent approaches mitigate the negative influence of OOD samples by filtering them out from the unlabeled data. However, it is not clear whether directly removing the OOD samples is the best choice. Furthermore, why PL and DACT could perform differently in open-set SSL remains a mystery. In this paper, we thoroughly analyze various SSL methods (PL and DACT) on open-set SSL and discuss pros and cons of these two approaches separately. Based on our analysis, we propose Style Disturbance to improve traditional SSL methods on open-set SSL and experimentally show our approach can achieve state-of-the-art results on various datasets by utilizing OOD samples properly. We believe our study can bring new insights for SSL research.
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