Discovering gene annotations in biomedical text databases

<p>Abstract</p> <p>Background</p> <p>Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data.</p> <p>Results</p> <p>In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO) concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products.</p> <p>In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general.</p> <p>Conclusion</p> <p>GEANN is useful for two distinct purposes: (i) automating the annotation of genomic entities with Gene Ontology concepts, and (ii) providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values.</p

Theories for influencer identification in complex networks

In social and biological systems, the structural heterogeneity of interaction networks gives rise to the emergence of a small set of influential nodes, or influencers, in a series of dynamical processes. Although much smaller than the entire network, these influencers were observed to be able to shape the collective dynamics of large populations in different contexts. As such, the successful identification of influencers should have profound implications in various real-world spreading dynamics such as viral marketing, epidemic outbreaks and cascading failure. In this chapter, we first summarize the centrality-based approach in finding single influencers in complex networks, and then discuss the more complicated problem of locating multiple influencers from a collective point of view. Progress rooted in collective influence theory, belief-propagation and computer science will be presented. Finally, we present some applications of influencer identification in diverse real-world systems, including online social platforms, scientific publication, brain networks and socioeconomic systems.Comment: 24 pages, 6 figure

GIANT: Scalable Creation of a Web-scale Ontology

Understanding what online users may pay attention to is key to content recommendation and search services. These services will benefit from a highly structured and web-scale ontology of entities, concepts, events, topics and categories. While existing knowledge bases and taxonomies embody a large volume of entities and categories, we argue that they fail to discover properly grained concepts, events and topics in the language style of online population. Neither is a logically structured ontology maintained among these notions. In this paper, we present GIANT, a mechanism to construct a user-centered, web-scale, structured ontology, containing a large number of natural language phrases conforming to user attentions at various granularities, mined from a vast volume of web documents and search click graphs. Various types of edges are also constructed to maintain a hierarchy in the ontology. We present our graph-neural-network-based techniques used in GIANT, and evaluate the proposed methods as compared to a variety of baselines. GIANT has produced the Attention Ontology, which has been deployed in various Tencent applications involving over a billion users. Online A/B testing performed on Tencent QQ Browser shows that Attention Ontology can significantly improve click-through rates in news recommendation.Comment: Accepted as full paper by SIGMOD 202

Near Neighbor Search in Large Metric Spaces

Given user data, one often wants to find approximate matches in a large database. A good example of such a task is finding images similar to a given image in a large collection of images. We focus on the important and technically difficult case where each data element is high dimensional, or more generally, is represented by a point in a large metric spaceand distance calculations are computationally expensive. In this paper we introduce a data structure to solve this problem called a GNAT -- Geometric Near-neighbor Access Tree. It is based on the philosophy that the data structure should act as a hierarchical geometrical model of the data as opposed to a simple decomposition of the data that does not use its intrinsic geometry. In experiments, we find that GNAT&apos;s outperform previous data structures in a number of applications