Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction

<p>Abstract</p> <p>Background</p> <p>This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a gene and a pointer to a MEDLINE reference. In the suggested approach we merge two independent sentence extraction strategies. The first proposed strategy (LASt) uses argumentative features, inspired by discourse-analysis models. The second extraction scheme (GOEx) uses an automatic text categorizer to estimate the density of Gene Ontology categories in every sentence; thus providing a full ranking of all possible candidate GeneRiFs. A combination of the two approaches is proposed, which also aims at reducing the size of the selected segment by filtering out non-content bearing rhetorical phrases.</p> <p>Results</p> <p>Based on the TREC-2003 Genomics collection for GeneRiF identification, the LASt extraction strategy is already competitive (52.78%). When used in a combined approach, the extraction task clearly shows improvement, achieving a Dice score of over 57% (+10%).</p> <p>Conclusions</p> <p>Argumentative representation levels and conceptual density estimation using Gene Ontology contents appear complementary for functional annotation in proteomics.</p

FROM USER-GENERATED-CONTENT TO STRUCTURED KNOWLEDGE EXPLORING MULTI-ASPECT SENTENCE REPRESENTATION AND PROTOTYPE HIERARCHY BASED CATEGORIZATION FOR ORGANIZATION OF TEXT COLLECTIONS

Ph.DDOCTOR OF PHILOSOPH

A Relevance Feedback-Based System For Quickly Narrowing Biomedical Literature Search Result

The online literature is an important source that helps people find the information. The quick increase of online literature makes the manual search process for the most relevant information a very time-consuming task and leads to sifting through many results to find the relevant ones. The existing search engines and online databases return a list of results that satisfy the user\u27s search criteria. The list is often too long for the user to go through every hit if he/she does not exactly know what he/she wants or/and does not have time to review them one by one. My focus is on how to find biomedical literature in a fastest way. In this dissertation, I developed a biomedical literature search system that uses relevance feedback mechanism, fuzzy logic, text mining techniques and Unified Medical Language System. The system extracts and decodes information from the online biomedical documents and uses the extracted information to first filter unwanted documents and then ranks the related ones based on the user preferences. I used text mining techniques to extract PDF document features and used these features to filter unwanted documents with the help of fuzzy logic. The system extracts meaning and semantic relations between texts and calculates the similarity between documents using these relations. Moreover, I developed a fuzzy literature ranking method that uses fuzzy logic, text mining techniques and Unified Medical Language System. The ranking process is utilized based on fuzzy logic and Unified Medical Language System knowledge resources. The fuzzy ranking method uses semantic type and meaning concepts to map the relations between texts in documents. The relevance feedback-based biomedical literature search system is evaluated using a real biomedical data that created using dobutamine (drug name). The data set contains 1,099 original documents. To obtain coherent and reliable evaluation results, two physicians are involved in the system evaluation. Using (30-day mortality) as specific query, the retrieved result precision improves by 87.7% in three rounds, which shows the effectiveness of using relevance feedback, fuzzy logic and UMLS in the search process. Moreover, the fuzzy-based ranking method is evaluated in term of ranking the biomedical search result. Experiments show that the fuzzy-based ranking method improves the average ranking order accuracy by 3.35% and 29.55% as compared with UMLS meaning and semantic type methods respectively

Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot

<p>Abstract</p> <p>Background</p> <p>In the context of the BioCreative competition, where training data were very sparse, we investigated two complementary tasks: 1) given a Swiss-Prot triplet, containing a protein, a GO (Gene Ontology) term and a relevant article, extraction of a short passage that justifies the GO category assignement; 2) given a Swiss-Prot pair, containing a protein and a relevant article, automatic assignement of a set of categories.</p> <p>Methods</p> <p>Sentence is the basic retrieval unit. Our classifier computes a distance between each sentence and the GO category provided with the Swiss-Prot entry. The Text Categorizer computes a distance between each GO term and the text of the article. Evaluations are reported both based on annotator judgements as established by the competition and based on mean average precision measures computed using a curated sample of Swiss-Prot.</p> <p>Results</p> <p>Our system achieved the best recall and precision combination both for passage retrieval and text categorization as evaluated by official evaluators. However, text categorization results were far below those in other data-poor text categorization experiments The top proposed term is relevant in less that 20% of cases, while categorization with other biomedical controlled vocabulary, such as the Medical Subject Headings, we achieved more than 90% precision. We also observe that the scoring methods used in our experiments, based on the retrieval status value of our engines, exhibits effective confidence estimation capabilities.</p> <p>Conclusion</p> <p>From a comparative perspective, the combination of retrieval and natural language processing methods we designed, achieved very competitive performances. Largely data-independent, our systems were no less effective that data-intensive approaches. These results suggests that the overall strategy could benefit a large class of information extraction tasks, especially when training data are missing. However, from a user perspective, results were disappointing. Further investigations are needed to design applicable end-user text mining tools for biologists.</p

Exploratory search through large video corpora

Activity retrieval is a growing field in electrical engineering that specializes in the search and retrieval of relevant activities and events in video corpora. With the affordability and popularity of cameras for government, personal and retail use, the quantity of available video data is rapidly outscaling our ability to reason over it. Towards the end of empowering users to navigate and interact with the contents of these video corpora, we propose a framework for exploratory search that emphasizes activity structure and search space reduction over complex feature representations. Exploratory search is a user driven process wherein a person provides a system with a query describing the activity, event, or object he is interested in finding. Typically, this description takes the implicit form of one or more exemplar videos, but it can also involve an explicit description. The system returns candidate matches, followed by query refinement and iteration. System performance is judged by the run-time of the system and the precision/recall curve of of the query matches returned. Scaling is one of the primary challenges in video search. From vast web-video archives like youtube (1 billion videos and counting) to the 30 million active surveillance cameras shooting an estimated 4 billion hours of footage every week in the United States, trying to find a set of matches can be like looking for a needle in a haystack. Our goal is to create an efficient archival representation of video corpora that can be calculated in real-time as video streams in, and then enables a user to quickly get a set of results that match. First, we design a system for rapidly identifying simple queries in large-scale video corpora. Instead of focusing on feature design, our system focuses on the spatiotemporal relationships between those features as a means of disambiguating an activity of interest from background. We define a semantic feature vocabulary of concepts that are both readily extracted from video and easily understood by an operator. As data streams in, features are hashed to an inverted index and retrieved in constant time after the system is presented with a user's query. We take a zero-shot approach to exploratory search: the user manually assembles vocabulary elements like color, speed, size and type into a graph. Given that information, we perform an initial downsampling of the archived data, and design a novel dynamic programming approach based on genome-sequencing to search for similar patterns. Experimental results indicate that this approach outperforms other methods for detecting activities in surveillance video datasets. Second, we address the problem of representing complex activities that take place over long spans of space and time. Subgraph and graph matching methods have seen limited use in exploratory search because both problems are provably NP-hard. In this work, we render these problems computationally tractable by identifying the maximally discriminative spanning tree (MDST), and using dynamic programming to optimally reduce the archive data based on a custom algorithm for tree-matching in attributed relational graphs. We demonstrate the efficacy of this approach on popular surveillance video datasets in several modalities. Finally, we design an approach for successive search space reduction in subgraph matching problems. Given a query graph and archival data, our algorithm iteratively selects spanning trees from the query graph that optimize the expected search space reduction at each step until the archive converges. We use this approach to efficiently reason over video surveillance datasets, simulated data, as well as large graphs of protein data

Conspiracy in the Time of Corona: Automatic detection of Emerging Covid-19 Conspiracy Theories in Social Media and the News

Abstract Rumors and conspiracy theories thrive in environments of low confi- dence and low trust. Consequently, it is not surprising that ones related to the Covid-19 pandemic are proliferating given the lack of scientific consensus on the virus’s spread and containment, or on the long term social and economic ramifications of the pandemic. Among the stories currently circulating are ones suggesting that the 5G telecommunication network activates the virus, that the pandemic is a hoax perpetrated by a global cabal, that the virus is a bio-weapon released deliberately by the Chinese, or that Bill Gates is using it as cover to launch a broad vaccination program to facilitate a global surveillance regime. While some may be quick to dismiss these stories as having little impact on real-world behavior, recent events including the destruction of cell phone towers, racially fueled attacks against Asian Americans, demonstrations espousing resistance to public health orders, and wide-scale defiance of scientifically sound public mandates such as those to wear masks and practice social distancing, countermand such conclusions. Inspired by narrative theory, we crawl social media sites and news reports and, through the application of automated machine-learning methods, discover the underlying narrative frame- works supporting the generation of rumors and conspiracy theories. We show how the various narrative frameworks fueling these stories rely on the alignment of otherwise disparate domains of knowledge, and consider how they attach to the broader reporting on the pandemic. These alignments and attachments, which can be monitored in near real-time, may be useful for identifying areas in the news that are particularly vulnerable to reinterpretation by conspiracy theorists. Understanding the dynamics of storytelling on social media and the narrative frameworks that provide the generative basis for these stories may also be helpful for devising methods to disrupt their spread