Simulated evaluation of faceted browsing based on feature selection

In this paper we explore the limitations of facet based browsing which uses sub-needs of an information need for querying and organising the search process in video retrieval. The underlying assumption of this approach is that the search effectiveness will be enhanced if such an approach is employed for interactive video retrieval using textual and visual features. We explore the performance bounds of a faceted system by carrying out a simulated user evaluation on TRECVid data sets, and also on the logs of a prior user experiment with the system. We first present a methodology to reduce the dimensionality of features by selecting the most important ones. Then, we discuss the simulated evaluation strategies employed in our evaluation and the effect on the use of both textual and visual features. Facets created by users are simulated by clustering video shots using textual and visual features. The experimental results of our study demonstrate that the faceted browser can potentially improve the search effectiveness

A Systematic Review of Automated Query Reformulations in Source Code Search

Fixing software bugs and adding new features are two of the major maintenance tasks. Software bugs and features are reported as change requests. Developers consult these requests and often choose a few keywords from them as an ad hoc query. Then they execute the query with a search engine to find the exact locations within software code that need to be changed. Unfortunately, even experienced developers often fail to choose appropriate queries, which leads to costly trials and errors during a code search. Over the years, many studies attempt to reformulate the ad hoc queries from developers to support them. In this systematic literature review, we carefully select 70 primary studies on query reformulations from 2,970 candidate studies, perform an in-depth qualitative analysis (e.g., Grounded Theory), and then answer seven research questions with major findings. First, to date, eight major methodologies (e.g., term weighting, term co-occurrence analysis, thesaurus lookup) have been adopted to reformulate queries. Second, the existing studies suffer from several major limitations (e.g., lack of generalizability, vocabulary mismatch problem, subjective bias) that might prevent their wide adoption. Finally, we discuss the best practices and future opportunities to advance the state of research in search query reformulations.Comment: 81 pages, accepted at TOSE

Enhanced word embedding similarity measures using fuzzy rules for query expansion

© 2017 IEEE. Query expansion has been widely used to select additional words that are related to the original query words in the field of information retrieval. In this paper, we present a novel query expansion method that jointly uses fuzzy rules and a word embedding similarity calculation. The expansion words are generated using a word embedding method and selected according to their semantic similarity to the original query. Fuzzy rules are used to enhance the word similarity calculations and reweight expansion words. When measuring and ranking the relevance of a retrieved document, the original query and the expansion words with their weights are considered. We conduct experiments on the query expansion in document ranking tasks. Experimental results from the document ranking task show that the proposed method is able to significantly outperform state-of-the-art baseline methods

Neural Representations of Concepts and Texts for Biomedical Information Retrieval

Information retrieval (IR) methods are an indispensable tool in the current landscape of exponentially increasing textual data, especially on the Web. A typical IR task involves fetching and ranking a set of documents (from a large corpus) in terms of relevance to a user\u27s query, which is often expressed as a short phrase. IR methods are the backbone of modern search engines where additional system-level aspects including fault tolerance, scale, user interfaces, and session maintenance are also addressed. In addition to fetching documents, modern search systems may also identify snippets within the documents that are potentially most relevant to the input query. Furthermore, current systems may also maintain preprocessed structured knowledge derived from textual data as so called knowledge graphs, so certain types of queries that are posed as questions can be parsed as such; a response can be an output of one or more named entities instead of a ranked list of documents (e.g., what diseases are associated with EGFR mutations? ). This refined setup is often termed as question answering (QA) in the IR and natural language processing (NLP) communities. In biomedicine and healthcare, specialized corpora are often at play including research articles by scientists, clinical notes generated by healthcare professionals, consumer forums for specific conditions (e.g., cancer survivors network), and clinical trial protocols (e.g., www.clinicaltrials.gov). Biomedical IR is specialized given the types of queries and the variations in the texts are different from that of general Web documents. For example, scientific articles are more formal with longer sentences but clinical notes tend to have less grammatical conformity and are rife with abbreviations. There is also a mismatch between the vocabulary of consumers and the lingo of domain experts and professionals. Queries are also different and can range from simple phrases (e.g., COVID-19 symptoms ) to more complex implicitly fielded queries (e.g., chemotherapy regimens for stage IV lung cancer patients with ALK mutations ). Hence, developing methods for different configurations (corpus, query type, user type) needs more deliberate attention in biomedical IR. Representations of documents and queries are at the core of IR methods and retrieval methodology involves coming up with these representations and matching queries with documents based on them. Traditional IR systems follow the approach of keyword based indexing of documents (the so called inverted index) and matching query phrases against the document index. It is not difficult to see that this keyword based matching ignores the semantics of texts (synonymy at the lexeme level and entailment at phrase/clause/sentence levels) and this has lead to dimensionality reduction methods such as latent semantic indexing that generally have scale-related concerns; such methods also do not address similarity at the sentence level. Since the resurgence of neural network methods in NLP, the IR field has also moved to incorporate advances in neural networks into current IR methods. This dissertation presents four specific methodological efforts toward improving biomedical IR. Neural methods always begin with dense embeddings for words and concepts to overcome the limitations of one-hot encoding in traditional NLP/IR. In the first effort, we present a new neural pre-training approach to jointly learn word and concept embeddings for downstream use in applications. In the second study, we present a joint neural model for two essential subtasks of information extraction (IE): named entity recognition (NER) and entity normalization (EN). Our method detects biomedical concept phrases in texts and links them to the corresponding semantic types and entity codes. These first two studies provide essential tools to model textual representations as compositions of both surface forms (lexical units) and high level concepts with potential downstream use in QA. In the third effort, we present a document reranking model that can help surface documents that are likely to contain answers (e.g, factoids, lists) to a question in a QA task. The model is essentially a sentence matching neural network that learns the relevance of a candidate answer sentence to the given question parametrized with a bilinear map. In the fourth effort, we present another document reranking approach that is tailored for precision medicine use-cases. It combines neural query-document matching and faceted text summarization. The main distinction of this effort from previous efforts is to pivot from a query manipulation setup to transforming candidate documents into pseudo-queries via neural text summarization. Overall, our contributions constitute nontrivial advances in biomedical IR using neural representations of concepts and texts

Contextual Analysis of Large-Scale Biomedical Associations for the Elucidation and Prioritization of Genes and their Roles in Complex Disease

Vast amounts of biomedical associations are easily accessible in public resources, spanning gene-disease associations, tissue-specific gene expression, gene function and pathway annotations, and many other data types. Despite this mass of data, information most relevant to the study of a particular disease remains loosely coupled and difficult to incorporate into ongoing research. Current public databases are difficult to navigate and do not interoperate well due to the plethora of interfaces and varying biomedical concept identifiers used. Because no coherent display of data within a specific problem domain is available, finding the latent relationships associated with a disease of interest is impractical. This research describes a method for extracting the contextual relationships embedded within associations relevant to a disease of interest. After applying the method to a small test data set, a large-scale integrated association network is constructed for application of a network propagation technique that helps uncover more distant latent relationships. Together these methods are adept at uncovering highly relevant relationships without any a priori knowledge of the disease of interest. The combined contextual search and relevance methods power a tool which makes pertinent biomedical associations easier to find, easier to assimilate into ongoing work, and more prominent than currently available databases. Increasing the accessibility of current information is an important component to understanding high-throughput experimental results and surviving the data deluge

Green genes: bioinformatics and systems-biology innovations drive algal biotechnology.

Many species of microalgae produce hydrocarbons, polysaccharides, and other valuable products in significant amounts. However, large-scale production of algal products is not yet competitive against non-renewable alternatives from fossil fuel. Metabolic engineering approaches will help to improve productivity, but the exact metabolic pathways and the identities of the majority of the genes involved remain unknown. Recent advances in bioinformatics and systems-biology modeling coupled with increasing numbers of algal genome-sequencing projects are providing the means to address this. A multidisciplinary integration of methods will provide synergy for a systems-level understanding of microalgae, and thereby accelerate the improvement of industrially valuable strains. In this review we highlight recent advances and challenges to microalgal research and discuss future potential.We acknowledge support from the EU FP7 project SPLASH (Sustainable PoLymers from Algae Sugars and Hydrocarbons), grant agreement number 311956.This is the accepted manuscript. The final version is available from Cell/Elsevier at http://www.sciencedirect.com/science/article/pii/S016777991400196