The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

Description of an experimental on-line, minicomputer-based information retrieval system /

Thesis (M. S.)--University of Illinois at Urbana-Champaign.

Graph-based Vision-Language Model for Multi-Modal Retrieval of Fashion Products

Artificial Intelligence is reshaping the field of fashion industry in different ways. E-commerce retailers exploit their data through AI to enhance their search engines, make outfit suggestions and forecast the success of a specific fashion product. However, it is a challenging endeavour as the data they possess is huge, complex and multi-modal. The most common way to search for fashion products online is by matching keywords with phrases in the product's description which are often cluttered, inadequate and differ across collections and sellers. A customer may also browse an online store's taxonomy, although this is time-consuming and doesn't guarantee relevant items. With the advent of Deep Learning architectures, particularly Vision-Language models, ad-hoc solutions have been proposed to model both the product image and description to solve this problems. However, the suggested solutions do not exploit effectively the semantic or syntactic information of these modalities, and the unique qualities and relations of clothing items. In this work of thesis, a novel approach is proposed to address this issues, which aims to model and process images and text descriptions as graphs in order to exploit the relations inside and between each modality and employs specific techniques to extract syntactic and semantic information. The results obtained show promising performances on different tasks when compared to the present state-of-the-art deep learning architectures.

Intelligent Agent-based Multilingual Information Retrieval System

The goal of this work is to develop an Open Agent Architecture for Multilingual information retrieval from Relational Database. The query for information retrieval can be given in plain Hindi or Malayalam; two prominent regional languages of India. The system supports distributed processing of user requests through collaborating agents. Natural language processing techniques are used for meaning extraction from the plain query and information is given back to the user in his/ her native language. The system architecture is designed in a structured way so that it can be adapted to other regional languages of India

ANALYSIS AND VISUALIZATION OF FLOW FIELDS USING INFORMATION-THEORETIC TECHNIQUES AND GRAPH-BASED REPRESENTATIONS

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner. My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow patterns and how to pick good viewpoints to observe flow fields become critical. We treat streamline selection and viewpoint selection as symmetric problems and solve them simultaneously using the dual information channel [81]. To the best of my knowledge, this is the first attempt in flow visualization to combine these two selection problems in a unified approach. This work selects streamline in a view-independent manner and the selected streamlines will not change for all viewpoints. My another work [56] uses an information-theoretic approach to evaluate the importance of each streamline under various sample viewpoints and presents a solution for view-dependent streamline selection that guarantees coherent streamline update when the view changes gradually. When projecting 3D streamlines to 2D images for viewing, occlusion and clutter become inevitable. To address this challenge, we design FlowGraph [57, 58], a novel compound graph representation that organizes field line clusters and spatiotemporal regions hierarchically for occlusion-free and controllable visual exploration. We enable observation and exploration of the relationships among field line clusters, spatiotemporal regions and their interconnection in the transformed space. Most viewpoint selection methods only consider the external viewpoints outside of the flow field. This will not convey a clear observation when the flow field is clutter on the boundary side. Therefore, we propose a new way to explore flow fields by selecting several internal viewpoints around the flow features inside of the flow field and then generating a B-Spline curve path traversing these viewpoints to provide users with closeup views of the flow field for detailed observation of hidden or occluded internal flow features [54]. This work is also extended to deal with unsteady flow fields. Besides flow field visualization, some other topics relevant to visualization also attract my attention. In iGraph [31], we leverage a distributed system along with a tiled display wall to provide users with high-resolution visual analytics of big image and text collections in real time. Developing pedagogical visualization tools forms my other research focus. Since most cryptography algorithms use sophisticated mathematics, it is difficult for beginners to understand both what the algorithm does and how the algorithm does that. Therefore, we develop a set of visualization tools to provide users with an intuitive way to learn and understand these algorithms.

UNSUPERVISED INDEXING OF MEDLINE ARTICLES THROUGH GRAPH-BASED RANKING

The biomedical literature is extensively catalogued and indexed in MEDLINE. MEDLINE indexing is done by trained human indexers, who identify the most important concepts in each article, and is expensive and inconsistent. Automating the indexing task is difficult: the National Library of Medicine produces the Medical Text Indexer (MTI), which suggests potential indexing terms to the indexers. MTI’s output is not good enough to work unattended. In my thesis, I propose a different way to approach the indexing task called MEDRank. MEDRank creates graphs representing the concepts in biomedical articles and their relationships within the text, and applies graph-based ranking algorithms to identify the most important concepts in each article. I evaluate the performance of several automated indexing solutions, including my own, by comparing their output to the indexing terms selected by the human indexers. MEDRank outperformed all other evaluated indexing solutions, including MTI, in general indexing performance and precision. MEDRank can be used to cluster documents, index any kind of biomedical text with standard vocabularies, or could become part of MTI itself.

Implementation of an information-retrieval based CAI system /

Thesis (M. S.)--University of Illinois at Urbana-Champaign.

Information retrieval and machine translation : based on the International Conference for Standards on a Common Language for Machine Searching and Translation /

Mode of access: Internet.

Concept-based document readability in domain specific information retrieval

Domain specific information retrieval has become in demand. Not only domain experts, but also average non-expert users are interested in searching domain specific (e.g., medical and health) information from online resources. However, a typical problem to average users is that the search results are always a mixture of documents with different levels of readability. Non-expert users may want to see documents with higher readability on the top of the list. Consequently the search results need to be re-ranked in a descending order of readability. It is often not practical for domain experts to manually label the readability of documents for large databases. Computational models of readability needs to be investigated. However, traditional readability formulas are designed for general purpose text and insufficient to deal with technical materials for domain specific information retrieval. More advanced algorithms such as textual coherence model are computationally expensive for re-ranking a large number of retrieved documents. In this paper, we propose an effective and computationally tractable concept-based model of text readability. In addition to textual genres of a document, our model also takes into account domain specific knowledge, i.e., how the domain-specific concepts contained in the document affect the document’s readability. Three major readability formulas are proposed and applied to health and medical information retrieval. Experimental results show that our proposed readability formulas lead to remarkable improvements in terms of correlation with users’ readability ratings over four traditional readability measures.

An information foraging theory based user study of an adaptive user interaction framework for content-based image retrieval

This paper presents the design and results of a task-based user study, based on Information Foraging Theory, on a novel user interaction framework - uInteract - for content-based image retrieval (CBIR). The framework includes a four-factor user interaction model and an interactive interface. The user study involves three focused evaluations, 12 simulated real life search tasks with different complexity levels, 12 comparative systems and 50 subjects. Information Foraging Theory is applied to the user study design and the quantitative data analysis. The systematic findings have not only shown how effective and easy to use the uInteract framework is, but also illustrate the value of Information Foraging Theory for interpreting user interaction with CBIR. © 2011 Springer-Verlag Berlin Heidelberg.

Applying Information Foraging Theory to understand user interaction with content-based image retrieval

The paper proposes an ISE (Information goal, Search strategy, Evaluation threshold) user classification model based on Information Foraging Theory for understanding user interaction with content-based image retrieval (CBIR). The proposed model is verified by a multiple linear regression analysis based on 50 users' interaction features collected from a task-based user study of interactive CBIR systems. To our best knowledge, this is the first principled user classification model in CBIR verified by a formal and systematic qualitative analysis of extensive user interaction data. Copyright 2010 ACM.

Improving cross language information retrieval using corpus based query suggestion approach

Users seeking information may not find relevant information pertaining to their information need in a specific language. But information may be available in a language different from their own, but users may not know that language. Thus users may experience difficulty in accessing the information present in different languages. Since the retrieval process depends on the translation of the user query, there are many issues in getting the right translation of the user query. For a pair of languages chosen by a user, resources, like incomplete dictionary, inaccurate machine translation system may exist. These resources may be insufficient to map the query terms in one language to its equivalent terms in another language. Also for a given query, there might exist multiple correct translations. The underlying corpus evidence may suggest a clue to select a probable set of translations that could eventually perform a better information retrieval. In this paper, we present a cross language information retrieval approach to effectively retrieve information present in a language other than the language of the user query using the corpus driven query suggestion approach. The idea is to utilize the corpus based evidence of one language to improve the retrieval and re-ranking of news documents in the other language. We use FIRE corpora - Tamil and English news collections in our experiments and illustrate the effectiveness of the proposed cross language information retrieval approach.

Self-supervised information retrieval: a novel approach based on Deep Metric Learning and Neural Language Models

Most of the existing open-source search engines, utilize keyword or tf-idf based techniques to find relevant documents and web pages relative to an input query. Although these methods, with the help of a page rank or knowledge graphs, proved to be effective in some cases, they often fail to retrieve relevant instances for more complicated queries that would require a semantic understanding to be exploited. In this Thesis, a self-supervised information retrieval system based on transformers is employed to build a semantic search engine over the library of Gruppo Maggioli company. Semantic search or search with meaning can refer to an understanding of the query, instead of simply finding words matches and, in general, it represents knowledge in a way suitable for retrieval. We chose to investigate a new self-supervised strategy to handle the training of unlabeled data based on the creation of pairs of ’artificial’ queries and the respective positive passages. We claim that by removing the reliance on labeled data, we may use the large volume of unlabeled material on the web without being limited to languages or domains where labeled data is abundant.

Supporting content-based image retrieval and computer-aided diagnosis systems with association rule-based techniques

In this work, we take advantage of association rule mining to support two types of medical systems: the Content-based Image Retrieval (CBIR) systems and the Computer-Aided Diagnosis (CAD) systems. For content-based retrieval, association rules are employed to reduce the dimensionality of the feature vectors that represent the images and to improve the precision of the similarity queries. We refer to the association rule-based method to improve CBIR systems proposed here as Feature selection through Association Rules (FAR). To improve CAD systems, we propose the Image Diagnosis Enhancement through Association rules (IDEA) method. Association rules are employed to suggest a second opinion to the radiologist or a preliminary diagnosis of a new image. A second opinion automatically obtained can either accelerate the process of diagnosing or to strengthen a hypothesis, increasing the probability of a prescribed treatment be successful. Two new algorithms are proposed to support the IDEA method: to pre-process low-level features and to propose a preliminary diagnosis based on association rules. We performed several experiments to validate the proposed methods. The results indicate that association rules can be successfully applied to improve CBIR and CAD systems, empowering the arsenal of techniques to support medical image analysis in medical systems. (C) 2009 Elsevier B.V. All rights reserved.