Improving average ranking precision in user searches for biomedical research datasets

Availability of research datasets is keystone for health and life science study reproducibility and scientific progress. Due to the heterogeneity and complexity of these data, a main challenge to be overcome by research data management systems is to provide users with the best answers for their search queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we investigate a novel ranking pipeline to improve the search of datasets used in biomedical experiments. Our system comprises a query expansion model based on word embeddings, a similarity measure algorithm that takes into consideration the relevance of the query terms, and a dataset categorisation method that boosts the rank of datasets matching query constraints. The system was evaluated using a corpus with 800k datasets and 21 annotated user queries. Our system provides competitive results when compared to the other challenge participants. In the official run, it achieved the highest infAP among the participants, being +22.3% higher than the median infAP of the participant's best submissions. Overall, it is ranked at top 2 if an aggregated metric using the best official measures per participant is considered. The query expansion method showed positive impact on the system's performance increasing our baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively. Our similarity measure algorithm seems to be robust, in particular compared to Divergence From Randomness framework, having smaller performance variations under different training conditions. Finally, the result categorization did not have significant impact on the system's performance. We believe that our solution could be used to enhance biomedical dataset management systems. In particular, the use of data driven query expansion methods could be an alternative to the complexity of biomedical terminologies

Description of the LTG system used for MUC-7

The basic building blocks in our muc system are reusable text handling tools which wehave been developing and using for a number of years at the Language Technology Group. They are modular tools with stream input/output; each tooldoesavery speci c job, but can be combined with other tools in a unix pipeline. Di erent combinations of the same tools can thus be used in a pipeline for completing di erent tasks. Our architecture imposes an additional constraint on the input/output streams: they should have a common syntactic format. For this common format we chose eXtensible Markup Language (xml). xml is an o cial, simpli ed version of Standard Generalised Markup Language (sgml), simpli ed to make processing easier [3]. Wewere involved in the developmentofthexml standard, building on our expertise in the design of our own Normalised sgml (nsl) and nsl tool lt nsl [10], and our xml tool lt xml [11]. A detailed comparison of this sgml-oriented architecture with more traditional data-base oriented architectures can be found in [9]. A tool in our architecture is thus a piece of software which uses an api for all its access to xml and sgml data and performs a particular task: exploiting markup which has previously been added by other tools, removing markup, or adding new markup to the stream(s) without destroying the previously adde

Multi modal multi-semantic image retrieval

PhDThe rapid growth in the volume of visual information, e.g. image, and video can overwhelm users’ ability to find and access the specific visual information of interest to them. In recent years, ontology knowledge-based (KB) image information retrieval techniques have been adopted into in order to attempt to extract knowledge from these images, enhancing the retrieval performance. A KB framework is presented to promote semi-automatic annotation and semantic image retrieval using multimodal cues (visual features and text captions). In addition, a hierarchical structure for the KB allows metadata to be shared that supports multi-semantics (polysemy) for concepts. The framework builds up an effective knowledge base pertaining to a domain specific image collection, e.g. sports, and is able to disambiguate and assign high level semantics to ‘unannotated’ images. Local feature analysis of visual content, namely using Scale Invariant Feature Transform (SIFT) descriptors, have been deployed in the ‘Bag of Visual Words’ model (BVW) as an effective method to represent visual content information and to enhance its classification and retrieval. Local features are more useful than global features, e.g. colour, shape or texture, as they are invariant to image scale, orientation and camera angle. An innovative approach is proposed for the representation, annotation and retrieval of visual content using a hybrid technique based upon the use of an unstructured visual word and upon a (structured) hierarchical ontology KB model. The structural model facilitates the disambiguation of unstructured visual words and a more effective classification of visual content, compared to a vector space model, through exploiting local conceptual structures and their relationships. The key contributions of this framework in using local features for image representation include: first, a method to generate visual words using the semantic local adaptive clustering (SLAC) algorithm which takes term weight and spatial locations of keypoints into account. Consequently, the semantic information is preserved. Second a technique is used to detect the domain specific ‘non-informative visual words’ which are ineffective at representing the content of visual data and degrade its categorisation ability. Third, a method to combine an ontology model with xi a visual word model to resolve synonym (visual heterogeneity) and polysemy problems, is proposed. The experimental results show that this approach can discover semantically meaningful visual content descriptions and recognise specific events, e.g., sports events, depicted in images efficiently. Since discovering the semantics of an image is an extremely challenging problem, one promising approach to enhance visual content interpretation is to use any associated textual information that accompanies an image, as a cue to predict the meaning of an image, by transforming this textual information into a structured annotation for an image e.g. using XML, RDF, OWL or MPEG-7. Although, text and image are distinct types of information representation and modality, there are some strong, invariant, implicit, connections between images and any accompanying text information. Semantic analysis of image captions can be used by image retrieval systems to retrieve selected images more precisely. To do this, a Natural Language Processing (NLP) is exploited firstly in order to extract concepts from image captions. Next, an ontology-based knowledge model is deployed in order to resolve natural language ambiguities. To deal with the accompanying text information, two methods to extract knowledge from textual information have been proposed. First, metadata can be extracted automatically from text captions and restructured with respect to a semantic model. Second, the use of LSI in relation to a domain-specific ontology-based knowledge model enables the combined framework to tolerate ambiguities and variations (incompleteness) of metadata. The use of the ontology-based knowledge model allows the system to find indirectly relevant concepts in image captions and thus leverage these to represent the semantics of images at a higher level. Experimental results show that the proposed framework significantly enhances image retrieval and leads to narrowing of the semantic gap between lower level machinederived and higher level human-understandable conceptualisation

A Review of Codebook Models in Patch-Based Visual Object Recognition

The codebook model-based approach, while ignoring any structural aspect in vision, nonetheless provides state-of-the-art performances on current datasets. The key role of a visual codebook is to provide a way to map the low-level features into a fixed-length vector in histogram space to which standard classifiers can be directly applied. The discriminative power of such a visual codebook determines the quality of the codebook model, whereas the size of the codebook controls the complexity of the model. Thus, the construction of a codebook is an important step which is usually done by cluster analysis. However, clustering is a process that retains regions of high density in a distribution and it follows that the resulting codebook need not have discriminant properties. This is also recognised as a computational bottleneck of such systems. In our recent work, we proposed a resource-allocating codebook, to constructing a discriminant codebook in a one-pass design procedure that slightly outperforms more traditional approaches at drastically reduced computing times. In this review we survey several approaches that have been proposed over the last decade with their use of feature detectors, descriptors, codebook construction schemes, choice of classifiers in recognising objects, and datasets that were used in evaluating the proposed methods

Knowledge Nodes: the Building Blocks of a Distributed Approach to Knowledge Management

Abstract: In this paper we criticise the objectivistic approach that underlies most current systems for Knowledge Management. We show that such an approach is incompatible with the very nature of what is to be managed (i.e., knowledge), and we argue that this may partially explain why most knowledge management systems are deserted by users. We propose a different approach - called distributed knowledge management - in which subjective and social (in a word, contextual) aspects of knowledge are seriously taken into account. Finally, we present a general technological architecture in which these ideas are implemented by introducing the concept of knowledge node

Towards Effective Codebookless Model for Image Classification

The bag-of-features (BoF) model for image classification has been thoroughly studied over the last decade. Different from the widely used BoF methods which modeled images with a pre-trained codebook, the alternative codebook free image modeling method, which we call Codebookless Model (CLM), attracted little attention. In this paper, we present an effective CLM that represents an image with a single Gaussian for classification. By embedding Gaussian manifold into a vector space, we show that the simple incorporation of our CLM into a linear classifier achieves very competitive accuracy compared with state-of-the-art BoF methods (e.g., Fisher Vector). Since our CLM lies in a high dimensional Riemannian manifold, we further propose a joint learning method of low-rank transformation with support vector machine (SVM) classifier on the Gaussian manifold, in order to reduce computational and storage cost. To study and alleviate the side effect of background clutter on our CLM, we also present a simple yet effective partial background removal method based on saliency detection. Experiments are extensively conducted on eight widely used databases to demonstrate the effectiveness and efficiency of our CLM method