Khresmoi Professional: Multilingual Semantic Search for Medical Professionals

There is increasing interest in and need for innovative solutions to medical search. In this paper we present the EU funded Khresmoi medical search and access system, currently in year 3 of 4 of development across 12 partners . The Khresmoi system uses a component based architecture housed in the cloud to allow for the development of several innovative applications to support target users medical information needs. The Khresmoi search systems based on this architecture have been designed to support the multilingual and multimod al information needs of three target groups the general public, general practitioners and consultant radiologists. In this paper we focus on the presentation of the systems to support the latter two groups using semantic, multilingual text and image based (including 2D and 3D radiology images) search

Using Prior Information from the Medical Literature in GWAS of Oral Cancer Identifies Novel Susceptibility Variant on Chromosome 4 - the AdAPT Method

Background: Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS. Methods: We developed a method that searches through PubMed abstracts for pre-assigned keywords and key concepts, and uses this information to assign prior probabilities of association for each single nucleotide polymorphism (SNP) with the phenotype of interest - the Adjusting Association Priors with Text (AdAPT) method. Association results from a GWAS can subsequently be ranked in the context of these priors using the Bayes False Discovery Probability (BFDP) framework. We initially tested AdAPT by comparing rankings of known susceptibility alleles in a previous lung cancer GWAS, and subsequently applied it in a two-phase GWAS of oral cancer. Results: Known lung cancer susceptibility SNPs were consistently ranked higher by AdAPT BFDPs than by p-values. In the oral cancer GWAS, we sought to replicate the top five SNPs as ranked by AdAPT BFDPs, of which rs991316, located in the ADH gene region of 4q23, displayed a statistically significant association with oral cancer risk in the replication phase (per-rare-allele log additive p-value [p(trend)] = 2.5 x 10(-3)). The combined OR for having one additional rare allele was 0.83 (95% CI: 0.76-0.90), and this association was independent of previously identified susceptibility SNPs that are associated with overall UADT cancer in this gene region. We also investigated if rs991316 was associated with other cancers of the upper aerodigestive tract (UADT), but no additional association signal was found. Conclusion: This study highlights the potential utility of systematically incorporating prior knowledge from the medical literature in genome-wide analyses using the AdAPT methodology. AdAPT is available online (url: http://services.gate.ac.uk/lld/gwas/service/config)

Khresmoi: Multimodal Multilingual Medical Information Search

Khresmoi is a European Integrated Project developing a multilingual multimodal search and access system for medical and health information and documents. It addresses the challenges of searching through huge amounts of medical data, including general medical information available on the internet, as well as radiology data in hospital archives. It is developing novel semantic search and visual search techniques for the medical domain. At the MIE Village of the Future, Khresmoi proposes to have two interactive demonstrations of the system under development, as well as an overview oral presentation and potentially some poster presentation

Khresmoi – multilingual semantic search of medical text and images

The Khresmoi project is developing a multilingual multimodal search and access system for medical and health information and documents. This scientific demonstration presents the current state of the Khresmoi integrated system, which includes components for text and image annotation, semantic search, search by image similarity and machine translation. The flexibility in adapting the system to varying requirements for different types of medical information search is demonstrated through two instantiations of the system, one aimed at medical professionals in general and the second aimed at radiologists. The key innovations of the Khresmoi system are the integration of multiple software components in a flexible scalable medical search system, the use of annotation cycles including manual correction to improve semantic search, and the possibility to do large scale visual similarity search on 2D and 3D (CT, MR) medical images

Designing a General Framework for Text Alignment: Case Studies with Two South Asian Languages

Building machine translation systems for many South Asian languages (such as Hindi, Gujarati, etc.) using statistical methods is problematic. The primary reason is insufficient parallel data to learn accurate word alignment. Additionally, these languages are morphologically rich and have free word order. When it is difficult to rely purely on statistical methods due to insufficient data, research shows that better performance can be obtained by building hybrid systems that rely on language specific resources, such as morphological analysers or dictionaries, as well as statistical methods. However, it is difficult to find such language specific resources for many South Asian languages. Since languages such as Hindi, Gujarati, Urdu, Bengali, Punjabi and Marathi are all very similar in structure and the main differences lie in the script and vocabulary used for these languages, we hypothesise that it is possible to develop resources for one of these languages and generalize the approach to allow rapid bootstrapping of similar resources for the other closely related languages -- with minimal effort and similar accuracies. To verify this, we develop a few resources for the Hindi language, including a sentence alignment algorithm, a morphological analyser and a transliteration similarity component and generalize the approach to allow rapid bootstrapping of similar resources for the Gujarati language. We show that the approach works on both the Hindi and Gujarati languages and achieves results that are comparable to similar state-of-the-art (SOA) resources available for these languages. We also hypothesise that it is possible to develop a high performance hybrid word alignment algorithm that relies on such language specific resources. To verify this, we design, implement and evaluate a novel English-Hindi hybrid word alignment system that uses the Hindi specific resources developed by us. Not only do we show our word alignment system outperforms other SOA English-Hindi word alignment systems, but also how simple it is to adapt it to the English-Gujarati language pair

Khresmoi - multilingual semantic search of medical text and images

Khresmoi is a European Integrated Project developing a multilingual multimodal search and access system for medical and health information and documents. It addresses the challenges of searching through huge amounts of medical data, including general medical information available on the internet, as well as radiology data in hospital archives. It is developing novel semantic search and visual search techniques for the medical domain. At the MIE Village of the Future, Khresmoi proposes to have two interactive demonstrations of the system under development, as well as an overview oral presentation and potentially some poster presentations

English-Hindi Transliteration using Multiple Similarity Metrics

In this paper, we present an approach to measure the transliteration similarity of English-Hindi word pairs. Our approach has two components. First we propose a bi-directional mapping between one or more characters in the Devanagari script and one or more characters in the Roman script (pronounced as in English). This allows a given Hindi word written in Devanagari to be transliterated into the Roman script and vice-versa. Second, we present an algorithm for computing a similarity measure that is a variant of Dice’s coefficient measure and the LCSR measure and which also takes into account the constraints needed to match English-Hindi transliterated words. Finally, by evaluating various similarity metrics individually and together under a multiple measure agreement scenario, we show that it is possible to achieve a 0.92 f-measure in identifying English-Hindi word pairs that are transliterations. In order to assess the portability of our approach to other similar languages we adapt our system to the Gujarati language. 1