Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

STEM: stacked threshold-based entity matching for knowledge base generation

One of the major issues encountered in the generation of knowledge bases is the integration of data coming from a collection of heterogeneous data sources. A key essential task when integrating data instances is the entity matching. Entity matching is based on the definition of a similarity measure among entities and on the classification of the entity pair as a match if the similarity exceeds a certain threshold. This parameter introduces a trade-off between the precision and the recall of the algorithm, as higher values of the threshold lead to higher precision and lower recall, and lower values lead to higher recall and lower precision. In this paper, we propose a stacking approach for threshold-based classifiers. It runs several instances of classifiers corresponding to different thresholds and use their predictions as a feature vector for a supervised learner. We show that this approach is able to break the trade-off between the precision and recall of the algorithm, increasing both at the same time and enhancing the overall performance of the algorithm. We also show that this hybrid approach performs better and is less dependent on the amount of available training data with respect to a supervised learning approach that directly uses properties’ similarity values. In order to test the generality of the claim, we have run experimental tests using two different threshold-based classifiers on two different data sets. Finally, we show a concrete use case describing the implementation of the proposed approach in the generation of the 3cixty Nice knowledge base

Knowledge Discovery and Management within Service Centers

These days, most enterprise service centers deploy Knowledge Discovery and Management (KDM) systems to address the challenge of timely delivery of a resourceful service request resolution while efficiently utilizing the huge amount of data. These KDM systems facilitate prompt response to the critical service requests and if possible then try to prevent the service requests getting triggered in the first place. Nevertheless, in most cases, information required for a request resolution is dispersed and suppressed under the mountain of irrelevant information over the Internet in unstructured and heterogeneous formats. These heterogeneous data sources and formats complicate the access to reusable knowledge and increase the response time required to reach a resolution. Moreover, the state-of-the art methods neither support effective integration of domain knowledge with the KDM systems nor promote the assimilation of reusable knowledge or Intellectual Capital (IC). With the goal of providing an improved service request resolution within the shortest possible time, this research proposes an IC Management System. The proposed tool efficiently utilizes domain knowledge in the form of semantic web technology to extract the most valuable information from those raw unstructured data and uses that knowledge to formulate service resolution model as a combination of efficient data search, classification, clustering, and recommendation methods. Our proposed solution also handles the technology categorization of a service request which is very crucial in the request resolution process. The system has been extensively evaluated with several experiments and has been used in a real enterprise customer service center

Site-Specific Rules Extraction in Precision Agriculture

El incremento sostenible en la producción alimentaria para satisfacer las necesidades de una población mundial en aumento es un verdadero reto cuando tenemos en cuenta el impacto constante de plagas y enfermedades en los cultivos. Debido a las importantes pérdidas económicas que se producen, el uso de tratamientos químicos es demasiado alto; causando contaminación del medio ambiente y resistencia a distintos tratamientos. En este contexto, la comunidad agrícola divisa la aplicación de tratamientos más específicos para cada lugar, así como la validación automática con la conformidad legal. Sin embargo, la especificación de estos tratamientos se encuentra en regulaciones expresadas en lenguaje natural. Por este motivo, traducir regulaciones a una representación procesable por máquinas está tomando cada vez más importancia en la agricultura de precisión.Actualmente, los requisitos para traducir las regulaciones en reglas formales están lejos de ser cumplidos; y con el rápido desarrollo de la ciencia agrícola, la verificación manual de la conformidad legal se torna inabordable.En esta tesis, el objetivo es construir y evaluar un sistema de extracción de reglas para destilar de manera efectiva la información relevante de las regulaciones y transformar las reglas de lenguaje natural a un formato estructurado que pueda ser procesado por máquinas. Para ello, hemos separado la extracción de reglas en dos pasos. El primero es construir una ontología del dominio; un modelo para describir los desórdenes que producen las enfermedades en los cultivos y sus tratamientos. El segundo paso es extraer información para poblar la ontología. Puesto que usamos técnicas de aprendizaje automático, implementamos la metodología MATTER para realizar el proceso de anotación de regulaciones. Una vez creado el corpus, construimos un clasificador de categorías de reglas que discierne entre obligaciones y prohibiciones; y un sistema para la extracción de restricciones en reglas, que reconoce información relevante para retener el isomorfismo con la regulación original. Para estos componentes, empleamos, entre otra técnicas de aprendizaje profundo, redes neuronales convolucionales y “Long Short- Term Memory”. Además, utilizamos como baselines algoritmos más tradicionales como “support-vector machines” y “random forests”.Como resultado, presentamos la ontología PCT-O, que ha sido alineada con otras ontologías como NCBI, PubChem, ChEBI y Wikipedia. El modelo puede ser utilizado para la identificación de desórdenes, el análisis de conflictos entre tratamientos y la comparación entre legislaciones de distintos países. Con respecto a los sistemas de extracción, evaluamos empíricamente el comportamiento con distintas métricas, pero la métrica F1 es utilizada para seleccionar los mejores sistemas. En el caso del clasificador de categorías de reglas, el mejor sistema obtiene un macro F1 de 92,77% y un F1 binario de 85,71%. Este sistema usa una red “bidirectional long short-term memory” con “word embeddings” como entrada. En relación al extractor de restricciones de reglas, el mejor sistema obtiene un micro F1 de 88,3%. Este extractor utiliza como entrada una combinación de “character embeddings” junto a “word embeddings” y una red neuronal “bidirectional long short-term memory”.<br /

Mining complex trees for hidden fruit : a graph–based computational solution to detect latent criminal networks : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Information Technology at Massey University, Albany, New Zealand.

The detection of crime is a complex and difficult endeavour. Public and private organisations – focusing on law enforcement, intelligence, and compliance – commonly apply the rational isolated actor approach premised on observability and materiality. This is manifested largely as conducting entity-level risk management sourcing ‘leads’ from reactive covert human intelligence sources and/or proactive sources by applying simple rules-based models. Focusing on discrete observable and material actors simply ignores that criminal activity exists within a complex system deriving its fundamental structural fabric from the complex interactions between actors - with those most unobservable likely to be both criminally proficient and influential. The graph-based computational solution developed to detect latent criminal networks is a response to the inadequacy of the rational isolated actor approach that ignores the connectedness and complexity of criminality. The core computational solution, written in the R language, consists of novel entity resolution, link discovery, and knowledge discovery technology. Entity resolution enables the fusion of multiple datasets with high accuracy (mean F-measure of 0.986 versus competitors 0.872), generating a graph-based expressive view of the problem. Link discovery is comprised of link prediction and link inference, enabling the high-performance detection (accuracy of ~0.8 versus relevant published models ~0.45) of unobserved relationships such as identity fraud. Knowledge discovery uses the fused graph generated and applies the “GraphExtract” algorithm to create a set of subgraphs representing latent functional criminal groups, and a mesoscopic graph representing how this set of criminal groups are interconnected. Latent knowledge is generated from a range of metrics including the “Super-broker” metric and attitude prediction. The computational solution has been evaluated on a range of datasets that mimic an applied setting, demonstrating a scalable (tested on ~18 million node graphs) and performant (~33 hours runtime on a non-distributed platform) solution that successfully detects relevant latent functional criminal groups in around 90% of cases sampled and enables the contextual understanding of the broader criminal system through the mesoscopic graph and associated metadata. The augmented data assets generated provide a multi-perspective systems view of criminal activity that enable advanced informed decision making across the microscopic mesoscopic macroscopic spectrum

record linkage of banks and municipalities through multiple criteria and neural networks

Record linkage aims to identify records from multiple data sources that refer to the same entity of the real world. It is a well known data quality process studied since the second half of the last century, with an established pipeline and a rich literature of case studies mainly covering census, administrative or health domains. In this paper, a method to recognize matching records from real municipalities and banks through multiple similarity criteria and a Neural Network classifier is proposed: starting from a labeled subset of the available data, first several similarity measures are combined and weighted to build a feature vector, then a Multi-Layer Perceptron (MLP) network is trained and tested to find matching pairs. For validation, seven real datasets have been used (three from banks and four from municipalities), purposely chosen in the same geographical area to increase the probability of matches. The training only involved two municipalities, while testing involved all sources (municipalities vs. municipalities, banks vs banks and and municipalities vs. banks). The proposed method scored remarkable results in terms of both precision and recall, clearly outperforming threshold-based competitors

Beyond Volume: The Impact of Complex Healthcare Data on the Machine Learning Pipeline

From medical charts to national census, healthcare has traditionally operated under a paper-based paradigm. However, the past decade has marked a long and arduous transformation bringing healthcare into the digital age. Ranging from electronic health records, to digitized imaging and laboratory reports, to public health datasets, today, healthcare now generates an incredible amount of digital information. Such a wealth of data presents an exciting opportunity for integrated machine learning solutions to address problems across multiple facets of healthcare practice and administration. Unfortunately, the ability to derive accurate and informative insights requires more than the ability to execute machine learning models. Rather, a deeper understanding of the data on which the models are run is imperative for their success. While a significant effort has been undertaken to develop models able to process the volume of data obtained during the analysis of millions of digitalized patient records, it is important to remember that volume represents only one aspect of the data. In fact, drawing on data from an increasingly diverse set of sources, healthcare data presents an incredibly complex set of attributes that must be accounted for throughout the machine learning pipeline. This chapter focuses on highlighting such challenges, and is broken down into three distinct components, each representing a phase of the pipeline. We begin with attributes of the data accounted for during preprocessing, then move to considerations during model building, and end with challenges to the interpretation of model output. For each component, we present a discussion around data as it relates to the healthcare domain and offer insight into the challenges each may impose on the efficiency of machine learning techniques.Comment: Healthcare Informatics, Machine Learning, Knowledge Discovery: 20 Pages, 1 Figur