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 /

Text Mining Methods for Analyzing Online Health Information and Communication

The Internet provides an alternative way to share health information. Specifically, social network systems such as Twitter, Facebook, Reddit, and disease specific online support forums are increasingly being used to share information on health related topics. This could be in the form of personal health information disclosure to seek suggestions or answering other patients\u27 questions based on their history. This social media uptake gives a new angle to improve the current health communication landscape with consumer generated content from social platforms. With these online modes of communication, health providers can offer more immediate support to the people seeking advice. Non-profit organizations and federal agencies can also diffuse preventative information in such networks for better outcomes. Researchers in health communication can mine user generated content on social networks to understand themes and derive insights into patient experiences that may be impractical to glean through traditional surveys. The main difficulty in mining social health data is in separating the signal from the noise. Social data is characterized by informal nature of content, typos, emoticons, tonal variations (e.g. sarcasm), and ambiguities arising from polysemous words, all of which make it difficult in building automated systems for deriving insights from such sources. In this dissertation, we present four efforts to mine health related insights from user generated social data. In the first effort, we build a model to identify marketing tweets on electronic cigarettes (e-cigs) and assess different topics in marketing and non-marketing messages on e-cigs on Twitter. In our next effort, we build ensemble models to classify messages on a mental health forum for triaging posts whose authors need immediate attention from trained moderators to prevent self-harm. The third effort deals with models from our participation in a shared task on identifying tweets that discuss adverse drug reactions and those that mention medication intake. In the final task, we build a classifier that identifies whether a particular tweet about the popular Juul e-cig indicates the tweeter actually using the product. Our methods range from linear classifiers (e.g., logistic regression), classical nonlinear models (e.g., nearest neighbors), recent deep neural networks (e.g., convolutional neural networks), and ensembles of all these models in using different supervised training regimens (e.g., co-training). The focus is more on task specific system building than on building specific individual models. Overall, we demonstrate that it is possible to glean insights from social data on health related topics through natural language processing and machine learning with use-cases from substance use and mental health

Optimizing text mining methods for improving biomedical natural language processing

The overwhelming amount and the increasing rate of publication in the biomedical domain make it difficult for life sciences researchers to acquire and maintain all information that is necessary for their research. Pubmed (the primary citation database for the biomedical literature) currently contains over 21 million article abstracts and more than one million of them were published in 2020 alone. Even though existing article databases provide capable keyword search services, typical everyday-life queries usually return thousands of relevant articles. For instance, a cancer research scientist may need to acquire a complete list of genes that interact with BRCA1 (breast cancer 1) gene. The PubMed keyword search for BRCA1 returns over 16,500 article abstracts, making manual inspection of the retrieved documents impractical. Missing even one of the interacting gene partners in this scenario may jeopardize successful development of a potential new drug or vaccine. Although manually curated databases of biomolecular interactions exist, they are usually not up-to-date and they require notable human effort to maintain. To summarize, new discoveries are constantly being shared within the community via scientific publishing, but unfortunately the probability of missing vital information for research in life sciences is increasing. In response to this problem, the biomedical natural language processing (BioNLP) community of researchers has emerged and strives to assist life sciences researchers by building modern language processing and text mining tools that can be applied at large-scale and scan the whole publicly available literature and extract, classify, and aggregate the information found within, thus keeping life sciences researchers always up-to-date with the recent relevant discoveries and facilitating their research in numerous fields such as molecular biology, biomedical engineering, bioinformatics, genetics engineering and biochemistry. My research has almost exclusively focused on biomedical relation and event extraction tasks. These foundational information extraction tasks deal with automatic detection of biological processes, interactions and relations described in the biomedical literature. Precisely speaking, biomedical relation and event extraction systems can scan through a vast amount of biomedical texts and automatically detect and extract the semantic relations of biomedical named entities (e.g. genes, proteins, chemical compounds, and diseases). The structured outputs of such systems (i.e., the extracted relations or events) can be stored as relational databases or molecular interaction networks which can easily be queried, filtered, analyzed, visualized and integrated with other structured data sources. Extracting biomolecular interactions has always been the primary interest of BioNLP researcher because having knowledge about such interactions is crucially important in various research areas including precision medicine, drug discovery, drug repurposing, hypothesis generation, construction and curation of signaling pathways, and protein function and structure prediction. State-of-the-art relation and event extraction methods are based on supervised machine learning, requiring manually annotated data for training. Manual annotation for the biomedical domain requires domain expertise and it is time-consuming. Hence, having minimal training data for building information extraction systems is a common case in the biomedical domain. This demands development of methods that can make the most out of available training data and this thesis gathers all my research efforts and contributions in that direction. It is worth mentioning that biomedical natural language processing has undergone a revolution since I started my research in this field almost ten years ago. As a member of the BioNLP community, I have witnessed the emergence, improvement– and in some cases, the disappearance–of many methods, each pushing the performance of the best previous method one step further. I can broadly divide the last ten years into three periods. Once I started my research, feature-based methods that relied on heavy feature engineering were dominant and popular. Then, significant advancements in the hardware technology, as well as several breakthroughs in the algorithms and methods enabled machine learning practitioners to seriously utilize artificial neural networks for real-world applications. In this period, convolutional, recurrent, and attention-based neural network models became dominant and superior. Finally, the introduction of transformer-based language representation models such as BERT and GPT impacted the field and resulted in unprecedented performance improvements on many data sets. When reading this thesis, I demand the reader to take into account the course of history and judge the methods and results based on what could have been done in that particular period of the history

Affective computing for smart operations: a survey and comparative analysis of the available tools, libraries and web services

In this paper, we make a deep search of the available tools in the market, at the current state of the art of Sentiment Analysis. Our aim is to optimize the human response in Datacenter Operations, using a combination of research tools, that allow us to decrease human error in general operations, managing Complex Infrastructures. The use of Sentiment Analysis tools is the first step for extending our capabilities for optimizing the human interface. Using different data collections from a variety of data sources, our research provides a very interesting outcome. In our final testing, we have found that the three main commercial platforms (IBM Watson, Google Cloud and Microsoft Azure) get the same accuracy (89-90%). for the different datasets tested, based on Artificial Neural Network and Deep Learning techniques. The other stand-alone Applications or APIs, like Vader or MeaninCloud, get a similar accuracy level in some of the datasets, using a different approach, semantic Networks, such as Concepnet1, but the model can easily be optimized above 90% of accuracy, just adjusting some parameter of the semantic model. This paper points to future directions for optimizing DataCenter Operations Management and decreasing human error in complex environments

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Review of trends in health social media analysis

This paper surveys recent publications (2008-2017) on using social media data to study public health. The survey describes the main topics being discussed in forums and presents short information about methods and tools used for analysis health social media. We put especial attention on adverse drug reaction detection problem (ADR)

Exploring Text Mining and Analytics for Applications in Public Security: An in-depth dive into a systematic literature review

Text mining and related analytics emerge as a technological approach to support human activities in extracting useful knowledge through texts in several formats. From a managerial point of view, it can help organizations in planning and decision-making processes, providing information that was not previously evident through textual materials produced internally or even externally. In this context, within the public/governmental scope, public security agencies are great beneficiaries of the tools associated with text mining, in several aspects, from applications in the criminal area to the collection of people's opinions and sentiments about the actions taken to promote their welfare. This article reports details of a systematic literature review focused on identifying the main areas of text mining application in public security, the most recurrent technological tools, and future research directions. The searches covered four major article bases (Scopus, Web of Science, IEEE Xplore, and ACM Digital Library), selecting 194 materials published between 2014 and the first half of 2021, among journals, conferences, and book chapters. There were several findings concerning the targets of the literature review, as presented in the results of this article