End to end approach for i2b2 2012 challenge based on Cross-lingual models

BACKGROUND - We propose a Cross-lingual approach to i2b2 2012 challenge for Clinical Records focused on the temporal relations in clinical narratives. Corpus of discharge summaries annotated with temporal information was provided for automatically extracting : (1) clinically significant events, including both clinical concepts such as problems, tests, treatments, and clinical departments, and events relevant to the patient’s clinical timeline, such as admissions, transfers between departments, etc; (2) temporal expressions, referring to the dates, times, duration, or frequencies in the clinical text. The values of the extracted temporal expressions had to be normalized to an ISO specification standard; and (3) temporal relations, among the clinical events and temporal expressions. GOALS - The objectives involved in the current work consists on outperforming previous State of the Art for the i2b2 2012 challenge and adapting Cross-lingual model into clinical specific domain with low Data resources available. METHODS - The task has been conceived as a pipeline of different modules, an event and temporal expression token-classifier and a text-classifier for relation extraction, each of them independently developed from the other. We used XLM-RoBERTa Cross-lingual model. RESULTS - For event detection, the proposed token-classifier obtains a 0.91 Span F1. For temporal expressions, our sentence-classifier achieves a 0.91 Span F1. For temporal relation, we propose sentence classifier based on sequential-taggers that performs at 0.29 F1 measure.DESKRIBAPENA - Narratiba klinikoen domeinuan i2b2 2012 erronkarako hizkuntzarteko ikuspegia jorratzen duen soluzioa proposatzen dugu. Erronka honek txosten medikuetan islatzen diren gertaeren arteko denbora-erlazioak iragartzea du helburu. Horretarako, lan hau alde batetik (1) klinikoki esanguratsuak diren gertaerak, adibidez, kontzeptu klinikoak, probak, tratamenduak, sail klinikoak eta bestetik, (2) denbora-adierazpenak, adibidez, txostenak esleituta duen data, denbora, iraupen edo maiztasuna adierazten duten espresioak antzeman eta bukatzeko gertaera klinikoen eta (3) denbora-adierazpenen arteako erlazioak anotatuta duen corpus batetik abiatzen da. HELBURUAK - Lanaren helburuak i2b2 2012 artearen egoera hobetzea eta Cross-lingual modeloa Data baliabide baxuak dituen domeinu kliniko espezifikora egokitzea dira. METODOAK - Lana modulu desberdinetako hobi gisa ulertu da, gertaera eta denbora-adierazpenetarako sekuentzia-markatzaileak, eta denbora-erlaziorako perpaus-sailkatzailea, independenteki garatu dira. XLM-RoBERTa Cross-lingual modeloa erabili izan da lan honetan. EMAITZAK - Gertaerak atzemateko, 0.91 Span F1 exekutatzen duen sekuentzia-markatzailea proposatzen dugu. Denbora-adierazpenetarako, 0.91 Span F1 egiten duen sekuentzia-markatzailea bat proposatzen dugu. Denbora-erlaziorako, 0.29 F1 neurria egiten duten sekuentzia-markatzaileetan oinarritutako perpaus-sailkatzailea proposatzen dugu

End to end approach for i2b2 2012 challenge based on Cross-lingual models

BACKGROUND - We propose a Cross-lingual approach to i2b2 2012 challenge for Clinical Records focused on the temporal relations in clinical narratives. Corpus of discharge summaries annotated with temporal information was provided for automatically extracting : (1) clinically significant events, including both clinical concepts such as problems, tests, treatments, and clinical departments, and events relevant to the patient’s clinical timeline, such as admissions, transfers between departments, etc; (2) temporal expressions, referring to the dates, times, duration, or frequencies in the clinical text. The values of the extracted temporal expressions had to be normalized to an ISO specification standard; and (3) temporal relations, among the clinical events and temporal expressions. GOALS - The objectives involved in the current work consists on outperforming previous State of the Art for the i2b2 2012 challenge and adapting Cross-lingual model into clinical specific domain with low Data resources available. METHODS - The task has been conceived as a pipeline of different modules, an event and temporal expression token-classifier and a text-classifier for relation extraction, each of them independently developed from the other. We used XLM-RoBERTa Cross-lingual model. RESULTS - For event detection, the proposed token-classifier obtains a 0.91 Span F1. For temporal expressions, our sentence-classifier achieves a 0.91 Span F1. For temporal relation, we propose sentence classifier based on sequential-taggers that performs at 0.29 F1 measure.DESKRIBAPENA - Narratiba klinikoen domeinuan i2b2 2012 erronkarako hizkuntzarteko ikuspegia jorratzen duen soluzioa proposatzen dugu. Erronka honek txosten medikuetan islatzen diren gertaeren arteko denbora-erlazioak iragartzea du helburu. Horretarako, lan hau alde batetik (1) klinikoki esanguratsuak diren gertaerak, adibidez, kontzeptu klinikoak, probak, tratamenduak, sail klinikoak eta bestetik, (2) denbora-adierazpenak, adibidez, txostenak esleituta duen data, denbora, iraupen edo maiztasuna adierazten duten espresioak antzeman eta bukatzeko gertaera klinikoen eta (3) denbora-adierazpenen arteako erlazioak anotatuta duen corpus batetik abiatzen da. HELBURUAK - Lanaren helburuak i2b2 2012 artearen egoera hobetzea eta Cross-lingual modeloa Data baliabide baxuak dituen domeinu kliniko espezifikora egokitzea dira. METODOAK - Lana modulu desberdinetako hobi gisa ulertu da, gertaera eta denbora-adierazpenetarako sekuentzia-markatzaileak, eta denbora-erlaziorako perpaus-sailkatzailea, independenteki garatu dira. XLM-RoBERTa Cross-lingual modeloa erabili izan da lan honetan. EMAITZAK - Gertaerak atzemateko, 0.91 Span F1 exekutatzen duen sekuentzia-markatzailea proposatzen dugu. Denbora-adierazpenetarako, 0.91 Span F1 egiten duen sekuentzia-markatzailea bat proposatzen dugu. Denbora-erlaziorako, 0.29 F1 neurria egiten duten sekuentzia-markatzaileetan oinarritutako perpaus-sailkatzailea proposatzen dugu

Identificador automático de relaciones temporales en textos clínicos basado en redes neuronales

Resumen: el proyecto constituye una aproximación de un identificador automático de relaciones temporales en textos clínicos basado en redes neuronales, el sistema es funcional y cuenta con la evidencia de un prototipo de alta fidelidad capaz de concretar la aplicación de técnicas ‘natural language processing’ NLP, ‘machine learning’ ML y ‘deep learning’ DL. En cuanto a la estructura del proyecto, cuenta con una introducción, que busca nutrir al lector de información suficiente para apoyar la lectura técnica, además se expone el Documento de Objetivos del Proyecto, donde se puede encontrar toda la información relativa a la gestión del proyecto, por otro lado se expone un compendio del estado del arte, en que nos hemos inspirado para las aproximaciones realizadas hasta el prototipo de alta fidelidad, después se detalla el: análisis, diseño e implementación realizados para el desarrollo del prototipo de alta fidelidad del sistema basado en BiLSTM + CRF, así como otros experimentos realizados, este desarrollo cuenta con resultados parciales que se exponen en las pruebas y de paso se contrastan con la competición internacional ‘i2b2’, actualizando el estado del arte en extracción de conceptos clínicos y expresiones temporales, por último se tratan los prototipos generados durante el proyecto, y se concluye con una crítica del proyecto, así como los trabajos futuros a realizar sobre el mismo. Por último, consideramos que sería buena idea la utilización del presente proyecto para futuras aproximaciones a nuevas áreas de aplicación, ya que el sistema descrito se considera genérico, y la dificultad en dichos acercamientos residiría en la generación del conjunto de entrenamiento pudiendo aprovecharse el formato IOB de dicha tarea, y unos ‘word embeddings’ pre entrenados concretamente para el acercamiento que se realice.Abstract: the project is an approximation to an automatic temporal relation identifier for clinical texts based on neural networks, the system is functional an has an evident high fidelity prototype that could accurate how to apply techniques as: natural language processing NLP, machine learning ML and deep learning DL. The project structure has an introduction to immerse lecturer into technical signature, moreover it has a project objectives document where it could be found all management information used to manage the project, in addition it has a state of the art summary into which we inspired our experiments trough the final prototype, later we detail the process of: analysis, design and implementation, based on BiLSTM + CRF to achieve high fidelity prototype, and other experiments made, we also have partial results summarized in testing section and we contrast the system with ‘i2b2’ international challenge, in this case we update the current state of the art in clinical concept extraction and time expression extraction tasks, finally we show the prototypes made for the system, and we review the work made, and besides we expose the future works on system. We finally suggest the use of the present work in future approximations into new application areas, because of the system is generic and the difficult would be in the data generation, it could be used the IOB format and pre trained word embedding s relative to the task studied.Laburpena: proiektua da sare neuronaletan oinarritutako testu klinikoetako denborazko erlazioko identifikatzaile automatikoko hurbilketa, sistema funtzionala da eta du ‘processing-a language naturala’ teknika aplikazioa NLP-a, ‘learning-a’ ML ‘machine-a’ eta ‘learning-a’ DL ‘deep-a’ zehazteko goi-fidelitate gaiko prototipo baten ziurtasuna. Proiektuaren, sarrerarekiko kontuaren irakurketa teknikoaren alde agertzeko informazio nahikoko elikatzea irakurleari| bilatzen duenaren, egiturari dagokionez gainera Proiektuaren Helburuetako Dokumentua erakusten da, proiektuaren kudeaketari buruzko informazio guztia aurki dezakeen tokian, bestalde erakusten da artearen egoeraren| laburpen bat, egindako goi-fidelitate-prototiporainoko hurbilketetarako inspirazioa hartu dugunaren, gero zehazten du: analisiak, diseinua eta inplementazioa BiLSTM-etan oinarritutako sistemaren goi-fidelitateko prototipoaren garapenerako egindakoak + CRF-a, egindako beste esperimentu batzuk bezala horrela, garapen honek ditu probetan eta iragaitzaz erakusten diren emaitza partzialak egiaztatzen dute ‘i2b2' nazioarteko lehiaketarekin, artearen egoera kontzeptu klinikoko erauzketan etadenborazko adierazpenetan eguneratuz, azkenik proiektuan zehar sortutako prototipoak tratatzen dira, eta amaitzen du proiektuaren kritikarekin, baita ere beraren gainean egiteko etorkizuneko lanekin. Azkenik, pentsatzen dugu ideia ona izango litzatekeela aplikazio-area berrietara etorkizuneko hurbiltzeetarako oraingo| proiektuaren erabilera, deskribatutako sistema generikotzat hartzen denez gero, eta aipaturiko hurbiltzeetako zailtasuna entrenamendu-tmultzoan etzango litzatekeela IOB-a aipaturiko zereginaren formatua, eta ‘embeddings-a’ zehazki egiten den hurbiltzerako aurre entrenatutako ‘word’ batzuk aprobetxatu ahal izanez

El color: interacción armónica y formal en el espacio cotidiano para la creación de escenarios alternos a la realidad

La siguiente investigación aborda la representación alterna de lugares cotidianos mediante la pintura junto con la aplicación formal del color en la obra. Cómo fue el proceso para realizar estas pinturas y qué conceptos guían la creación de estos mundos alternos. El color fue el punto de partida e instrumento esencial para la creación de estos mundos alternos, por eso se ahonda el tema de la cromática en el capítulo uno. Ahí se indaga acerca del origen del color, sus propiedades, sus teorías y modos de aplicación formal; cómo algunos movimientos artísticos usaron el lenguaje cromático para sus diferentes fines y cómo ha sido un componente importante en el desarrollo de la pintura. Al ser el lenguaje pictórico el medio de expresión para este proyecto es necesario analizar cuál es su fin y significado. En el capítulo dos se habla acerca de cómo el concepto de pintura ha evolucionado con el paso del tiempo concluyendo en lo que significa actualmente para el arte contemporáneo, ahí realizo algunas interpretaciones personales acerca de la pintura y como está vinculada a la representación alterna de los lugares urbanos/cotidianos. También se trata acerca de cómo estos sitios funcionan como un soporte de ideas para el artista y qué componentes se hallan inmersos. En el capítulo tres se detalla los métodos de cómo fueron realizadas las pinturas, cómo se desarrolló y concluyó el proyecto y qué medios fueron usados para la creación de las imágenes. Se encuentra también una pequeña reseña acerca de cómo y dónde se realizó la exposición individual “Cromáticas Urbanas Alternas

Advances in monolingual and crosslingual automatic disability annotation in Spanish

Background Unlike diseases, automatic recognition of disabilities has not received the same attention in the area of medical NLP. Progress in this direction is hampered by obstacles like the lack of annotated corpus. Neural architectures learn to translate sequences from spontaneous representations into their corresponding standard representations given a set of samples. The aim of this paper is to present the last advances in monolingual (Spanish) and crosslingual (from English to Spanish and vice versa) automatic disability annotation. The task consists of identifying disability mentions in medical texts written in Spanish within a collection of abstracts from journal papers related to the biomedical domain. Results In order to carry out the task, we have combined deep learning models that use different embedding granularities for sequence to sequence tagging with a simple acronym and abbreviation detection module to boost the coverage. Conclusions Our monolingual experiments demonstrate that a good combination of different word embedding representations provide better results than single representations, significantly outperforming the state of the art in disability annotation in Spanish. Additionally, we have experimented crosslingual transfer (zero-shot) for disability annotation between English and Spanish with interesting results that might help overcoming the data scarcity bottleneck, specially significant for the disabilities.This work was partially funded by the Spanish Ministry of Science and Innovation (MCI/AEI/FEDER, UE, DOTT-HEALTH/PAT-MED PID2019-106942RB-C31), the Basque Government (IXA IT1570-22), MCIN/AEI/ 10.13039/501100011033 and European Union NextGeneration EU/PRTR (DeepR3, TED2021-130295B-C31) and the EU ERA-Net CHIST-ERA and the Spanish Research Agency (ANTIDOTE PCI2020-120717-2)

The successful use of a submersible ultrasound to confirm pregnancy on free swimming bull sharks, Carcharhinus leucas, in a provisioned shark site

A prototype, fully submersible, high definition ultrasound was used to determine the reproductive state of wild, free-swimming bull sharks, Carcharhinus leucas, at a provisioned shark diving site in Playa del Carmen, Mexico. During two opportunistic dives, the presence of embryos was confirmed in three female sharks (greater than 2.0 m total length) and emphasizes the importance of developing and linking emerging technologies with shark diving sites for the conservation of elasmobranch species

Sistema Edmo como prototipo para la caracterización de suelos superficiales

Actually there are several sophisticated mechanisms subsurface information, the idea is to make a geophone-type system composed of Arduino with sensors by which we can acquire the time when a Rayleigh wave travels from sensor to sensor, using the program as a tool for interpretation of these data, to then determine the speed at which the Rayleigh wave travels so we can predict the type of soil according to the recorded speed. This has advantages of being adapted to detect waves in any axis (x, y and z) simultaneously or individually. This system is new, practical and economical.Actualmente existen varios mecanismos sofisticados para obtener información del subsuelo, la idea consiste en hacer un sistema tipo geófono conformado de placa Arduino con sensores por medio del cual podemos adquirir el tiempo en que viaja una onda de Rayleigh (onda superficial) de sensor a sensor, usando la programación como herramienta de interpretación de estos datos, para posteriormente determinar la velocidad en la que viaja la onda de Rayleigh y así poder predecir el tipo de suelo según la velocidad registrada. Este posee la ventajas de ser adaptado para detectar ondas en cualquier eje (eje x, y, z) al mismo tiempo o individualmente. Este sistema resulta novedoso, práctico y económico

Thallium-induced DNA damage, genetic, and epigenetic alterations

Thallium (Tl) is a toxic heavy metal responsible for noxious effects in living organisms. As a pollutant, Tl can be found in the environment at high concentrations, especially in industrial areas. Systemic toxicity induced by this toxic metal can affect cell metabolism, including redox alterations, mitochondrial dysfunction, and activation of apoptotic signaling pathways. Recent focus on Tl toxicity has been devoted to the characterization of its effects at the nuclear level, with emphasis on DNA, which, in turn, may be responsible for cytogenetic damage, mutations, and epigenetic changes. In this work, we review and discuss past and recent evidence on the toxic effects of Tl at the systemic level and its effects on DNA. We also address Tl’s role in cancer and its control

Drosophila histone locus bodies form by hierarchical recruitment of components

An assembly process involving sequential recruitment of components and hierarchical dependency drives formation of the nuclear structures known as histone locus bodies

First LIGO search for gravitational wave bursts from cosmic (super)strings

We report on a matched-filter search for gravitational wave bursts from cosmic string cusps using LIGO data from the fourth science run (S4) which took place in February and March 2005. No gravitational waves were detected in 14.9 days of data from times when all three LIGO detectors were operating. We interpret the result in terms of a frequentist upper limit on the rate of gravitational wave bursts and use the limits on the rate to constrain the parameter space (string tension, reconnection probability, and loop sizes) of cosmic string models.Comment: 11 pages, 3 figures. Replaced with version submitted to PR