BIOSMILE web search: a web application for annotating biomedical entities and relations

BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein–protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form. To date, BWS has been field tested by over 30 biologists and questionnaires have shown that subjects are highly satisfied with its capabilities and usability. BWS is accessible free of charge at http://bioservices.cse.yzu.edu.tw/BWS

Neural Approaches to Relational Aspect-Based Sentiment Analysis. Exploring generalizations across words and languages

Jebbara S. Neural Approaches to Relational Aspect-Based Sentiment Analysis. Exploring generalizations across words and languages. Bielefeld: Universität Bielefeld; 2020.Everyday, vast amounts of unstructured, textual data are shared online in digital form. Websites such as forums, social media sites, review sites, blogs, and comment sections offer platforms to express and discuss opinions and experiences. Understanding the opinions in these resources is valuable for e.g. businesses to support market research and customer service but also individuals, who can benefit from the experiences and expertise of others. In this thesis, we approach the topic of opinion extraction and classification with neural network models. We regard this area of sentiment analysis as a relation extraction problem in which the sentiment of some opinion holder towards a certain aspect of a product, theme, or event needs to be extracted. In accordance with this framework, our main contributions are the following: 1. We propose a full system addressing all subtasks of relational sentiment analysis. 2. We investigate how semantic web resources can be leveraged in a neural-network-based model for the extraction of opinion targets and the classification of sentiment labels. Specifically, we experiment with enhancing pretrained word embeddings using the lexical resource WordNet. Furthermore, we enrich a purely text-based model with SenticNet concepts and observe an improvement for sentiment classification. 3. We examine how opinion targets can be automatically identified in noisy texts. Customer reviews, for instance, are prone to contain misspelled words and are difficult to process due to their domain-specific language. We integrate information about the character structure of a word into a sequence labeling system using character-level word embeddings and show their positive impact on the system's performance. We reveal encoded character patterns of the learned embeddings and give a nuanced view of the obtained performance differences. 4. Opinion target extraction usually relies on supervised learning approaches. We address the lack of available annotated data for specific languages by proposing a zero-shot cross-lingual approach for the extraction of opinion target expressions. We leverage multilingual word embeddings that share a common vector space across various languages and incorporate these into a convolutional neural network architecture. Our experiments with 5 languages give promising results: We can successfully train a model on annotated data of a source language and perform accurate prediction on a target language without ever using any annotated samples in that target language

Exploratory Content Analysis Using Text Data Mining: Corporate Citizenship Reports of Seven US Companes from 2004 to 2012

This study demonstrates the use of Text Data Mining (TDM) for exploring the content of a collection of Corporate Citizenship(CC) reports. The collection analyzed comprises CC reports produced by seven Dow Jones companies (Citi, Coca-Cola, ExxonMobil, General Motors, Intel, McDonalds and Microsoft) in2004, 2008 and 2012.Exploratory con-tent analysis using TDM enables insights for CC professionals and analysts, in less time using fewer resources, which in turn could help them explore collaboration opportunities around supply chains, re-training programs, and alternative risk mitigation strategies in terms of governance and compliance. In addition, TDM, using supervised machine learning on the whole collection (or corpus) as well as unsupervised machine learning on document collections by year, suggests the integration of CC considerations related to environmental sustain-ability in CC report components discussing the core business of some firms. This method has been used in many contexts in which a collection of documents needs to be categorized and/or analyzed to uncover new patterns and relationships

Assorted, Archetypal and Annotated Two Million (3A2M) Cooking Recipes Dataset based on Active Learning

Cooking recipes allow individuals to exchange culinary ideas and provide food preparation instructions. Due to a lack of adequate labeled data, categorizing raw recipes found online to the appropriate food genres is a challenging task in this domain. Utilizing the knowledge of domain experts to categorize recipes could be a solution. In this study, we present a novel dataset of two million culinary recipes labeled in respective categories leveraging the knowledge of food experts and an active learning technique. To construct the dataset, we collect the recipes from the RecipeNLG dataset. Then, we employ three human experts whose trustworthiness score is higher than 86.667% to categorize 300K recipe by their Named Entity Recognition (NER) and assign it to one of the nine categories: bakery, drinks, non-veg, vegetables, fast food, cereals, meals, sides and fusion. Finally, we categorize the remaining 1900K recipes using Active Learning method with a blend of Query-by-Committee and Human In The Loop (HITL) approaches. There are more than two million recipes in our dataset, each of which is categorized and has a confidence score linked with it. For the 9 genres, the Fleiss Kappa score of this massive dataset is roughly 0.56026. We believe that the research community can use this dataset to perform various machine learning tasks such as recipe genre classification, recipe generation of a specific genre, new recipe creation, etc. The dataset can also be used to train and evaluate the performance of various NLP tasks such as named entity recognition, part-of-speech tagging, semantic role labeling, and so on. The dataset will be available upon publication: https://tinyurl.com/3zu4778y

Script acquisition : a crowdsourcing and text mining approach

According to Grice’s (1975) theory of pragmatics, people tend to omit basic information when participating in a conversation (or writing a narrative) under the assumption that left out details are already known or can be inferred from commonsense knowledge by the hearer (or reader). Writing and understanding of texts makes particular use of a specific kind of common-sense knowledge, referred to as script knowledge. Schank and Abelson (1977) proposed Scripts as a model of human knowledge represented in memory that stores the frequent habitual activities, called scenarios, (e.g. eating in a fast food restaurant, etc.), and the different courses of action in those routines. This thesis addresses measures to provide a sound empirical basis for high-quality script models. We work on three key areas related to script modeling: script knowledge acquisition, script induction and script identification in text. We extend the existing repository of script knowledge bases in two different ways. First, we crowdsource a corpus of 40 scenarios with 100 event sequence descriptions (ESDs) each, thus going beyond the size of previous script collections. Second, the corpus is enriched with partial alignments of ESDs, done by human annotators. The crowdsourced partial alignments are used as prior knowledge to guide the semi-supervised script-induction algorithm proposed in this dissertation. We further present a semi-supervised clustering approach to induce script structure from crowdsourced descriptions of event sequences by grouping event descriptions into paraphrase sets and inducing their temporal order. The proposed semi-supervised clustering model better handles order variation in scripts and extends script representation formalism, Temporal Script graphs, by incorporating "arbitrary order" equivalence classes in order to allow for the flexible event order inherent in scripts. In the third part of this dissertation, we introduce the task of scenario detection, in which we identify references to scripts in narrative texts. We curate a benchmark dataset of annotated narrative texts, with segments labeled according to the scripts they instantiate. The dataset is the first of its kind. The analysis of the annotation shows that one can identify scenario references in text with reasonable reliability. Subsequently, we proposes a benchmark model that automatically segments and identifies text fragments referring to given scenarios. The proposed model achieved promising results, and therefore opens up research on script parsing and wide coverage script acquisition.Gemäß der Grice’schen (1975) Pragmatiktheorie neigen Menschen dazu, grundlegende Informationen auszulassen, wenn sie an einem Gespräch teilnehmen (oder eine Geschichte schreiben). Dies geschieht unter der Annahme, dass die ausgelassenen Details bereits bekannt sind, oder vom Hörer (oder Leser) aus Weltwissen erschlossen werden können. Besonders beim Schreiben und Verstehen von Text wird Verwendung einer spezifischen Art von solchem Weltwissen gemacht, welches auch Skriptwissen genannt wird. Schank und Abelson (1977) erdachten Skripte als ein Modell menschlichen Wissens, welches im menschlichen Gedächtnis gespeichert ist und häufige Alltags-Aktivitäten sowie deren typischen Ablauf beinhaltet. Solche Skript-Aktivitäten werden auch als Szenarios bezeichnet und umfassen zum Beispiel Im Restaurant Essen etc. Diese Dissertation widmet sich der Bereitstellung einer soliden empirischen Grundlage zur Akquisition qualitativ hochwertigen Skriptwissens. Wir betrachten drei zentrale Aspekte im Bereich der Skriptmodellierung: Akquisition ition von Skriptwissen, Skript-Induktion und Skriptidentifizierung in Text. Wir erweitern das bereits bestehende Repertoire und Skript-Datensätzen in 2 Bereichen. Erstens benutzen wir Crowdsourcing zur Erstellung eines Korpus, das 40 Szenarien mit jeweils 100 Ereignissequenzbeschreibungen (Event Sequence Descriptions, ESDs) beinhaltet, und welches somit größer als bestehende Skript- Datensätze ist. Zweitens erweitern wir das Korpus mit partiellen ESD-Alignierungen, die von Hand annotiert werden. Die partiellen Alignierungen werden dann als Vorwissen für einen halbüberwachten Algorithmus zur Skriptinduktion benutzt, der im Rahmen dieser Dissertation vorgestellt wird. Wir präsentieren außerdem einen halbüberwachten Clusteringansatz zur Induktion von Skripten, basierend auf Ereignissequenzen, die via Crowdsourcing gesammelt wurden. Hierbei werden einzelne Ereignisbeschreibungen gruppiert, um Paraphrasenmengen und der deren temporale Ordnung abzuleiten. Der vorgestellte Clusteringalgorithmus ist im Stande, Variationen in der typischen Reihenfolge in Skripte besser abzubilden und erweitert damit einen Formalismus zur Skriptrepräsentation, temporale Skriptgraphen. Dies wird dadurch bewerkstelligt, dass Equivalenzklassen von Beschreibungen mit "arbiträrer Reihenfolge" genutzt werden, die es erlauben, eine flexible Ereignisordnung abzubilden, die inhärent bei Skripten vorhanden ist. Im dritten Teil der vorliegenden Arbeit führen wir den Task der SzenarioIdentifikation ein, also der automatischen Identifikation von Skriptreferenzen in narrativen Texten. Wir erstellen einen Benchmark-Datensatz mit annotierten narrativen Texten, in denen einzelne Segmente im Bezug auf das Skript, welches sie instantiieren, markiert wurden. Dieser Datensatz ist der erste seiner Art. Eine Analyse der Annotation zeigt, dass Referenzen zu Szenarien im Text mit annehmbarer Akkuratheit vorhergesagt werden können. Zusätzlich stellen wir ein Benchmark-Modell vor, welches Textfragmente automatisch erstellt und deren Szenario identifiziert. Das vorgestellte Modell erreicht erfolgversprechende Resultate und öffnet damit einen Forschungszweig im Bereich des Skript-Parsens und der Skript-Akquisition im großen Stil

FrameNet annotation for multimodal corpora: devising a methodology for the semantic representation of text-image interactions in audiovisual productions

Multimodal analyses have been growing in importance within several approaches to Cognitive Linguistics and applied fields such as Natural Language Understanding. Nonetheless fine-grained semantic representations of multimodal objects are still lacking, especially in terms of integrating areas such as Natural Language Processing and Computer Vision, which are key for the implementation of multimodality in Computational Linguistics. In this dissertation, we propose a methodology for extending FrameNet annotation to the multimodal domain, since FrameNet can provide fine-grained semantic representations, particularly with a database enriched by Qualia and other interframal and intraframal relations, as it is the case of FrameNet Brasil. To make FrameNet Brasil able to conduct multimodal analysis, we outlined the hypothesis that similarly to the way in which words in a sentence evoke frames and organize their elements in the syntactic locality accompanying them, visual elements in video shots may, also, evoke frames and organize their elements on the screen or work complementarily with the frame evocation patterns of the sentences narrated simultaneously to their appearance on screen, providing different profiling and perspective options for meaning construction. The corpus annotated for testing the hypothesis is composed of episodes of a Brazilian TV Travel Series critically acclaimed as an exemplar of good practices in audiovisual composition. The TV genre chosen also configures a novel experimental setting for research on integrated image and text comprehension, since, in this corpus, text is not a direct description of the image sequence but correlates with it indirectly in a myriad of ways. The dissertation also reports on an eye-tracker experiment conducted to validate the approach proposed to a text-oriented annotation. The experiment demonstrated that it is not possible to determine that text impacts gaze directly and was taken as a reinforcement to the approach of valorizing modes combination. Last, we present the Frame2 dataset, the product of the annotation task carried out for the corpus following both the methodology and guidelines proposed. The results achieved demonstrate that, at least for this TV genre but possibly also for others, a fine-grained semantic annotation tackling the diverse correlations that take place in a multimodal setting provides new perspective in multimodal comprehension modeling. Moreover, multimodal annotation also enriches the development of FrameNets, to the extent that correlations found between modalities can attest the modeling choices made by those building frame-based resources.Análises multimodais vêm crescendo em importância em várias abordagens da Linguística Cognitiva e em diversas áreas de aplicação, como o da Compreensão de Linguagem Natural. No entanto, há significativa carência de representações semânticas refinadas de objetos multimodais, especialmente em termos de integração de áreas como Processamento de Linguagem Natural e Visão Computacional, que são fundamentais para a implementação de multimodalidade no campo da Linguística Computacional. Nesta tese, propomos uma metodologia para estender o método de anotação da FrameNet ao domínio multimodal, uma vez que a FrameNet pode fornecer representações semânticas refinadas, particularmente com um banco de dados enriquecido por Qualia e outras relações interframe e intraframe, como é o caso do FrameNet Brasil. Para tornar a FrameNet Brasil capaz de realizar análises multimodais, delineamos a hipótese de que, assim como as palavras em uma frase evocam frames e organizam seus elementos na localidade sintática que os acompanha, os elementos visuais nos planos de vídeo também podem evocar frames e organizar seus elementos na tela ou trabalhar de forma complementar aos padrões de evocação de frames das sentenças narradas simultaneamente ao seu aparecimento na tela, proporcionando diferentes perfis e opções de perspectiva para a construção de sentido. O corpus anotado para testar a hipótese é composto por episódios de um programa televisivo de viagens brasileiro aclamado pela crítica como um exemplo de boas práticas em composição audiovisual. O gênero televisivo escolhido também configura um novo conjunto experimental para a pesquisa em imagem integrada e compreensão textual, uma vez que, neste corpus, o texto não é uma descrição direta da sequência de imagens, mas se correlaciona com ela indiretamente em uma miríade de formas diversa. A Tese também relata um experimento de rastreamento ocular realizado para validar a abordagem proposta para uma anotação orientada por texto. O experimento demonstrou que não é possível determinar que o texto impacta diretamente o direcionamento do olhar e foi tomado como um reforço para a abordagem de valorização da combinação de modos. Por fim, apresentamos o conjunto de dados Frame2, produto da tarefa de anotação realizada para o corpus seguindo a metodologia e as diretrizes propostas. Os resultados obtidos demonstram que, pelo menos para esse gênero de TV, mas possivelmente também para outros, uma anotação semântica refinada que aborde as diversas correlações que ocorrem em um ambiente multimodal oferece uma nova perspectiva na modelagem da compreensão multimodal. Além disso, a anotação multimodal também enriquece o desenvolvimento de FrameNets, na medida em que as correlações encontradas entre as modalidades podem atestar as escolhas de modelagem feitas por aqueles que criam recursos baseados em frames.CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superio