Bi-Encoders based Species Normalization -- Pairwise Sentence Learning to Rank

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named entity normalization heavily rely on dictionaries, manually created rules, and high-quality representative features such as lexical or morphological characteristics. However, recent research has investigated the use of neural network-based models to reduce dependence on dictionaries, manually crafted rules, and features. Despite these advancements, the performance of these models is still limited due to the lack of sufficiently large training datasets. These models have a tendency to overfit small training corpora and exhibit poor generalization when faced with previously unseen entities, necessitating the redesign of rules and features. Contribution: We present a novel deep learning approach for named entity normalization, treating it as a pair-wise learning to rank problem. Our method utilizes the widely-used information retrieval algorithm Best Matching 25 to generate candidate concepts, followed by the application of bi-directional encoder representation from the encoder (BERT) to re-rank the candidate list. Notably, our approach eliminates the need for feature-engineering or rule creation. We conduct experiments on species entity types and evaluate our method against state-of-the-art techniques using LINNAEUS and S800 biomedical corpora. Our proposed approach surpasses existing methods in linking entities to the NCBI taxonomy. To the best of our knowledge, there is no existing neural network-based approach for species normalization in the literature

Automatic inference of causal reasoning chains from student essays

While there has been an increasing focus on higher-level thinking skills arising from the Common Core Standards, many high-school and middle-school students struggle to combine and integrate information from multiple sources when writing essays. Writing is an important learning skill, and there is increasing evidence that writing about a topic develops a deeper understanding in the student. However, grading essays is time consuming for teachers, resulting in an increasing focus on shallower forms of assessment that are easier to automate, such as multiple-choice tests. Existing essay grading software has attempted to ease this burden but relies on shallow lexico-syntactic features and is unable to understand the structure or validity of a student’s arguments or explanations. Without the ability to understand a student’s reasoning processes, it is impossible to write automated formative assessment systems to assist students with improving their thinking skills through essay writing. In order to understand the arguments put forth in an explanatory essay in the science domain, we need a method of representing the causal structure of a piece of explanatory text. Psychologists use a representation called a causal model to represent a student\u27s understanding of an explanatory text. This consists of a number of core concepts, and a set of causal relations linking them into one or more causal chains, forming a causal model. In this thesis I present a novel system for automatically constructing causal models from student scientific essays using Natural Language Processing (NLP) techniques. The problem was decomposed into 4 sub-problems - assigning essay concepts to words, detecting causal-relations between these concepts, resolving coreferences within each essay, and using the structure of the whole essay to reconstruct a causal model. Solutions to each of these sub-problems build upon the predictions from the solutions to earlier problems, forming a sequential pipeline of models. Designing a system in this way allows later models to correct for false positive predictions from downstream models. However, this also has the disadvantage that errors made in earlier models can propagate through the system, negatively impacting the upstream models, and limiting their accuracy. Producing robust solutions for the initial 2 sub problems, detecting concepts, and parsing causal relations between them, was critical in building a robust system. A number of sequence labeling models were trained to classify the concepts associated with each word, with the most effective approach being a bidirectional recurrent neural network (RNN), a deep learning model commonly applied to word labeling problems. This is because the RNN used pre-trained word embeddings to better generalize to rarer words, and was able to use information from both ends of each sentence to infer a word\u27s concept. The concepts predicted by this model were then used to develop causal relation parsing models for detecting causal connections between these concepts. A shift-reduce dependency parsing model was trained using the SEARN algorithm and out-performed a number of other approaches by better utilizing the structure of the problem and directly optimizing the error metric used. Two pre-trained coreference resolution systems were used to resolve coreferences within the essays. However a word tagging model trained to predict anaphors combined with a heuristic for determining the antecedent out-performed these two systems. Finally, a model was developed for parsing a causal model from an entire essay, utilizing the solutions to the three previous problems. A beam search algorithm was used to produce multiple parses for each sentence, which in turn were combined to generate multiple candidate causal models for each student essay. A reranking algorithm was then used to select the optimal causal model from all of the generated candidates. An important contribution of this work is that it represents a system for parsing a complete causal model of a scientific essay from a student\u27s written answer. Existing systems have been developed to parse individual causal relations, but no existing system attempts to parse a sequence of linked causal relations forming a causal model from an explanatory scientific essay. It is hoped that this work can lead to the development of more robust essay grading software and formative assessment tools, and can be extended to build solutions for extracting causality from text in other domains. In addition, I also present 2 novel approaches for optimizing the micro-F1 score within the design of two of the algorithms studied: the dependency parser and the reranking algorithm. The dependency parser uses a custom cost function to estimate the impact of parsing mistakes on the overall micro-F1 score, while the reranking algorithm allows the micro-F1 score to be optimized by tuning the beam search parameter to balance recall and precision

Information extraction from multimedia web documents: an open-source platform and testbed

The LivingKnowledge project aimed to enhance the current state of the art in search, retrieval and knowledge management on the web by advancing the use of sentiment and opinion analysis within multimedia applications. To achieve this aim, a diverse set of novel and complementary analysis techniques have been integrated into a single, but extensible software platform on which such applications can be built. The platform combines state-of-the-art techniques for extracting facts, opinions and sentiment from multimedia documents, and unlike earlier platforms, it exploits both visual and textual techniques to support multimedia information retrieval. Foreseeing the usefulness of this software in the wider community, the platform has been made generally available as an open-source project. This paper describes the platform design, gives an overview of the analysis algorithms integrated into the system and describes two applications that utilise the system for multimedia information retrieval

A Multi-task Learning Approach for Improving Product Title Compression with User Search Log Data

It is a challenging and practical research problem to obtain effective compression of lengthy product titles for E-commerce. This is particularly important as more and more users browse mobile E-commerce apps and more merchants make the original product titles redundant and lengthy for Search Engine Optimization. Traditional text summarization approaches often require a large amount of preprocessing costs and do not capture the important issue of conversion rate in E-commerce. This paper proposes a novel multi-task learning approach for improving product title compression with user search log data. In particular, a pointer network-based sequence-to-sequence approach is utilized for title compression with an attentive mechanism as an extractive method and an attentive encoder-decoder approach is utilized for generating user search queries. The encoding parameters (i.e., semantic embedding of original titles) are shared among the two tasks and the attention distributions are jointly optimized. An extensive set of experiments with both human annotated data and online deployment demonstrate the advantage of the proposed research for both compression qualities and online business values.Comment: 8 Pages, accepted at AAAI 201

Factoid question answering for spoken documents

In this dissertation, we present a factoid question answering system, specifically tailored for Question Answering (QA) on spoken documents. This work explores, for the first time, which techniques can be robustly adapted from the usual QA on written documents to the more difficult spoken documents scenario. More specifically, we study new information retrieval (IR) techniques designed for speech, and utilize several levels of linguistic information for the speech-based QA task. These include named-entity detection with phonetic information, syntactic parsing applied to speech transcripts, and the use of coreference resolution. Our approach is largely based on supervised machine learning techniques, with special focus on the answer extraction step, and makes little use of handcrafted knowledge. Consequently, it should be easily adaptable to other domains and languages. In the work resulting of this Thesis, we have impulsed and coordinated the creation of an evaluation framework for the task of QA on spoken documents. The framework, named QAst, provides multi-lingual corpora, evaluation questions, and answers key. These corpora have been used in the QAst evaluation that was held in the CLEF workshop for the years 2007, 2008 and 2009, thus helping the developing of state-of-the-art techniques for this particular topic. The presentend QA system and all its modules are extensively evaluated on the European Parliament Plenary Sessions English corpus composed of manual transcripts and automatic transcripts obtained by three different Automatic Speech Recognition (ASR) systems that exhibit significantly different word error rates. This data belongs to the CLEF 2009 track for QA on speech transcripts. The main results confirm that syntactic information is very useful for learning to rank question candidates, improving results on both manual and automatic transcripts unless the ASR quality is very low. Overall, the performance of our system is comparable or better than the state-of-the-art on this corpus, confirming the validity of our approach.En aquesta Tesi, presentem un sistema de Question Answering (QA) factual, especialment ajustat per treballar amb documents orals. En el desenvolupament explorem, per primera vegada, quines tècniques de les habitualment emprades en QA per documents escrit són suficientment robustes per funcionar en l'escenari més difícil de documents orals. Amb més especificitat, estudiem nous mètodes de Information Retrieval (IR) dissenyats per tractar amb la veu, i utilitzem diversos nivells d'informació linqüística. Entre aquests s'inclouen, a saber: detecció de Named Entities utilitzant informació fonètica, "parsing" sintàctic aplicat a transcripcions de veu, i també l'ús d'un sub-sistema de detecció i resolució de la correferència. La nostra aproximació al problema es recolza en gran part en tècniques supervisades de Machine Learning, estant aquestes enfocades especialment cap a la part d'extracció de la resposta, i fa servir la menor quantitat possible de coneixement creat per humans. En conseqüència, tot el procés de QA pot ser adaptat a altres dominis o altres llengües amb relativa facilitat. Un dels resultats addicionals de la feina darrere d'aquesta Tesis ha estat que hem impulsat i coordinat la creació d'un marc d'avaluació de la taska de QA en documents orals. Aquest marc de treball, anomenat QAst (Question Answering on Speech Transcripts), proporciona un corpus de documents orals multi-lingüe, uns conjunts de preguntes d'avaluació, i les respostes correctes d'aquestes. Aquestes dades han estat utilitzades en les evaluacionis QAst que han tingut lloc en el si de les conferències CLEF en els anys 2007, 2008 i 2009; d'aquesta manera s'ha promogut i ajudat a la creació d'un estat-de-l'art de tècniques adreçades a aquest problema en particular. El sistema de QA que presentem i tots els seus particulars sumbòduls, han estat avaluats extensivament utilitzant el corpus EPPS (transcripcions de les Sessions Plenaries del Parlament Europeu) en anglès, que cónté transcripcions manuals de tots els discursos i també transcripcions automàtiques obtingudes mitjançant tres reconeixedors automàtics de la parla (ASR) diferents. Els reconeixedors tenen característiques i resultats diferents que permetes una avaluació quantitativa i qualitativa de la tasca. Aquestes dades pertanyen a l'avaluació QAst del 2009. Els resultats principals de la nostra feina confirmen que la informació sintàctica és mol útil per aprendre automàticament a valorar la plausibilitat de les respostes candidates, millorant els resultats previs tan en transcripcions manuals com transcripcions automàtiques, descomptat que la qualitat de l'ASR sigui molt baixa. En general, el rendiment del nostre sistema és comparable o millor que els altres sistemes pertanyents a l'estat-del'art, confirmant així la validesa de la nostra aproximació

Linking named entities to Wikipedia

Natural language is fraught with problems of ambiguity, including name reference. A name in text can refer to multiple entities just as an entity can be known by different names. This thesis examines how a mention in text can be linked to an external knowledge base (KB), in our case, Wikipedia. The named entity linking (NEL) task requires systems to identify the KB entry, or Wikipedia article, that a mention refers to; or, if the KB does not contain the correct entry, return NIL. Entity linking systems can be complex and we present a framework for analysing their different components, which we use to analyse three seminal systems which are evaluated on a common dataset and we show the importance of precise search for linking. The Text Analysis Conference (TAC) is a major venue for NEL research. We report on our submissions to the entity linking shared task in 2010, 2011 and 2012. The information required to disambiguate entities is often found in the text, close to the mention. We explore apposition, a common way for authors to provide information about entities. We model syntactic and semantic restrictions with a joint model that achieves state-of-the-art apposition extraction performance. We generalise from apposition to examine local descriptions specified close to the mention. We add local description to our state-of-the-art linker by using patterns to extract the descriptions and matching against this restricted context. Not only does this make for a more precise match, we are also able to model failure to match. Local descriptions help disambiguate entities, further improving our state-of-the-art linker. The work in this thesis seeks to link textual entity mentions to knowledge bases. Linking is important for any task where external world knowledge is used and resolving ambiguity is fundamental to advancing research into these problems