Spain

Epidemiologists study the global impact of the spread of viruses by considering information on the DNA sequence and structure of viruses, as well as relying on accurate metadata. Although accurate localized geographical data is critical for creating maps of the locations of viruses and their migration paths, most publicly available databases, such as GenBank, provide insufficient details on the matter, limited to country or state level. Therefore, a manual inspection of biomedical articles is vital for obtaining more detailed information about the locations of the viruses.

COLING 2020

TIMBERT: Toponym Identifier For The Medical Domain Based on BERT

toponym identification

medical domain

sequence labeling

bert

Congratulations to all the researchers who have qualified for the AMA Research Challenge virtual poster symposium and semifinals!

Welcome to the **largest national, multi-specialty research event** featuring research from nearly 1,000 medical students, residents, fellows, and international medical graduates across six topic areas - basic science, clinical and translational research, clinical vignettes, health systems science, medical education, and public health and health policy.

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The 2025 AMA Research Challenge includes the following symposium halls:
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At the conclusion of this event, the AMA announced the top five finalists who advanced to the AMA Research Challenge final round, presented their research to an elite panel of judges, and competed to win a $10,000 grand prize presented by Laurel Road.

**Addison Shenk, a fourth-year medical student from Edward Via Virginia College of Osteopathic Medicine, was the winner of the 2025 AMA Research Challenge and was awarded the grand prize of $10,000, presented by Laurel Road.**

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AMA Research Challenge 2025 

Join the AMA Research Challenge poster symposium and semifinals to explore top research posters and score posters in the semifinals (an AMA member exclusive opportunity).

poster

stages 

COLING, the International Conference on Computational Linguistics, is one of the premier conferences for natural language processing and computational linguistics. Often grouped within the field of artificial intelligence, but actually pre-dating the development of artificial intelligence, advances in computational linguistics and natural language processing are now some of the major drivers behind the use of artificial intelligence for commercial and social applications – for example, on-line search, machine translation and with voice-assisted conversational devices.

First established in 1965, the biennial COLING conference is held in diverse parts of the globe and attracts participants from both top-ranked research centers and emerging countries. Today, the most important developments in our field are taking place not only in universities and academic research institutes, but also in industrial research departments and in technological startups. COLING conferences provide opportunities for all these communities to showcase their exciting developments.

COLING, the International Conference on Computational Linguistics, is one of the premier conferences for natural language processing and computational linguistics. Often grouped within the field of artificial intelligence, but actually pre-dating the development of artificial intelligence, advances in computational linguistics and natural language processing are now some of the major drivers behind the use of artificial intelligence for commercial and social applications – for example, on-line search, machine translation and with voice-assisted conversational devices.

The lack of annotated data is a big issue for building reliable NLP systems for most of the world’slanguages. But this problem can be alleviated by automatic data generation. In this paper, wepresent a new data augmentation method for artificially creating new dependency-annotated sen-tences. The main idea is to swap subtrees between annotated sentences while enforcing strongconstraints on those trees to ensure maximal grammaticality of the new sentences. We also pro-pose a method to perform low-resource experiments using resource-rich languages by mimickinglow-resource languages by sampling sentences under a low-resource distribution. In a series ofexperiments, we show that our newly proposed data augmentation method outperforms previousproposals using the same basic inputs.

Data Augmentation via Subtree Swapping for Dependency Parsing of Low-Resource Languages

Emotion-cause pair extraction (ECPE) aims at extracting emotions and causes as pairs from documents, where each pair contains an emotion clause and a set of cause clauses. Existing approaches address the task by first extracting emotion and cause clauses via two binary classifiers separately, and then training another binary classifier to pair them up. However, the extracted emotion-cause pairs of different emotion types cannot be distinguished from each other through simple binary classifiers, which limits the applicability of the existing approaches. Moreover, such two-step approaches may suffer from possible cascading errors. In this paper, to address the first problem, we assign emotion type labels to emotion and cause clauses so that emotion- cause pairs of different emotion types can be easily distinguished. As for the second problem, we reformulate the ECPE task as a unified sequence labeling task, which can extract multiple emotion-cause pairs in an end-to-end fashion. We propose an approach composed of a convolution neural network for encoding neighboring information and two Bidirectional Long-Short Term Memory networks for two auxiliary tasks. Experiment results demonstrate the feasibility and effectiveness of our approaches.

A Unified Sequence Labeling Model for Emotion Cause Pair Extraction

A promising application of AI to healthcare is the retrieval of information from electronic health records (EHRs), e.g. to aid clinicians in finding relevant information for a consultation or to recruit suitable patients for a study.
This requires search capabilities far beyond simple string matching, including the retrieval of concepts (diagnoses, symptoms, medications, etc.) related to the one in question. 
The suitability of AI methods for such applications is tested by predicting the relatedness of concepts with known relatedness scores.
However, all existing biomedical concept relatedness datasets are notoriously small and consist of hand-picked concept pairs.
We open-source a novel concept relatedness benchmark overcoming these issues: it is six times larger than existing datasets 
and concept pairs are chosen based on co-occurrence in EHRs, ensuring their relevance for the application of interest.
We present an in-depth analysis of our new dataset and compare it to existing ones, highlighting that it is not only larger but also complements existing datasets in terms of the types of concepts included.
Initial experiments with state-of-the-art embedding methods show that our dataset is a challenging new benchmark for testing concept relatedness models.

Biomedical Concept Relatedness - A large EHR based benchmark

An essential task of most Question Answering (QA) systems is to re-rank the set of answer candidates, i.e., Answer Sentence Selection (AS2). These candidates are typically sentences either extracted from one or more documents preserving their natural order or retrieved by a search engine. Most state-of-the-art approaches to the task use huge neural models, such as BERT, or complex attentive architectures.
In this paper, we argue that by exploiting the intrinsic structure of the original rank together with an effective word-relatedness encoder, we achieve the highest accuracy among the cost-efficient models, with two orders of magnitude fewer parameters than the current state of the art. Our model takes 9.5 seconds to train on the WikiQA dataset, i.e., very fast in comparison with the 18 minutes required by a standard BERT-base fine-tuning.

A Study on Efficiency, Accuracy and Document Structure for Answer Sentence Selection

Sentence matching aims to identify the special relationship between two sentences, and plays a key role in many natural language processing tasks. However, previous studies mainly focused on exploiting either syntactic or semantic information for sentence matching, and no studies consider integrating both of them. In this study, we propose integrating syntax and semantics into BERT with sentence matching. In particular, we use an implicit syntax and semantics integration method that is less sensitive to the output structure information. Thus the implicit integration can alleviate the error propagation problem. The experimental results show that our approach has achieved state-of-the-art or competitive performance on several sentence matching datasets, demonstrating the benefits of implicitly integrating syntactic and semantic features in sentence matching.


Sentence Matching with Syntax- and Semantics-Aware BERT

We perform a corpus analysis to develop a representation of the knowledge and reasoning used to interpret indirect speech acts. An indirect speech act (ISA) is an utterance whose intended meaning is different from its literal meaning. We focus on those speech acts in which slight changes in situational or contextual information can switch the dominant intended meaning of an utterance from direct to indirect or vice-versa. We computationalize how various contextual features can influence a speaker’s beliefs, and how these beliefs can influence the intended meaning and choice of the surface form of an utterance. We axiomatize the domain-general patterns of reasoning involved, and implement a proof-of-concept architecture using Answer Set Programming. Our model is presented as a contribution to cognitive science and psycholinguistics, so representational decisions are justified by existing theoretical work.

Reasoning Requirements for Indirect Speech Acts

We reduce the model size of pre-trained word embeddings by a factor of $200$ while preserving its quality. Previous studies in this direction created a smaller word embedding model by reconstructing pre-trained word representations from those of subwords, which allows to store only a smaller number of subword embeddings in the memory. However, previous studies that train the reconstruction models using only target words cannot reduce the model size extremely while preserving its quality. Inspired by the observation of words with similar meanings having similar embeddings, our reconstruction training learns the global relationships among words, which can be employed in various models for word embedding reconstruction. Experimental results on word similarity benchmarks show that the proposed method improves the performance of the all subword-based reconstruction models.

Tiny Word Embeddings Using Globally Informed Reconstruction

Complex question answering (CQA) over raw text is a challenging task. A prominent approach to this task is based on the programmer-interpreter framework, where the programmer maps the question into a sequence of reasoning actions and the interpreter then executes these actions on the raw text. Learning an effective CQA model requires large amounts of human-annotated data, consisting of the ground-truth sequence of reasoning actions, which is time-consuming and expensive to collect at scale. In this paper, we address the challenge of learning a high-quality programmer (parser) by projecting natural human-generated questions into unnatural machinegenerated questions which are more convenient to parse. We firstly generate synthetic (question, action sequence) pairs by a data generator, and train a semantic parser that associates synthetic questions with their corresponding action sequences. To capture the diversity when applied to natural questions, we learn a projection model to map natural questions into their most similar unnatural questions for which the parser can work well. Without any natural training data, our projection model provides high-quality action sequences for the CQA task. Experimental results show that the QA model trained exclusively with synthetic data outperforms its state-of-the-art counterpart trained on human-labeled data.

Understanding Unnatural Questions Improves Reasoning over Text

This paper studies the problem of generating a summary for a given sentence-image pair. Existing multimodal sequence-to-sequence approaches mainly focus on enhancing the decoder by visual signals, while ignoring that the image can improve the ability of the encoder to identify highlights of a news event or a document. Thus, we propose a multimodal selective gate network that considers reciprocal relationships between textual and multi-level visual features, including global image descriptor, activation grids, and object proposals, to select highlights of the event when encoding the source sentence. In addition, we introduce a modality regularization to encourage the summary to capture the highlights embedded in the image more accurately. To verify the generalization of our model, we adopt the multimodal selective gate to the text-based decoder and multimodal-based decoder. Experimental results on a public multimodal sentence summarization dataset demonstrate the advantage of our models over baselines. Further analysis suggests that our proposed multimodal selective gate network can effectively select important information in the input sentence.

Multimodal Sentence Summarization via Multimodal Selective Encoding

Pre-trained language models provide the foundations for state-of-the-art performance across a wide range of natural language processing tasks, including text classification. However, most classification datasets assume a large amount labeled data, which is commonly not the case in practical settings. In particular, in this paper we compare the performance of a light-weight linear classifier based on word embeddings, i.e., fastText (Joulin et al., 2017), versus a pre-trained language model, i.e., BERT (Devlin et al., 2019), across a wide range of datasets and classification tasks. In general, results show the importance of domain-specific unlabeled data, both in the form of word embeddings or language models. As for the comparison, BERT outperforms all baselines in standard datasets with large training sets. However, in settings with small training datasets a simple method like fastText coupled with domain-specific word embeddings performs equally well or better than BERT, even when pre-trained on domain-specific data.

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