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Publications

Publications by Alípio Jorge

2023

A Biomedical Entity Extraction Pipeline for Oncology Health Records in Portuguese

Authors
Sousa, H; Pasquali, A; Jorge, A; Santos, CS; Lopes, MA;

Publication
38TH ANNUAL ACM SYMPOSIUM ON APPLIED COMPUTING, SAC 2023

Abstract
Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved..1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

2023

tieval: An Evaluation Framework for Temporal Information Extraction Systems

Authors
Sousa, H; Jorge, A; Campos, R;

Publication
PROCEEDINGS OF THE 46TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL, SIGIR 2023

Abstract
Temporal information extraction (TIE) has attracted a great deal of interest over the last two decades. Such endeavors have led to the development of a significant number of datasets. Despite its benefits, having access to a large volume of corpora makes it difficult to benchmark TIE systems. On the one hand, different datasets have different annotation schemes, which hinders the comparison between competitors across different corpora. On the other hand, the fact that each corpus is disseminated in a different format requires a considerable engineering effort for a researcher/practitioner to develop parsers for all of them. These constraints force researchers to select a limited amount of datasets to evaluate their systems which consequently limits the comparability of the systems. Yet another obstacle to the comparability of TIE systems is the evaluation metric employed. While most research works adopt traditional metrics such as precision, recall, and..1, a few others prefer temporal awareness - a metric tailored to be more comprehensive on the evaluation of temporal systems. Although the reason for the absence of temporal awareness in the evaluation of most systems is not clear, one of the factors that certainly weighs on this decision is the need to implement the temporal closure algorithm, which is neither straightforward to implement nor easily available. All in all, these problems have limited the fair comparison between approaches and consequently, the development of TIE systems. To mitigate these problems, we have developed tieval, a Python library that provides a concise interface for importing different corpora and is equipped with domain-specific operations that facilitate system evaluation. In this paper, we present the first public release of tieval and highlight its most relevant features. The library is available as open source, under MIT License, at PyPI1 and GitHub(2).

2023

A survey on narrative extraction from textual data

Authors
Santana, B; Campos, R; Amorim, E; Jorge, A; Silvano, P; Nunes, S;

Publication
ARTIFICIAL INTELLIGENCE REVIEW

Abstract
Narratives are present in many forms of human expression and can be understood as a fundamental way of communication between people. Computational understanding of the underlying story of a narrative, however, may be a rather complex task for both linguists and computational linguistics. Such task can be approached using natural language processing techniques to automatically extract narratives from texts. In this paper, we present an in depth survey of narrative extraction from text, providing a establishing a basis/framework for the study roadmap to the study of this area as a whole as a means to consolidate a view on this line of research. We aim to fulfill the current gap by identifying important research efforts at the crossroad between linguists and computer scientists. In particular, we highlight the importance and complexity of the annotation process, as a crucial step for the training stage. Next, we detail methods and approaches regarding the identification and extraction of narrative components, their linkage and understanding of likely inherent relationships, before detailing formal narrative representation structures as an intermediate step for visualization and data exploration purposes. We then move into the narrative evaluation task aspects, and conclude this survey by highlighting important open issues under the domain of narratives extraction from texts that are yet to be explored.

2022

Probing Commonsense Knowledge in Pre-trained Language Models with Sense-level Precision and Expanded Vocabulary

Authors
Loureiro, D; Jorge, AM;

Publication
CoRR

Abstract

2022

ORSUM 2022 - 5th Workshop on Online Recommender Systems and User Modeling

Authors
Vinagre, J; Jorge, AM; Ghossein, MA; Bifet, A;

Publication
RecSys '22: Sixteenth ACM Conference on Recommender Systems, Seattle, WA, USA, September 18 - 23, 2022

Abstract
Modern online systems for user modeling and recommendation need to continuously deal with complex data streams generated by users at very fast rates. This can be overwhelming for systems and algorithms designed to train recommendation models in batches, given the continuous and potentially fast change of content, context and user preferences or intents. Therefore, it is important to investigate methods able to transparently and continuously adapt to the inherent dynamics of user interactions, preferably for long periods of time. Online models that continuously learn from such flows of data are gaining attention in the recommender systems community, given their natural ability to deal with data generated in dynamic, complex environments. User modeling and personalization can particularly benefit from algorithms capable of maintaining models incrementally and online. The objective of this workshop is to foster contributions and bring together a growing community of researchers and practitioners interested in online, adaptive approaches to user modeling, recommendation and personalization, and their implications regarding multiple dimensions, such as evaluation, reproducibility, privacy, fairness and transparency. © 2022 Owner/Author.

2022

LMMS reloaded: Transformer-based sense embeddings for disambiguation and beyond

Authors
Loureiro, D; Mário Jorge, A; Camacho Collados, J;

Publication
ARTIFICIAL INTELLIGENCE

Abstract
Distributional semantics based on neural approaches is a cornerstone of Natural Language Processing, with surprising connections to human meaning representation as well. Recent Transformer-based Language Models have proven capable of producing contextual word representations that reliably convey sense-specific information, simply as a product of self supervision. Prior work has shown that these contextual representations can be used to accurately represent large sense inventories as sense embeddings, to the extent that a distance-based solution to Word Sense Disambiguation (WSD) tasks outperforms models trained specifically for the task. Still, there remains much to understand on how to use these Neural Language Models (NLMs) to produce sense embeddings that can better harness each NLM's meaning representation abilities. In this work we introduce a more principled approach to leverage information from all layers of NLMs, informed by a probing analysis on 14 NLM variants. We also emphasize the versatility of these sense embeddings in contrast to task-specific models, applying them on several sense-related tasks, besides WSD, while demonstrating improved performance using our proposed approach over prior work focused on sense embeddings. Finally, we discuss unexpected findings regarding layer and model performance variations, and potential applications for downstream tasks.& nbsp;

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