Antonio Jimeno Yepes

Qingyu Chen, Alexis Allot, Robert Leaman et al.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Yuxi Liu, Zhenhao Zhang, Antonio Jimeno Yepes et al.

Building models for health prediction based on Electronic Health Records (EHR) has become an active research area. EHR patient journey data consists of patient time-ordered clinical events/visits from patients. Most existing studies focus on modeling long-term dependencies between visits, without explicitly taking short-term correlations between consecutive visits into account, where irregular time intervals, incorporated as auxiliary information, are fed into health prediction models to capture latent progressive patterns of patient journeys. We present a novel deep neural network with four modules to take into account the contributions of various variables for health prediction: i) the Stacked Attention module strengthens the deep semantics in clinical events within each patient journey and generates visit embeddings, ii) the Short-Term Temporal Attention module models short-term correlations between consecutive visit embeddings while capturing the impact of time intervals within those visit embeddings, iii) the Long-Term Temporal Attention module models long-term dependencies between visit embeddings while capturing the impact of time intervals within those visit embeddings, iv) and finally, the Coupled Attention module adaptively aggregates the outputs of Short-Term Temporal Attention and Long-Term Temporal Attention modules to make health predictions. Experimental results on MIMIC-III demonstrate superior predictive accuracy of our model compared to existing state-of-the-art methods, as well as the interpretability and robustness of this approach. Furthermore, we found that modeling short-term correlations contributes to local priors generation, leading to improved predictive modeling of patient journeys.

Yuxi Liu, Zhenhao Zhang, Shaowen Qin et al.

Predicting the risk of in-hospital mortality from electronic health records (EHRs) has received considerable attention. Such predictions will provide early warning of a patient's health condition to healthcare professionals so that timely interventions can be taken. This prediction task is challenging since EHR data are intrinsically irregular, with not only many missing values but also varying time intervals between medical records. Existing approaches focus on exploiting the variable correlations in patient medical records to impute missing values and establishing time-decay mechanisms to deal with such irregularity. This paper presents a novel contrastive learning-based imputation-prediction network for predicting in-hospital mortality risks using EHR data. Our approach introduces graph analysis-based patient stratification modeling in the imputation process to group similar patients. This allows information of similar patients only to be used, in addition to personal contextual information, for missing value imputation. Moreover, our approach can integrate contrastive learning into the proposed network architecture to enhance patient representation learning and predictive performance on the classification task. Experiments on two real-world EHR datasets show that our approach outperforms the state-of-the-art approaches in both imputation and prediction tasks.

Yuxi Liu, Zhenhao Zhang, Shaowen Qin et al.

The Intensive Care Unit (ICU) is one of the most important parts of a hospital, which admits critically ill patients and provides continuous monitoring and treatment. Various patient outcome prediction methods have been attempted to assist healthcare professionals in clinical decision-making. Existing methods focus on measuring the similarity between patients using deep neural networks to capture the hidden feature structures. However, the higher-order relationships are ignored, such as patient characteristics (e.g., diagnosis codes) and their causal effects on downstream clinical predictions. In this paper, we propose a novel Hypergraph Convolutional Network that allows the representation of non-pairwise relationships among diagnosis codes in a hypergraph to capture the hidden feature structures so that fine-grained patient similarity can be calculated for personalized mortality risk prediction. Evaluation using a publicly available eICU Collaborative Research Database indicates that our method achieves superior performance over the state-of-the-art models on mortality risk prediction. Moreover, the results of several case studies demonstrated the effectiveness and robustness of the model decisions.

Yuxi Liu, Shaowen Qin, Antonio Jimeno Yepes et al.

Predicting the health risks of patients using Electronic Health Records (EHR) has attracted considerable attention in recent years, especially with the development of deep learning techniques. Health risk refers to the probability of the occurrence of a specific health outcome for a specific patient. The predicted risks can be used to support decision-making by healthcare professionals. EHRs are structured patient journey data. Each patient journey contains a chronological set of clinical events, and within each clinical event, there is a set of clinical/medical activities. Due to variations of patient conditions and treatment needs, EHR patient journey data has an inherently high degree of missingness that contains important information affecting relationships among variables, including time. Existing deep learning-based models generate imputed values for missing values when learning the relationships. However, imputed data in EHR patient journey data may distort the clinical meaning of the original EHR patient journey data, resulting in classification bias. This paper proposes a novel end-to-end approach to modeling EHR patient journey data with Integrated Convolutional and Recurrent Neural Networks. Our model can capture both long- and short-term temporal patterns within each patient journey and effectively handle the high degree of missingness in EHR data without any imputation data generation. Extensive experimental results using the proposed model on two real-world datasets demonstrate robust performance as well as superior prediction accuracy compared to existing state-of-the-art imputation-based prediction methods.

Ying Xu, Xu Zhong, Antonio Jimeno Yepes et al.

We introduce a grey-box adversarial attack and defence framework for sentiment classification. We address the issues of differentiability, label preservation and input reconstruction for adversarial attack and defence in one unified framework. Our results show that once trained, the attacking model is capable of generating high-quality adversarial examples substantially faster (one order of magnitude less in time) than state-of-the-art attacking methods. These examples also preserve the original sentiment according to human evaluation. Additionally, our framework produces an improved classifier that is robust in defending against multiple adversarial attacking methods. Code is available at: https://github.com/ibm-aur-nlp/adv-def-text-dist.

Xu Zhong, Elaheh ShafieiBavani, Antonio Jimeno Yepes

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

Xu Zhong, Jianbin Tang, Antonio Jimeno Yepes

Recognizing the layout of unstructured digital documents is an important step when parsing the documents into structured machine-readable format for downstream applications. Deep neural networks that are developed for computer vision have been proven to be an effective method to analyze layout of document images. However, document layout datasets that are currently publicly available are several magnitudes smaller than established computing vision datasets. Models have to be trained by transfer learning from a base model that is pre-trained on a traditional computer vision dataset. In this paper, we develop the PubLayNet dataset for document layout analysis by automatically matching the XML representations and the content of over 1 million PDF articles that are publicly available on PubMed Central. The size of the dataset is comparable to established computer vision datasets, containing over 360 thousand document images, where typical document layout elements are annotated. The experiments demonstrate that deep neural networks trained on PubLayNet accurately recognize the layout of scientific articles. The pre-trained models are also a more effective base mode for transfer learning on a different document domain. We release the dataset (https://github.com/ibm-aur-nlp/PubLayNet) to support development and evaluation of more advanced models for document layout analysis.

Antonio Jimeno Yepes, Yao You, Jan Milczek et al.

Chunking information is a key step in Retrieval Augmented Generation (RAG). Current research primarily centers on paragraph-level chunking. This approach treats all texts as equal and neglects the information contained in the structure of documents. We propose an expanded approach to chunk documents by moving beyond mere paragraph-level chunking to chunk primary by structural element components of documents. Dissecting documents into these constituent elements creates a new way to chunk documents that yields the best chunk size without tuning. We introduce a novel framework that evaluates how chunking based on element types annotated by document understanding models contributes to the overall context and accuracy of the information retrieved. We also demonstrate how this approach impacts RAG assisted Question & Answer task performance. Our research includes a comprehensive analysis of various element types, their role in effective information retrieval, and the impact they have on the quality of RAG outputs. Findings support that element type based chunking largely improve RAG results on financial reporting. Through this research, we are also able to answer how to uncover highly accurate RAG.

Antonio Jimeno Yepes, Pieter Barnard

Large Language Models (LLMs) have unveiled remarkable capabilities in understanding and generating both natural language and code, but LLM reasoning is prone to hallucination and struggle with complex, novel scenarios, often getting stuck on partial or incorrect solutions. However, the inherent ability of Evolutionary Algorithms (EAs) to explore extensive and complex search spaces makes them particularly effective in scenarios where traditional optimization methodologies may falter. However, EAs explore a vast search space when applied to complex problems. To address the computational bottleneck of evaluating large populations, particularly crucial for complex evolutionary tasks, we introduce a highly efficient evaluation framework. This implementation maintains compatibility with existing primitive definitions, ensuring the generation of valid individuals. Using LLMs, we propose an enhanced evolutionary search strategy that enables a more focused exploration of expansive solution spaces. LLMs facilitate the generation of superior candidate solutions, as evidenced by empirical results demonstrating their efficacy in producing improved outcomes.

Renyu Li, Antonio Jimeno Yepes, Yao You et al.

Multi-modal generative document parsing systems challenge traditional evaluation: unlike deterministic OCR or layout models, they often produce semantically correct yet structurally divergent outputs. Conventional metrics-CER, WER, IoU, or TEDS-misclassify such diversity as error, penalizing valid interpretations and obscuring system behavior. We introduce SCORE (Structural and COntent Robust Evaluation), an interpretation-agnostic framework that integrates (i) adjusted edit distance for robust content fidelity, (ii) token-level diagnostics to distinguish hallucinations from omissions, (iii) table evaluation with spatial tolerance and semantic alignment, and (iv) hierarchy-aware consistency checks. Together, these dimensions enable evaluation that embraces representational diversity while enforcing semantic rigor. Across 1,114 pages spanning a holistic benchmark and a field dataset, SCORE consistently revealed cross-dataset performance patterns missed by standard metrics. In 2-5% of pages with ambiguous table structures, traditional metrics penalized systems by 12-25% on average, leading to distorted rankings. SCORE corrected these cases, recovering equivalence between alternative but valid interpretations. Moreover, by normalizing generative outputs into a format-agnostic representation, SCORE reproduces traditional scores (e.g., table F1 up to 0.93) without requiring object-detection pipelines, demonstrating that generative parsing alone suffices for comprehensive evaluation. By exposing how interpretive diversity impacts evaluation outcomes and providing multi-dimensional, interpretable diagnostics, SCORE establishes foundational principles for semantically grounded, fair, and practical benchmarking of modern document parsing systems.

Antonio Jimeno Yepes

Deep learning methods minimise the empirical risk using loss functions such as the cross entropy loss. When minimising the empirical risk, the generalisation of the learnt function still depends on the performance on the training data, the Vapnik-Chervonenkis(VC)-dimension of the function and the number of training examples. Neural networks have a large number of parameters, which correlates with their VC-dimension that is typically large but not infinite, and typically a large number of training instances are needed to effectively train them. In this work, we explore how to optimize feature mappings using neural network with the intention to reduce the effective VC-dimension of the hyperplane found in the space generated by the mapping. An interpretation of the results of this study is that it is possible to define a loss that controls the VC-dimension of the separating hyperplane. We evaluate this approach and observe that the performance when using this method improves when the size of the training set is small.

Antonio Jimeno Yepes, Xu Zhong, Douglas Burdick

Scientific literature contain important information related to cutting-edge innovations in diverse domains. Advances in natural language processing have been driving the fast development in automated information extraction from scientific literature. However, scientific literature is often available in unstructured PDF format. While PDF is great for preserving basic visual elements, such as characters, lines, shapes, etc., on a canvas for presentation to humans, automatic processing of the PDF format by machines presents many challenges. With over 2.5 trillion PDF documents in existence, these issues are prevalent in many other important application domains as well. Our ICDAR 2021 Scientific Literature Parsing Competition (ICDAR2021-SLP) aims to drive the advances specifically in document understanding. ICDAR2021-SLP leverages the PubLayNet and PubTabNet datasets, which provide hundreds of thousands of training and evaluation examples. In Task A, Document Layout Recognition, submissions with the highest performance combine object detection and specialised solutions for the different categories. In Task B, Table Recognition, top submissions rely on methods to identify table components and post-processing methods to generate the table structure and content. Results from both tasks show an impressive performance and opens the possibility for high performance practical applications.

Simon Šuster, Karin Verspoor, Timothy Baldwin et al.

The COVID-19 pandemic has driven ever-greater demand for tools which enable efficient exploration of biomedical literature. Although semi-structured information resulting from concept recognition and detection of the defining elements of clinical trials (e.g. PICO criteria) has been commonly used to support literature search, the contributions of this abstraction remain poorly understood, especially in relation to text-based retrieval. In this study, we compare the results retrieved by a standard search engine with those filtered using clinically-relevant concepts and their relations. With analysis based on the annotations from the TREC-COVID shared task, we obtain quantitative as well as qualitative insights into characteristics of relational and concept-based literature exploration. Most importantly, we find that the relational concept selection filters the original retrieved collection in a way that decreases the proportion of unjudged documents and increases the precision, which means that the user is likely to be exposed to a larger number of relevant documents.

David Martinez Iraola, Antonio Jimeno Yepes

The focus of this paper is to address the knowledge acquisition bottleneck for Named Entity Recognition (NER) of mutations, by analysing different approaches to build manually-annotated data. We address first the impact of using a single annotator vs two annotators, in order to measure whether multiple annotators are required. Once we evaluate the performance loss when using a single annotator, we apply different methods to sample the training data for second annotation, aiming at improving the quality of the dataset without requiring a full pass. We use held-out double-annotated data to build two scenarios with different types of rankings: similarity-based and confidence based. We evaluate both approaches on: (i) their ability to identify training instances that are erroneous (cases where single-annotator labels differ from double-annotation after discussion), and (ii) on Mutation NER performance for state-of-the-art classifiers after integrating the fixes at different thresholds.

Stefan Maetschke, David Martinez Iraola, Pieter Barnard et al.

Current Artificial Intelligence (AI) methods, most based on deep learning, have facilitated progress in several fields, including computer vision and natural language understanding. The progress of these AI methods is measured using benchmarks designed to solve challenging tasks, such as visual question answering. A question remains of how much understanding is leveraged by these methods and how appropriate are the current benchmarks to measure understanding capabilities. To answer these questions, we have analysed existing benchmarks and their understanding capabilities, defined by a set of understanding capabilities, and current research streams. We show how progress has been made in benchmark development to measure understanding capabilities of AI methods and we review as well how current methods develop understanding capabilities.

Karin Verspoor, Simon Šuster, Yulia Otmakhova et al.

We present COVID-SEE, a system for medical literature discovery based on the concept of information exploration, which builds on several distinct text analysis and natural language processing methods to structure and organise information in publications, and augments search by providing a visual overview supporting exploration of a collection to identify key articles of interest. We developed this system over COVID-19 literature to help medical professionals and researchers explore the literature evidence, and improve findability of relevant information. COVID-SEE is available at http://covid-see.com.

Elaheh ShafieiBavani, Antonio Jimeno Yepes, Xu Zhong et al.

Due to the exponential growth of biomedical literature, event and relation extraction are important tasks in biomedical text mining. Most work only focus on relation extraction, and detect a single entity pair mention on a short span of text, which is not ideal due to long sentences that appear in biomedical contexts. We propose an approach to both relation and event extraction, for simultaneously predicting relationships between all mention pairs in a text. We also perform an empirical study to discuss different network setups for this purpose. The best performing model includes a set of multi-head attentions and convolutions, an adaptation of the transformer architecture, which offers self-attention the ability to strengthen dependencies among related elements, and models the interaction between features extracted by multiple attention heads. Experiment results demonstrate that our approach outperforms the state of the art on a set of benchmark biomedical corpora including BioNLP 2009, 2011, 2013 and BioCreative 2017 shared tasks.

Antonio Jimeno Yepes

Named entity recognition (NER) is used to identify relevant entities in text. A bidirectional LSTM (long short term memory) encoder with a neural conditional random fields (CRF) decoder (biLSTM-CRF) is the state of the art methodology. In this work, we have done an analysis of several methods that intend to optimize the performance of networks based on this architecture, which in some cases encourage overfitting avoidance. These methods target exploration of parameter space, regularization of LSTMs and penalization of confident output distributions. Results show that the optimization methods improve the performance of the biLSTM-CRF NER baseline system, setting a new state of the art performance for the CoNLL-2003 Spanish set with an F1 of 87.18.

Quan Tran, Andrew MacKinlay, Antonio Jimeno Yepes

Recurrent Neural Network models are the state-of-the-art for Named Entity Recognition (NER). We present two innovations to improve the performance of these models. The first innovation is the introduction of residual connections between the Stacked Recurrent Neural Network model to address the degradation problem of deep neural networks. The second innovation is a bias decoding mechanism that allows the trained system to adapt to non-differentiable and externally computed objectives, such as the entity-based F-measure. Our work improves the state-of-the-art results for both Spanish and English languages on the standard train/development/test split of the CoNLL 2003 Shared Task NER dataset.

Antonio Jimeno Yepes, Jianbin Tang, Benjamin Scott Mashford

Deep Neural Networks (DNN) achieve human level performance in many image analytics tasks but DNNs are mostly deployed to GPU platforms that consume a considerable amount of power. New hardware platforms using lower precision arithmetic achieve drastic reductions in power consumption. More recently, brain-inspired spiking neuromorphic chips have achieved even lower power consumption, on the order of milliwatts, while still offering real-time processing. However, for deploying DNNs to energy efficient neuromorphic chips the incompatibility between continuous neurons and synaptic weights of traditional DNNs, discrete spiking neurons and synapses of neuromorphic chips need to be overcome. Previous work has achieved this by training a network to learn continuous probabilities, before it is deployed to a neuromorphic architecture, such as IBM TrueNorth Neurosynaptic System, by random sampling these probabilities. The main contribution of this paper is a new learning algorithm that learns a TrueNorth configuration ready for deployment. We achieve this by training directly a binary hardware crossbar that accommodates the TrueNorth axon configuration constrains and we propose a different neuron model. Results of our approach trained on electroencephalogram (EEG) data show a significant improvement with previous work (76% vs 86% accuracy) while maintaining state of the art performance on the MNIST handwritten data set.

A. K. M. Sabbir, Antonio Jimeno Yepes, Ramakanth Kavuluru

Biomedical word sense disambiguation (WSD) is an important intermediate task in many natural language processing applications such as named entity recognition, syntactic parsing, and relation extraction. In this paper, we employ knowledge-based approaches that also exploit recent advances in neural word/concept embeddings to improve over the state-of-the-art in biomedical WSD using the MSH WSD dataset as the test set. Our methods involve weak supervision - we do not use any hand-labeled examples for WSD to build our prediction models; however, we employ an existing well known named entity recognition and concept mapping program, MetaMap, to obtain our concept vectors. Over the MSH WSD dataset, our linear time (in terms of numbers of senses and words in the test instance) method achieves an accuracy of 92.24% which is an absolute 3% improvement over the best known results obtained via unsupervised or knowledge-based means. A more expensive approach that we developed relies on a nearest neighbor framework and achieves an accuracy of 94.34%. Employing dense vector representations learned from unlabeled free text has been shown to benefit many language processing tasks recently and our efforts show that biomedical WSD is no exception to this trend. For a complex and rapidly evolving domain such as biomedicine, building labeled datasets for larger sets of ambiguous terms may be impractical. Here, we show that weak supervision that leverages recent advances in representation learning can rival supervised approaches in biomedical WSD. However, external knowledge bases (here sense inventories) play a key role in the improvements achieved.

Antonio Jimeno Yepes, Jianbin Tang

Deep Neural Networks (DNN) have achieved human level performance in many image analytics tasks but DNNs are mostly deployed to GPU platforms that consume a considerable amount of power. Brain-inspired spiking neuromorphic chips consume low power and can be highly parallelized. However, for deploying DNNs to energy efficient neuromorphic chips the incompatibility between continuous neurons and synaptic weights of traditional DNNs, discrete spiking neurons and synapses of neuromorphic chips has to be overcome. Previous work has achieved this by training a network to learn continuous probabilities and deployment to a neuromorphic architecture by random sampling these probabilities. An ensemble of sampled networks is needed to approximate the performance of the trained network. In the work presented in this paper, we have extended previous research by directly learning binary synaptic crossbars. Results on MNIST show that better performance can be achieved with a small network in one time step (92.7% maximum observed accuracy vs 95.98% accuracy in our work). Top results on a larger network are similar to previously published results (99.42% maximum observed accuracy vs 99.45% accuracy in our work). More importantly, in our work a smaller ensemble is needed to achieve similar or better accuracy than previous work, which translates into significantly decreased energy consumption for both networks. Results of our work are stable since they do not require random sampling.

Antonio Jimeno Yepes

Word sense disambiguation helps identifying the proper sense of ambiguous words in text. With large terminologies such as the UMLS Metathesaurus ambiguities appear and highly effective disambiguation methods are required. Supervised learning algorithm methods are used as one of the approaches to perform disambiguation. Features extracted from the context of an ambiguous word are used to identify the proper sense of such a word. The type of features have an impact on machine learning methods, thus affect disambiguation performance. In this work, we have evaluated several types of features derived from the context of the ambiguous word and we have explored as well more global features derived from MEDLINE using word embeddings. Results show that word embeddings improve the performance of more traditional features and allow as well using recurrent neural network classifiers based on Long-Short Term Memory (LSTM) nodes. The combination of unigrams and word embeddings with an SVM sets a new state of the art performance with a macro accuracy of 95.97 in the MSH WSD data set.