Simon Suster

Also published as: Simon Šuster


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Integrating Higher-Level Semantics into Robust Biomedical Name Representations
Pieter Fivez | Simon Suster | Walter Daelemans
Proceedings of the 12th International Workshop on Health Text Mining and Information Analysis

Neural encoders of biomedical names are typically considered robust if representations can be effectively exploited for various downstream NLP tasks. To achieve this, encoders need to model domain-specific biomedical semantics while rivaling the universal applicability of pretrained self-supervised representations. Previous work on robust representations has focused on learning low-level distinctions between names of fine-grained biomedical concepts. These fine-grained concepts can also be clustered together to reflect higher-level, more general semantic distinctions, such as grouping the names nettle sting and tick-borne fever together under the description puncture wound of skin. It has not yet been empirically confirmed that training biomedical name encoders on fine-grained distinctions automatically leads to bottom-up encoding of such higher-level semantics. In this paper, we show that this bottom-up effect exists, but that it is still relatively limited. As a solution, we propose a scalable multi-task training regime for biomedical name encoders which can also learn robust representations using only higher-level semantic classes. These representations can generalise both bottom-up as well as top-down among various semantic hierarchies. Moreover, we show how they can be used out-of-the-box for improved unsupervised detection of hypernyms, while retaining robust performance on various semantic relatedness benchmarks.

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Conceptual Grounding Constraints for Truly Robust Biomedical Name Representations
Pieter Fivez | Simon Suster | Walter Daelemans
Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume

Effective representation of biomedical names for downstream NLP tasks requires the encoding of both lexical as well as domain-specific semantic information. Ideally, the synonymy and semantic relatedness of names should be consistently reflected by their closeness in an embedding space. To achieve such robustness, prior research has considered multi-task objectives when training neural encoders. In this paper, we take a next step towards truly robust representations, which capture more domain-specific semantics while remaining universally applicable across different biomedical corpora and domains. To this end, we use conceptual grounding constraints which more effectively align encoded names to pretrained embeddings of their concept identifiers. These constraints are effective even when using a Deep Averaging Network, a simple feedforward encoding architecture that allows for scaling to large corpora while remaining sufficiently expressive. We empirically validate our approach using multiple tasks and benchmarks, which assess both literal synonymy as well as more general semantic relatedness.

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Scalable Few-Shot Learning of Robust Biomedical Name Representations
Pieter Fivez | Simon Suster | Walter Daelemans
Proceedings of the 20th Workshop on Biomedical Language Processing

Recent research on robust representations of biomedical names has focused on modeling large amounts of fine-grained conceptual distinctions using complex neural encoders. In this paper, we explore the opposite paradigm: training a simple encoder architecture using only small sets of names sampled from high-level biomedical concepts. Our encoder post-processes pretrained representations of biomedical names, and is effective for various types of input representations, both domain-specific or unsupervised. We validate our proposed few-shot learning approach on multiple biomedical relatedness benchmarks, and show that it allows for continual learning, where we accumulate information from various conceptual hierarchies to consistently improve encoder performance. Given these findings, we propose our approach as a low-cost alternative for exploring the impact of conceptual distinctions on robust biomedical name representations.

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Are we there yet? Exploring clinical domain knowledge of BERT models
Madhumita Sushil | Simon Suster | Walter Daelemans
Proceedings of the 20th Workshop on Biomedical Language Processing

We explore whether state-of-the-art BERT models encode sufficient domain knowledge to correctly perform domain-specific inference. Although BERT implementations such as BioBERT are better at domain-based reasoning than those trained on general-domain corpora, there is still a wide margin compared to human performance on these tasks. To bridge this gap, we explore whether supplementing textual domain knowledge in the medical NLI task: a) by further language model pretraining on the medical domain corpora, b) by means of lexical match algorithms such as the BM25 algorithm, c) by supplementing lexical retrieval with dependency relations, or d) by using a trained retriever module, can push this performance closer to that of humans. We do not find any significant difference between knowledge supplemented classification as opposed to the baseline BERT models, however. This is contrary to the results for evidence retrieval on other tasks such as open domain question answering (QA). By examining the retrieval output, we show that the methods fail due to unreliable knowledge retrieval for complex domain-specific reasoning. We conclude that the task of unsupervised text retrieval to bridge the gap in existing information to facilitate inference is more complex than what the state-of-the-art methods can solve, and warrants extensive research in the future.

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Contextual explanation rules for neural clinical classifiers
Madhumita Sushil | Simon Suster | Walter Daelemans
Proceedings of the 20th Workshop on Biomedical Language Processing

Several previous studies on explanation for recurrent neural networks focus on approaches that find the most important input segments for a network as its explanations. In that case, the manner in which these input segments combine with each other to form an explanatory pattern remains unknown. To overcome this, some previous work tries to find patterns (called rules) in the data that explain neural outputs. However, their explanations are often insensitive to model parameters, which limits the scalability of text explanations. To overcome these limitations, we propose a pipeline to explain RNNs by means of decision lists (also called rules) over skipgrams. For evaluation of explanations, we create a synthetic sepsis-identification dataset, as well as apply our technique on additional clinical and sentiment analysis datasets. We find that our technique persistently achieves high explanation fidelity and qualitatively interpretable rules.


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Improved Topic Representations of Medical Documents to Assist COVID-19 Literature Exploration
Yulia Otmakhova | Karin Verspoor | Timothy Baldwin | Simon Šuster
Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020

Efficient discovery and exploration of biomedical literature has grown in importance in the context of the COVID-19 pandemic, and topic-based methods such as latent Dirichlet allocation (LDA) are a useful tool for this purpose. In this study we compare traditional topic models based on word tokens with topic models based on medical concepts, and propose several ways to improve topic coherence and specificity.


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CliCR: a Dataset of Clinical Case Reports for Machine Reading Comprehension
Simon Šuster | Walter Daelemans
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers)

We present a new dataset for machine comprehension in the medical domain. Our dataset uses clinical case reports with around 100,000 gap-filling queries about these cases. We apply several baselines and state-of-the-art neural readers to the dataset, and observe a considerable gap in performance (20% F1) between the best human and machine readers. We analyze the skills required for successful answering and show how reader performance varies depending on the applicable skills. We find that inferences using domain knowledge and object tracking are the most frequently required skills, and that recognizing omitted information and spatio-temporal reasoning are the most difficult for the machines.

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Rule induction for global explanation of trained models
Madhumita Sushil | Simon Šuster | Walter Daelemans
Proceedings of the 2018 EMNLP Workshop BlackboxNLP: Analyzing and Interpreting Neural Networks for NLP

Understanding the behavior of a trained network and finding explanations for its outputs is important for improving the network’s performance and generalization ability, and for ensuring trust in automated systems. Several approaches have previously been proposed to identify and visualize the most important features by analyzing a trained network. However, the relations between different features and classes are lost in most cases. We propose a technique to induce sets of if-then-else rules that capture these relations to globally explain the predictions of a network. We first calculate the importance of the features in the trained network. We then weigh the original inputs with these feature importance scores, simplify the transformed input space, and finally fit a rule induction model to explain the model predictions. We find that the output rule-sets can explain the predictions of a neural network trained for 4-class text classification from the 20 newsgroups dataset to a macro-averaged F-score of 0.80. We make the code available at

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Revisiting neural relation classification in clinical notes with external information
Simon Šuster | Madhumita Sushil | Walter Daelemans
Proceedings of the Ninth International Workshop on Health Text Mining and Information Analysis

Recently, segment convolutional neural networks have been proposed for end-to-end relation extraction in the clinical domain, achieving results comparable to or outperforming the approaches with heavy manual feature engineering. In this paper, we analyze the errors made by the neural classifier based on confusion matrices, and then investigate three simple extensions to overcome its limitations. We find that including ontological association between drugs and problems, and data-induced association between medical concepts does not reliably improve the performance, but that large gains are obtained by the incorporation of semantic classes to capture relation triggers.


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A Short Review of Ethical Challenges in Clinical Natural Language Processing
Simon Šuster | Stéphan Tulkens | Walter Daelemans
Proceedings of the First ACL Workshop on Ethics in Natural Language Processing

Clinical NLP has an immense potential in contributing to how clinical practice will be revolutionized by the advent of large scale processing of clinical records. However, this potential has remained largely untapped due to slow progress primarily caused by strict data access policies for researchers. In this paper, we discuss the concern for privacy and the measures it entails. We also suggest sources of less sensitive data. Finally, we draw attention to biases that can compromise the validity of empirical research and lead to socially harmful applications.

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Unsupervised Context-Sensitive Spelling Correction of Clinical Free-Text with Word and Character N-Gram Embeddings
Pieter Fivez | Simon Šuster | Walter Daelemans
BioNLP 2017

We present an unsupervised context-sensitive spelling correction method for clinical free-text that uses word and character n-gram embeddings. Our method generates misspelling replacement candidates and ranks them according to their semantic fit, by calculating a weighted cosine similarity between the vectorized representation of a candidate and the misspelling context. We greatly outperform two baseline off-the-shelf spelling correction tools on a manually annotated MIMIC-III test set, and counter the frequency bias of an optimized noisy channel model, showing that neural embeddings can be successfully exploited to include context-awareness in a spelling correction model.


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Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts
Stéphan Tulkens | Simon Suster | Walter Daelemans
Proceedings of the 15th Workshop on Biomedical Natural Language Processing

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Bilingual Learning of Multi-sense Embeddings with Discrete Autoencoders
Simon Šuster | Ivan Titov | Gertjan van Noord
Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies


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From neighborhood to parenthood: the advantages of dependency representation over bigrams in Brown clustering
Simon Šuster | Gertjan van Noord
Proceedings of COLING 2014, the 25th International Conference on Computational Linguistics: Technical Papers