Pieter Fivez


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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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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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Mapping probability word problems to executable representations
Simon Suster | Pieter Fivez | Pietro Totis | Angelika Kimmig | Jesse Davis | Luc de Raedt | Walter Daelemans
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

While solving math word problems automatically has received considerable attention in the NLP community, few works have addressed probability word problems specifically. In this paper, we employ and analyse various neural models for answering such word problems. In a two-step approach, the problem text is first mapped to a formal representation in a declarative language using a sequence-to-sequence model, and then the resulting representation is executed using a probabilistic programming system to provide the answer. Our best performing model incorporates general-domain contextualised word representations that were finetuned using transfer learning on another in-domain dataset. We also apply end-to-end models to this task, which bring out the importance of the two-step approach in obtaining correct solutions to probability problems.

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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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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.