A common approach to automatically assigning diagnostic and procedural clinical codes to health records is to solve the task as a multi-label classification problem. Difficulties associated with this task stem from domain knowledge requirements, long document texts, large and imbalanced label space, reflecting the breadth and dependencies between medical diagnoses and procedures. Decisions in the healthcare domain also need to demonstrate sound reasoning, both when they are correct and when they are erroneous. Existing works address some of these challenges by incorporating external knowledge, which can be encoded into a graph-structured format. Incorporating graph structures on the output label space or between the input document and output label spaces have shown promising results in medical codes classification. Limited focus has been put on utilizing graph-based representation on the input document space. To partially bridge this gap, we represent clinical texts as graph-structured data through the UMLS Metathesaurus; we explore implicit graph representation through pre-trained knowledge graph embeddings and explicit domain-knowledge guided encoding of document concepts and relational information through graph neural networks. Our findings highlight the benefits of pre-trained knowledge graph embeddings in understanding model’s attention-based reasoning. In contrast, transparent domain knowledge guidance in graph encoder approaches is overshadowed by performance loss. Our qualitative analysis identifies limitations that contribute to prediction errors.

Temporal knowledge graph completion (TKGC) has become a popular approach for reasoning over the event and temporal knowledge graphs, targeting the completion of knowledge with accurate but missing information. In this context, tensor decomposition has successfully modeled interactions between entities and relations. Their effectiveness in static knowledge graph completion motivates us to introduce Time-LowFER, a family of parameter-efficient and time-aware extensions of the low-rank tensor factorization model LowFER. Noting several limitations in current approaches to represent time, we propose a cycle-aware time-encoding scheme for time features, which is model-agnostic and offers a more generalized representation of time. We implement our methods in a unified temporal knowledge graph embedding framework, focusing on time-sensitive data processing. The experiments show that our proposed methods perform on par or better than the state-of-the-art semantic matching models on two benchmarks.

Despite the advances in digital healthcare systems offering curated structured knowledge, much of the critical information still lies in large volumes of unlabeled and unstructured clinical texts. These texts, which often contain protected health information (PHI), are exposed to information extraction tools for downstream applications, risking patient identification. Existing works in de-identification rely on using large-scale annotated corpora in English, which often are not suitable in real-world multilingual settings. Pre-trained language models (LM) have shown great potential for cross-lingual transfer in low-resource settings. In this work, we empirically show the few-shot cross-lingual transfer property of LMs for named entity recognition (NER) and apply it to solve a low-resource and real-world challenge of code-mixed (Spanish-Catalan) clinical notes de-identification in the stroke domain. We annotate a gold evaluation dataset to assess few-shot setting performance where we only use a few hundred labeled examples for training. Our model improves the zero-shot F1-score from 73.7% to 91.2% on the gold evaluation set when adapting Multilingual BERT (mBERT) (CITATION) from the MEDDOCAN (CITATION) corpus with our few-shot cross-lingual target corpus. When generalized to an out-of-sample test set, the best model achieves a human-evaluation F1-score of 97.2%.

Relation extraction in the biomedical domain is challenging due to the lack of labeled data and high annotation costs, needing domain experts. Distant supervision is commonly used to tackle the scarcity of annotated data by automatically pairing knowledge graph relationships with raw texts. Such a pipeline is prone to noise and has added challenges to scale for covering a large number of biomedical concepts. We investigated existing broad-coverage distantly supervised biomedical relation extraction benchmarks and found a significant overlap between training and test relationships ranging from 26% to 86%. Furthermore, we noticed several inconsistencies in the data construction process of these benchmarks, and where there is no train-test leakage, the focus is on interactions between narrower entity types. This work presents a more accurate benchmark MedDistant19 for broad-coverage distantly supervised biomedical relation extraction that addresses these shortcomings and is obtained by aligning the MEDLINE abstracts with the widely used SNOMED Clinical Terms knowledge base. Lacking thorough evaluation with domain-specific language models, we also conduct experiments validating general domain relation extraction findings to biomedical relation extraction.

Recent advances in deep transformer models have achieved state-of-the-art in several natural language processing (NLP) tasks, whereas named entity recognition (NER) has traditionally benefited from long-short term memory (LSTM) networks. In this work, we present a Transformers based Transfer Learning framework for Named Entity Recognition (T2NER) created in PyTorch for the task of NER with deep transformer models. The framework is built upon the Transformers library as the core modeling engine and supports several transfer learning scenarios from sequential transfer to domain adaptation, multi-task learning, and semi-supervised learning. It aims to bridge the gap between the algorithmic advances in these areas by combining them with the state-of-the-art in transformer models to provide a unified platform that is readily extensible and can be used for both the transfer learning research in NER, and for real-world applications. The framework is available at: https://github.com/suamin/t2ner.

There has been a significant progress in the field of Extractive Question Answering (EQA) in the recent years. However, most of them are reliant on annotations of answer-spans in the corresponding passages. In this work, we address the problem of EQA when no annotations are present for the answer span, i.e., when the dataset contains only questions and corresponding passages. Our method is based on auto-encoding of the question that performs a question answering task during encoding and a question generation task during decoding. We show that our method performs well in a zero-shot setting and can provide an additional loss to boost performance for EQA.

Fact triples are a common form of structured knowledge used within the biomedical domain. As the amount of unstructured scientific texts continues to grow, manual annotation of these texts for the task of relation extraction becomes increasingly expensive. Distant supervision offers a viable approach to combat this by quickly producing large amounts of labeled, but considerably noisy, data. We aim to reduce such noise by extending an entity-enriched relation classification BERT model to the problem of multiple instance learning, and defining a simple data encoding scheme that significantly reduces noise, reaching state-of-the-art performance for distantly-supervised biomedical relation extraction. Our approach further encodes knowledge about the direction of relation triples, allowing for increased focus on relation learning by reducing noise and alleviating the need for joint learning with knowledge graph completion.

Contextualized word embeddings provide better initialization for neural networks that deal with various natural language understanding (NLU) tasks including Question Answering (QA) and more recently, Question Generation(QG). Apart from providing meaningful word representations, pre-trained transformer models (Vaswani et al., 2017), such as BERT (Devlin et al., 2019) also provide self-attentions which encode syntactic information that can be probed for dependency parsing (Hewitt and Manning, 2019) and POStagging (Coenen et al., 2019). In this paper, we show that the information from selfattentions of BERT are useful for language modeling of questions conditioned on paragraph and answer phrases. To control the attention span, we use semi-diagonal mask and utilize a shared model for encoding and decoding, unlike sequence-to-sequence. We further employ copy-mechanism over self-attentions to acheive state-of-the-art results for Question Generation on SQuAD v1.1 (Rajpurkar et al., 2016).