There is vivid research on adapting Large Language Models (LLMs) to perform a variety of tasks in high-stakes domains such as healthcare. Despite their popularity, there is a lack of understanding of the extent and contributing factors that allow LLMs to recall relevant knowledge and combine it with presented information in the clinical and biomedical domain: a fundamental pre-requisite for success on down-stream tasks.Addressing this gap, we use Multiple Choice and Abstractive Question Answering to conduct a large-scale empirical study on 22 datasets in three generalist and three specialist biomedical sub-domains. Our multifaceted analysis of the performance of 15 LLMs, further broken down by sub-domain, source of knowledge and model architecture, uncovers success factors such as instruction tuning that lead to improved recall and comprehension. We further show that while recently proposed domain-adapted models may lack adequate knowledge, directly fine-tuning on our collected medical knowledge datasets shows encouraging results, even generalising to unseen specialist sub-domains. We complement the quantitative results with a skill-oriented manual error analysis, which reveals a significant gap between the models’ capabilities to simply recall necessary knowledge and to integrate it with the presented context.To foster research and collaboration in this field we share M-QALM, our resources, standardised methodology, and evaluation results, with the research community to facilitate further advancements in clinical knowledge representation learning within language models.

Sentence representations are a critical component in NLP applications such as retrieval, question answering, and text classification. They capture the meaning of a sentence, enabling machines to understand and reason over human language. In recent years, significant progress has been made in developing methods for learning sentence representations, including unsupervised, supervised, and transfer learning approaches. However there is no literature review on sentence representations till now. In this paper, we provide an overview of the different methods for sentence representation learning, focusing mostly on deep learning models. We provide a systematic organization of the literature, highlighting the key contributions and challenges in this area. Overall, our review highlights the importance of this area in natural language processing, the progress made in sentence representation learning, and the challenges that remain. We conclude with directions for future research, suggesting potential avenues for improving the quality and efficiency of sentence representations.

Medical progress notes play a crucial role in documenting a patient’s hospital journey, including his or her condition, treatment plan, and any updates for healthcare providers. Automatic summarisation of a patient’s problems in the form of a “problem list” can aid stakeholders in understanding a patient’s condition, reducing workload and cognitive bias. BioNLP 2023 Shared Task 1A focusses on generating a list of diagnoses and problems from the provider’s progress notes during hospitalisation. In this paper, we introduce our proposed approach to this task, which integrates two complementary components. One component employs large language models (LLMs) for data augmentation; the other is an abstractive summarisation LLM with a novel pre-training objective for generating the patients’ problems summarised as a list. Our approach was ranked second among all submissions to the shared task. The performance of our model on the development and test datasets shows that our approach is more robust on unknown data, with an improvement of up to 3.1 points over the same size of the larger model.

Clinical notes in healthcare facilities are tagged with the International Classification of Diseases (ICD) code; a list of classification codes for medical diagnoses and procedures. ICD coding is a challenging multilabel text classification problem due to noisy clinical document inputs and long-tailed label distribution. Recent automated ICD coding efforts improve performance by encoding medical notes and codes with additional data and knowledge bases. However, most of them do not reflect how human coders generate the code: first, the coders select general code categories and then look for specific subcategories that are relevant to a patient’s condition. Inspired by this, we propose a two-stage decoding mechanism to predict ICD codes. Our model uses the hierarchical properties of the codes to split the prediction into two steps: At first, we predict the parent code and then predict the child code based on the previous prediction. Experiments on the public MIMIC-III data set have shown that our model performs well in single-model settings without external data or knowledge.

We propose two methods to make unsupervised domain adaptation (UDA) more parameter efficient using adapters – small bottleneck layers interspersed with every layer of the large-scale pre-trained language model (PLM). The first method deconstructs UDA into a two-step process: first by adding a domain adapter to learn domain-invariant information and then by adding a task adapter that uses domain-invariant information to learn task representations in the source domain. The second method jointly learns a supervised classifier while reducing the divergence measure. Compared to strong baselines, our simple methods perform well in natural language inference (MNLI) and the cross-domain sentiment classification task. We even outperform unsupervised domain adaptation methods such as DANN and DSN in sentiment classification, and we are within 0.85% F1 for natural language inference task, by fine-tuning only a fraction of the full model parameters. We release our code at this URL.

Automatic transfer of text between domains has become popular in recent times. One of its aims is to preserve the semantic content while adapting to the target domain. However, it does not explicitly maintain other attributes between the source and translated text: e.g., text length and descriptiveness. Maintaining constraints in transfer has several downstream applications, including data augmentation and debiasing. We introduce a method for such constrained unsupervised text style transfer by introducing two complementary losses to the generative adversarial network (GAN) family of models. Unlike the competing losses used in GANs, we introduce cooperative losses where the discriminator and the generator cooperate and reduce the same loss. The first is a contrastive loss and the second is a classification loss — aiming to regularize the latent space further and bring similar sentences closer together. We demonstrate that such training retains lexical, syntactic and domain-specific constraints between domains for multiple benchmark datasets, including ones where more than one attribute change. We show that the complementary cooperative losses improve text quality, according to both automated and human evaluation measures.

Logical structure recovery in scientific articles associates text with a semantic section of the article. Although previous work has disregarded the surrounding context of a line, we model this important information by employing line-level attention on top of a transformer-based scientific document processing pipeline. With the addition of loss function engineering and data augmentation techniques with semi-supervised learning, our method improves classification performance by 10% compared to a recent state-of-the-art model. Our parsimonious, text-only method achieves a performance comparable to that of other works that use rich document features such as font and spatial position, using less data without sacrificing performance, resulting in a lightweight training pipeline.

Domain divergence plays a significant role in estimating the performance of a model in new domains. While there is a significant literature on divergence measures, researchers find it hard to choose an appropriate divergence for a given NLP application. We address this shortcoming by both surveying the literature and through an empirical study. We develop a taxonomy of divergence measures consisting of three classes — Information-theoretic, Geometric, and Higher-order measures and identify the relationships between them. Further, to understand the common use-cases of these measures, we recognise three novel applications – 1) Data Selection, 2) Learning Representation, and 3) Decisions in the Wild – and use it to organise our literature. From this, we identify that Information-theoretic measures are prevalent for 1) and 3), and Higher-order measures are more common for 2). To further help researchers choose appropriate measures to predict drop in performance – an important aspect of Decisions in the Wild, we perform correlation analysis spanning 130 domain adaptation scenarios, 3 varied NLP tasks and 12 divergence measures identified from our survey. To calculate these divergences, we consider the current contextual word representations (CWR) and contrast with the older distributed representations. We find that traditional measures over word distributions still serve as strong baselines, while higher-order measures with CWR are effective.

The robustness of pretrained language models(PLMs) is generally measured using performance drops on two or more domains. However, we do not yet understand the inherent robustness achieved by contributions from different layers of a PLM. We systematically analyze the robustness of these representations layer by layer from two perspectives. First, we measure the robustness of representations by using domain divergence between two domains. We find that i) Domain variance increases from the lower to the upper layers for vanilla PLMs; ii) Models continuously pretrained on domain-specific data (DAPT)(Gururangan et al., 2020) exhibit more variance than their pretrained PLM counterparts; and that iii) Distilled models (e.g., DistilBERT) also show greater domain variance. Second, we investigate the robustness of representations by analyzing the encoded syntactic and semantic information using diagnostic probes. We find that similar layers have similar amounts of linguistic information for data from an unseen domain.

We introduce SciWING, an open-source soft-ware toolkit which provides access to state-of-the-art pre-trained models for scientific document processing (SDP) tasks, such as citation string parsing, logical structure recovery and citation intent classification. Compared to other toolkits, SciWING follows a full neural pipeline and provides a Python inter-face for SDP. When needed, SciWING provides fine-grained control for rapid experimentation with different models by swapping and stacking different modules. Transfer learning from general and scientific documents specific pre-trained transformers (i.e., BERT, SciBERT, etc.) can be performed. SciWING incorporates ready-to-use web and terminal-based applications and demonstrations to aid adoption and development. The toolkit is available from http://sciwing.io and the demos are available at http://rebrand.ly/sciwing-demo.