M-QALM: A Benchmark to Assess Clinical Reading Comprehension and Knowledge Recall in Large Language Models via Question Answering

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.

Automated Clinical Coding for Outpatient Departments

Computerised clinical coding approaches aim to automate the process of assigning a set of codes to medical records. While there is active research pushing the state of the art on clinical coding for hospitalized patients, the outpatient setting -- where doctors tend to non-hospitalised patients -- is overlooked. Although both settings can be formalised as a multi-label classification task, they present unique and distinct challenges, which raises the question of whether the success of inpatient clinical coding approaches translates to the outpatient setting. This paper is the first to investigate how well state-of-the-art deep learning-based clinical coding approaches work in the outpatient setting at hospital scale. To this end, we collect a large outpatient dataset comprising over 7 million notes documenting over half a million patients. We adapt four state-of-the-art clinical coding approaches to this setting and evaluate their potential to assist coders. We find evidence that clinical coding in outpatient settings can benefit from more innovations in popular inpatient coding benchmarks. A deeper analysis of the factors contributing to the success -- amount and form of data and choice of document representation -- reveals the presence of easy-to-solve examples, the coding of which can be completely automated with a low error rate.

MaxEnt Loss: Constrained Maximum Entropy for Calibration under Out-of-Distribution Shift

We present a new loss function that addresses the out-of-distribution (OOD) calibration problem. While many objective functions have been proposed to effectively calibrate models in-distribution, our findings show that they do not always fare well OOD. Based on the Principle of Maximum Entropy, we incorporate helpful statistical constraints observed during training, delivering better model calibration without sacrificing accuracy. We provide theoretical analysis and show empirically that our method works well in practice, achieving state-of-the-art calibration on both synthetic and real-world benchmarks.

PULSAR at MEDIQA-Sum 2023: Large Language Models Augmented by Synthetic Dialogue Convert Patient Dialogues to Medical Records

This paper describes PULSAR, our system submission at the ImageClef 2023 MediQA-Sum task on summarising patient-doctor dialogues into clinical records. The proposed framework relies on domain-specific pre-training, to produce a specialised language model which is trained on task-specific natural data augmented by synthetic data generated by a black-box LLM. We find limited evidence towards the efficacy of domain-specific pre-training and data augmentation, while scaling up the language model yields the best performance gains. Our approach was ranked second and third among 13 submissions on task B of the challenge. Our code is available at https://github.com/yuping-wu/PULSAR.

PULSAR: Pre-training with Extracted Healthcare Terms for Summarising Patients' Problems and Data Augmentation with Black-box Large Language Models

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 focuses 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.

A Two-Stage Decoder for Efficient ICD Coding

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 show that our model performs well in single-model settings without external data or knowledge.

Beyond Words: A Comprehensive Survey of Sentence Representations

Sentence representations have become a critical component in natural language processing applications, such as retrieval, question answering, and text classification. They capture the semantics and 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. In this paper, we provide an overview of the different methods for sentence representation learning, including both traditional and deep learning-based techniques. We provide a systematic organization of the literature on sentence representation learning, highlighting the key contributions and challenges in this area. Overall, our review highlights the progress made in sentence representation learning, the importance of this area in natural language processing, and the challenges that remain. We conclude with directions for future research, suggesting potential avenues for improving the quality and efficiency of sentence representations in NLP applications.

Mimic-IV-ICD: A new benchmark for eXtreme MultiLabel Classification

Clinical notes are assigned ICD codes - sets of codes for diagnoses and procedures. In the recent years, predictive machine learning models have been built for automatic ICD coding. However, there is a lack of widely accepted benchmarks for automated ICD coding models based on large-scale public EHR data. This paper proposes a public benchmark suite for ICD-10 coding using a large EHR dataset derived from MIMIC-IV, the most recent public EHR dataset. We implement and compare several popular methods for ICD coding prediction tasks to standardize data preprocessing and establish a comprehensive ICD coding benchmark dataset. This approach fosters reproducibility and model comparison, accelerating progress toward employing automated ICD coding in future studies. Furthermore, we create a new ICD-9 benchmark using MIMIC-IV data, providing more data points and a higher number of ICD codes than MIMIC-III. Our open-source code offers easy access to data processing steps, benchmark creation, and experiment replication for those with MIMIC-IV access, providing insights, guidance, and protocols to efficiently develop ICD coding models.

Generating near-infrared facial expression datasets with dimensional affect labels

Facial expression analysis has long been an active research area of computer vision. Traditional methods mainly analyse images for prototypical discrete emotions; as a result, they do not provide an accurate depiction of the complex emotional states in humans. Furthermore, illumination variance remains a challenge for face analysis in the visible light spectrum. To address these issues, we propose using a dimensional model based on valence and arousal to represent a wider range of emotions, in combination with near infra-red (NIR) imagery, which is more robust to illumination changes. Since there are no existing NIR facial expression datasets with valence-arousal labels available, we present two complementary data augmentation methods (face morphing and CycleGAN approach) to create NIR image datasets with dimensional emotion labels from existing categorical and/or visible-light datasets. Our experiments show that these generated NIR datasets are comparable to existing datasets in terms of data quality and baseline prediction performance.

AI Singapore Trusted Media Challenge Dataset

The development of powerful deep learning technologies has brought about some negative effects to both society and individuals. One such issue is the emergence of fake media. To tackle the issue, we have organized the Trusted Media Challenge (TMC) to explore how Artificial Intelligence (AI) technologies could be leveraged to combat fake media. Together with the challenge, we have released a challenge dataset which consists of 4,380 fake and 2,563 real videos. All these videos are accompanied with audios and different video and/or audio manipulation methods are adopted to produce different types of fake media. The videos in the dataset have various durations, background, illumination, a minimum resolution of 360p and may contain perturbations that mimic transmission errors and bad compression. We have also carried out a user study to demonstrate the quality of our composed dataset. The results show that our dataset has a promising quality and can fool human participants in many cases.