Interpretable phenotyping of Heart Failure patients with Dutch discharge letters

Objective: Heart failure (HF) patients present with diverse phenotypes affecting treatment and prognosis. This study evaluates models for phenotyping HF patients based on left ventricular ejection fraction (LVEF) classes, using structured and unstructured data, assessing performance and interpretability. Materials and Methods: The study analyzes all HF hospitalizations at both Amsterdam UMC hospitals (AMC and VUmc) from 2015 to 2023 (33,105 hospitalizations, 16,334 patients). Data from AMC were used for model training, and from VUmc for external validation. The dataset was unlabelled and included tabular clinical measurements and discharge letters. Silver labels for LVEF classes were generated by combining diagnosis codes, echocardiography results, and textual mentions. Gold labels were manually annotated for 300 patients for testing. Multiple Transformer-based (black-box) and Aug-Linear (white-box) models were trained and compared with baselines on structured and unstructured data. To evaluate interpretability, two clinicians annotated 20 discharge letters by highlighting information they considered relevant for LVEF classification. These were compared to SHAP and LIME explanations from black-box models and the inherent explanations of Aug-Linear models. Results: BERT-based and Aug-Linear models, using discharge letters alone, achieved the highest classification results (AUC=0.84 for BERT, 0.81 for Aug-Linear on external validation), outperforming baselines. Aug-Linear explanations aligned more closely with clinicians' explanations than post-hoc explanations on black-box models. Conclusions: Discharge letters emerged as the most informative source for phenotyping HF patients. Aug-Linear models matched black-box performance while providing clinician-aligned interpretability, supporting their use in transparent clinical decision-making.

What Does Neuro Mean to Cardio? Investigating the Role of Clinical Specialty Data in Medical LLMs

In this paper, we introduce S-MedQA, an English medical question-answering (QA) dataset for benchmarking large language models in fine-grained clinical specialties. We use S-MedQA to check the applicability of a popular hypothesis related to knowledge injection in the knowledge-intense scenario of medical QA, and show that: 1) training on data from a speciality does not necessarily lead to best performance on that specialty and 2) regardless of the specialty fine-tuned on, token probabilities of clinically relevant terms for all specialties increase consistently. Thus, we believe improvement gains come mostly from domain shifting (e.g., general to medical) rather than knowledge injection and suggest rethinking the role of fine-tuning data in the medical domain. We release S-MedQA and all code needed to reproduce all our experiments to the research community.

AnyMatch -- Efficient Zero-Shot Entity Matching with a Small Language Model

Entity matching (EM) is the problem of determining whether two records refer to same real-world entity, which is crucial in data integration, e.g., for product catalogs or address databases. A major drawback of many EM approaches is their dependence on labelled examples. We thus focus on the challenging setting of zero-shot entity matching where no labelled examples are available for an unseen target dataset. Recently, large language models (LLMs) have shown promising results for zero-shot EM, but their low throughput and high deployment cost limit their applicability and scalability. We revisit the zero-shot EM problem with AnyMatch, a small language model fine-tuned in a transfer learning setup. We propose several novel data selection techniques to generate fine-tuning data for our model, e.g., by selecting difficult pairs to match via an AutoML filter, by generating additional attribute-level examples, and by controlling label imbalance in the data. We conduct an extensive evaluation of the prediction quality and deployment cost of our model, in a comparison to thirteen baselines on nine benchmark datasets. We find that AnyMatch provides competitive prediction quality despite its small parameter size: it achieves the second-highest F1 score overall, and outperforms several other approaches that employ models with hundreds of billions of parameters. Furthermore, our approach exhibits major cost benefits: the average prediction quality of AnyMatch is within 4.4% of the state-of-the-art method MatchGPT with the proprietary trillion-parameter model GPT-4, yet AnyMatch requires four orders of magnitude less parameters and incurs a 3,899 times lower inference cost (in dollars per 1,000 tokens).

Evaluating Linguistic Capabilities of Multimodal LLMs in the Lens of Few-Shot Learning

The linguistic capabilities of Multimodal Large Language Models (MLLMs) are critical for their effective application across diverse tasks. This study aims to evaluate the performance of MLLMs on the VALSE benchmark, focusing on the efficacy of few-shot In-Context Learning (ICL), and Chain-of-Thought (CoT) prompting. We conducted a comprehensive assessment of state-of-the-art MLLMs, varying in model size and pretraining datasets. The experimental results reveal that ICL and CoT prompting significantly boost model performance, particularly in tasks requiring complex reasoning and contextual understanding. Models pretrained on captioning datasets show superior zero-shot performance, while those trained on interleaved image-text data benefit from few-shot learning. Our findings provide valuable insights into optimizing MLLMs for better grounding of language in visual contexts, highlighting the importance of the composition of pretraining data and the potential of few-shot learning strategies to improve the reasoning abilities of MLLMs.

LLM aided semi-supervision for Extractive Dialog Summarization

Generating high-quality summaries for chat dialogs often requires large labeled datasets. We propose a method to efficiently use unlabeled data for extractive summarization of customer-agent dialogs. In our method, we frame summarization as a question-answering problem and use state-of-the-art large language models (LLMs) to generate pseudo-labels for a dialog. We then use these pseudo-labels to fine-tune a chat summarization model, effectively transferring knowledge from the large LLM into a smaller specialized model. We demonstrate our method on the \tweetsumm dataset, and show that using 10% of the original labelled data set we can achieve 65.9/57.0/61.0 ROUGE-1/-2/-L, whereas the current state-of-the-art trained on the entire training data set obtains 65.16/55.81/64.37 ROUGE-1/-2/-L. In other words, in the worst case (i.e., ROUGE-L) we still effectively retain 94.7% of the performance while using only 10% of the data.

ViLMA: A Zero-Shot Benchmark for Linguistic and Temporal Grounding in Video-Language Models

With the ever-increasing popularity of pretrained Video-Language Models (VidLMs), there is a pressing need to develop robust evaluation methodologies that delve deeper into their visio-linguistic capabilities. To address this challenge, we present ViLMA (Video Language Model Assessment), a task-agnostic benchmark that places the assessment of fine-grained capabilities of these models on a firm footing. Task-based evaluations, while valuable, fail to capture the complexities and specific temporal aspects of moving images that VidLMs need to process. Through carefully curated counterfactuals, ViLMA offers a controlled evaluation suite that sheds light on the true potential of these models, as well as their performance gaps compared to human-level understanding. ViLMA also includes proficiency tests, which assess basic capabilities deemed essential to solving the main counterfactual tests. We show that current VidLMs' grounding abilities are no better than those of vision-language models which use static images. This is especially striking once the performance on proficiency tests is factored in. Our benchmark serves as a catalyst for future research on VidLMs, helping to highlight areas that still need to be explored.

Fixing confirmation bias in feature attribution methods via semantic match

Feature attribution methods have become a staple method to disentangle the complex behavior of black box models. Despite their success, some scholars have argued that such methods suffer from a serious flaw: they do not allow a reliable interpretation in terms of human concepts. Simply put, visualizing an array of feature contributions is not enough for humans to conclude something about a model's internal representations, and confirmation bias can trick users into false beliefs about model behavior. We argue that a structured approach is required to test whether our hypotheses on the model are confirmed by the feature attributions. This is what we call the "semantic match" between human concepts and (sub-symbolic) explanations. Building on the conceptual framework put forward in Cin\`a et al. [2023], we propose a structured approach to evaluate semantic match in practice. We showcase the procedure in a suite of experiments spanning tabular and image data, and show how the assessment of semantic match can give insight into both desirable (e.g., focusing on an object relevant for prediction) and undesirable model behaviors (e.g., focusing on a spurious correlation). We couple our experimental results with an analysis on the metrics to measure semantic match, and argue that this approach constitutes the first step towards resolving the issue of confirmation bias in XAI.

Soft-prompt tuning to predict lung cancer using primary care free-text Dutch medical notes

We investigate different natural language processing (NLP) approaches based on contextualised word representations for the problem of early prediction of lung cancer using free-text patient medical notes of Dutch primary care physicians. Because lung cancer has a low prevalence in primary care, we also address the problem of classification under highly imbalanced classes. Specifically, we use large Transformer-based pretrained language models (PLMs) and investigate: 1) how \textit{soft prompt-tuning} -- an NLP technique used to adapt PLMs using small amounts of training data -- compares to standard model fine-tuning; 2) whether simpler static word embedding models (WEMs) can be more robust compared to PLMs in highly imbalanced settings; and 3) how models fare when trained on notes from a small number of patients. We find that 1) soft-prompt tuning is an efficient alternative to standard model fine-tuning; 2) PLMs show better discrimination but worse calibration compared to simpler static word embedding models as the classification problem becomes more imbalanced; and 3) results when training models on small number of patients are mixed and show no clear differences between PLMs and WEMs. All our code is available open source in \url{https://bitbucket.org/aumc-kik/prompt_tuning_cancer_prediction/}.

Detecting Euphemisms with Literal Descriptions and Visual Imagery

This paper describes our two-stage system for the Euphemism Detection shared task hosted by the 3rd Workshop on Figurative Language Processing in conjunction with EMNLP 2022. Euphemisms tone down expressions about sensitive or unpleasant issues like addiction and death. The ambiguous nature of euphemistic words or expressions makes it challenging to detect their actual meaning within a context. In the first stage, we seek to mitigate this ambiguity by incorporating literal descriptions into input text prompts to our baseline model. It turns out that this kind of direct supervision yields remarkable performance improvement. In the second stage, we integrate visual supervision into our system using visual imageries, two sets of images generated by a text-to-image model by taking terms and descriptions as input. Our experiments demonstrate that visual supervision also gives a statistically significant performance boost. Our system achieved the second place with an F1 score of 87.2%, only about 0.9% worse than the best submission.

Endowing Language Models with Multimodal Knowledge Graph Representations

We propose a method to make natural language understanding models more parameter efficient by storing knowledge in an external knowledge graph (KG) and retrieving from this KG using a dense index. Given (possibly multilingual) downstream task data, e.g., sentences in German, we retrieve entities from the KG and use their multimodal representations to improve downstream task performance. We use the recently released VisualSem KG as our external knowledge repository, which covers a subset of Wikipedia and WordNet entities, and compare a mix of tuple-based and graph-based algorithms to learn entity and relation representations that are grounded on the KG multimodal information. We demonstrate the usefulness of the learned entity representations on two downstream tasks, and show improved performance on the multilingual named entity recognition task by $0.3\%$--$0.7\%$ F1, while we achieve up to $2.5\%$ improvement in accuracy on the visual sense disambiguation task. All our code and data are available in: \url{https://github.com/iacercalixto/visualsem-kg}.