Explainable ICD Coding via Entity Linking

Clinical coding is a critical task in healthcare, although traditional methods for automating clinical coding may not provide sufficient explicit evidence for coders in production environments. This evidence is crucial, as medical coders have to make sure there exists at least one explicit passage in the input health record that justifies the attribution of a code. We therefore propose to reframe the task as an entity linking problem, in which each document is annotated with its set of codes and respective textual evidence, enabling better human-machine collaboration. By leveraging parameter-efficient fine-tuning of Large Language Models (LLMs), together with constrained decoding, we introduce three approaches to solve this problem that prove effective at disambiguating clinical mentions and that perform well in few-shot scenarios.

From TOWER to SPIRE: Adding the Speech Modality to a Text-Only LLM

Large language models (LLMs) have shown remarkable performance and generalization capabilities across multiple languages and tasks, making them very attractive targets for multi-modality integration (e.g., images or speech). In this work, we extend an existing LLM to the speech modality via speech discretization and continued pre-training. In particular, we are interested in multilingual LLMs, such as TOWER, as their pre-training setting allows us to treat discretized speech input as an additional translation language. The resulting open-source model, SPIRE, is able to transcribe and translate English speech input while maintaining TOWER's original performance on translation-related tasks, showcasing that discretized speech input integration as an additional language is feasible during LLM adaptation. We make our code and models available to the community.

Evaluation of Multilingual Image Captioning: How far can we get with CLIP models?

The evaluation of image captions, looking at both linguistic fluency and semantic correspondence to visual contents, has witnessed a significant effort. Still, despite advancements such as the CLIPScore metric, multilingual captioning evaluation has remained relatively unexplored. This work presents several strategies, and extensive experiments, related to evaluating CLIPScore variants in multilingual settings. To address the lack of multilingual test data, we consider two different strategies: (1) using quality aware machine-translated datasets with human judgements, and (2) re-purposing multilingual datasets that target semantic inference and reasoning. Our results highlight the potential of finetuned multilingual models to generalize across languages and to handle complex linguistic challenges. Tests with machine-translated data show that multilingual CLIPScore models can maintain a high correlation with human judgements across different languages, and additional tests with natively multilingual and multicultural data further attest to the high-quality assessments.

Efficient Architectures for High Resolution Vision-Language Models

Vision-Language Models (VLMs) have recently experienced significant advancements. However, challenges persist in the accurate recognition of fine details within high resolution images, which limits performance in multiple tasks. This work introduces Pheye, a novel architecture that efficiently processes high-resolution images while training fewer parameters than similarly sized VLMs. Notably, Pheye achieves a high efficiency while maintaining strong performance, particularly in tasks that demand fine-grained image understanding and/or the handling of scene-text.

Multilingual Vision-Language Pre-training for the Remote Sensing Domain

Methods based on Contrastive Language-Image Pre-training (CLIP) are nowadays extensively used in support of vision-and-language tasks involving remote sensing data, such as cross-modal retrieval. The adaptation of CLIP to this specific domain has relied on model fine-tuning with the standard contrastive objective, using existing human-labeled image-caption datasets, or using synthetic data corresponding to image-caption pairs derived from other annotations over remote sensing images (e.g., object classes). The use of different pre-training mechanisms has received less attention, and only a few exceptions have considered multilingual inputs. This work proposes a novel vision-and-language model for the remote sensing domain, exploring the fine-tuning of a multilingual CLIP model and testing the use of a self-supervised method based on aligning local and global representations from individual input images, together with the standard CLIP objective. Model training relied on assembling pre-existing datasets of remote sensing images paired with English captions, followed by the use of automated machine translation into nine additional languages. We show that translated data is indeed helpful, e.g. improving performance also on English. Our resulting model, which we named Remote Sensing Multilingual CLIP (RS-M-CLIP), obtains state-of-the-art results in a variety of vision-and-language tasks, including cross-modal and multilingual image-text retrieval, or zero-shot image classification.

Evaluation of Code LLMs on Geospatial Code Generation

Software development support tools have been studied for a long time, with recent approaches using Large Language Models (LLMs) for code generation. These models can generate Python code for data science and machine learning applications. LLMs are helpful for software engineers because they increase productivity in daily work. An LLM can also serve as a "mentor" for inexperienced software developers, and be a viable learning support. High-quality code generation with LLMs can also be beneficial in geospatial data science. However, this domain poses different challenges, and code generation LLMs are typically not evaluated on geospatial tasks. Here, we show how we constructed an evaluation benchmark for code generation models, based on a selection of geospatial tasks. We categorised geospatial tasks based on their complexity and required tools. Then, we created a dataset with tasks that test model capabilities in spatial reasoning, spatial data processing, and geospatial tools usage. The dataset consists of specific coding problems that were manually created for high quality. For every problem, we proposed a set of test scenarios that make it possible to automatically check the generated code for correctness. In addition, we tested a selection of existing code generation LLMs for code generation in the geospatial domain. We share our dataset and reproducible evaluation code on a public GitHub repository, arguing that this can serve as an evaluation benchmark for new LLMs in the future. Our dataset will hopefully contribute to the development new models capable of solving geospatial coding tasks with high accuracy. These models will enable the creation of coding assistants tailored for geospatial applications.

Lisbon Computational Linguists at SemEval-2024 Task 2: Using A Mistral 7B Model and Data Augmentation

This paper describes our approach to the SemEval-2024 safe biomedical Natural Language Inference for Clinical Trials (NLI4CT) task, which concerns classifying statements about Clinical Trial Reports (CTRs). We explored the capabilities of Mistral-7B, a generalist open-source Large Language Model (LLM). We developed a prompt for the NLI4CT task, and fine-tuned a quantized version of the model using an augmented version of the training dataset. The experimental results show that this approach can produce notable results in terms of the macro F1-score, while having limitations in terms of faithfulness and consistency. All the developed code is publicly available on a GitHub repository

Dwell in the Beginning: How Language Models Embed Long Documents for Dense Retrieval

This study investigates the existence of positional biases in Transformer-based models for text representation learning, particularly in the context of web document retrieval. We build on previous research that demonstrated loss of information in the middle of input sequences for causal language models, extending it to the domain of representation learning. We examine positional biases at various stages of training for an encoder-decoder model, including language model pre-training, contrastive pre-training, and contrastive fine-tuning. Experiments with the MS-MARCO document collection reveal that after contrastive pre-training the model already generates embeddings that better capture early contents of the input, with fine-tuning further aggravating this effect.

Large Language Models for Captioning and Retrieving Remote Sensing Images

Image captioning and cross-modal retrieval are examples of tasks that involve the joint analysis of visual and linguistic information. In connection to remote sensing imagery, these tasks can help non-expert users in extracting relevant Earth observation information for a variety of applications. Still, despite some previous efforts, the development and application of vision and language models to the remote sensing domain have been hindered by the relatively small size of the available datasets and models used in previous studies. In this work, we propose RS-CapRet, a Vision and Language method for remote sensing tasks, in particular image captioning and text-image retrieval. We specifically propose to use a highly capable large decoder language model together with image encoders adapted to remote sensing imagery through contrastive language-image pre-training. To bridge together the image encoder and language decoder, we propose training simple linear layers with examples from combining different remote sensing image captioning datasets, keeping the other parameters frozen. RS-CapRet can then generate descriptions for remote sensing images and retrieve images from textual descriptions, achieving SOTA or competitive performance with existing methods. Qualitative results illustrate that RS-CapRet can effectively leverage the pre-trained large language model to describe remote sensing images, retrieve them based on different types of queries, and also show the ability to process interleaved sequences of images and text in a dialogue manner.

Accurate and Well-Calibrated ICD Code Assignment Through Attention Over Diverse Label Embeddings

Although the International Classification of Diseases (ICD) has been adopted worldwide, manually assigning ICD codes to clinical text is time-consuming, error-prone, and expensive, motivating the development of automated approaches. This paper describes a novel approach for automated ICD coding, combining several ideas from previous related work. We specifically employ a strong Transformer-based model as a text encoder and, to handle lengthy clinical narratives, we explored either (a) adapting the base encoder model into a Longformer, or (b) dividing the text into chunks and processing each chunk independently. The representations produced by the encoder are combined with a label embedding mechanism that explores diverse ICD code synonyms. Experiments with different splits of the MIMIC-III dataset show that the proposed approach outperforms the current state-of-the-art models in ICD coding, with the label embeddings significantly contributing to the good performance. Our approach also leads to properly calibrated classification results, which can effectively inform downstream tasks such as quantification.