A Unified Framework for Semi-Supervised Image Segmentation and Registration

Semi-supervised learning, which leverages both annotated and unannotated data, is an efficient approach for medical image segmentation, where obtaining annotations for the whole dataset is time-consuming and costly. Traditional semi-supervised methods primarily focus on extracting features and learning data distributions from unannotated data to enhance model training. In this paper, we introduce a novel approach incorporating an image registration model to generate pseudo-labels for the unannotated data, producing more geometrically correct pseudo-labels to improve the model training. Our method was evaluated on a 2D brain data set, showing excellent performance even using only 1\% of the annotated data. The results show that our approach outperforms conventional semi-supervised segmentation methods (e.g. teacher-student model), particularly in a low percentage of annotation scenario. GitHub: https://github.com/ruizhe-l/UniSegReg.

Llettuce: An Open Source Natural Language Processing Tool for the Translation of Medical Terms into Uniform Clinical Encoding

This paper introduces Llettuce, an open-source tool designed to address the complexities of converting medical terms into OMOP standard concepts. Unlike existing solutions such as the Athena database search and Usagi, which struggle with semantic nuances and require substantial manual input, Llettuce leverages advanced natural language processing, including large language models and fuzzy matching, to automate and enhance the mapping process. Developed with a focus on GDPR compliance, Llettuce can be deployed locally, ensuring data protection while maintaining high performance in converting informal medical terms to standardised concepts.

KemenkeuGPT: Leveraging a Large Language Model on Indonesia's Government Financial Data and Regulations to Enhance Decision Making

Data is crucial for evidence-based policymaking and enhancing public services, including those at the Ministry of Finance of the Republic of Indonesia. However, the complexity and dynamic nature of governmental financial data and regulations can hinder decision-making. This study investigates the potential of Large Language Models (LLMs) to address these challenges, focusing on Indonesia's financial data and regulations. While LLMs are effective in the financial sector, their use in the public sector in Indonesia is unexplored. This study undertakes an iterative process to develop KemenkeuGPT using the LangChain with Retrieval-Augmented Generation (RAG), prompt engineering and fine-tuning. The dataset from 2003 to 2023 was collected from the Ministry of Finance, Statistics Indonesia and the International Monetary Fund (IMF). Surveys and interviews with Ministry officials informed, enhanced and fine-tuned the model. We evaluated the model using human feedback, LLM-based evaluation and benchmarking. The model's accuracy improved from 35% to 61%, with correctness increasing from 48% to 64%. The Retrieval-Augmented Generation Assessment (RAGAS) framework showed that KemenkeuGPT achieved 44% correctness with 73% faithfulness, 40% precision and 60% recall, outperforming several other base models. An interview with an expert from the Ministry of Finance indicated that KemenkeuGPT has the potential to become an essential tool for decision-making. These results are expected to improve with continuous human feedback.

MrRegNet: Multi-resolution Mask Guided Convolutional Neural Network for Medical Image Registration with Large Deformations

Deformable image registration (alignment) is highly sought after in numerous clinical applications, such as computer aided diagnosis and disease progression analysis. Deep Convolutional Neural Network (DCNN)-based image registration methods have demonstrated advantages in terms of registration accuracy and computational speed. However, while most methods excel at global alignment, they often perform worse in aligning local regions. To address this challenge, this paper proposes a mask-guided encoder-decoder DCNN-based image registration method, named as MrRegNet. This approach employs a multi-resolution encoder for feature extraction and subsequently estimates multi-resolution displacement fields in the decoder to handle the substantial deformation of images. Furthermore, segmentation masks are employed to direct the model's attention toward aligning local regions. The results show that the proposed method outperforms traditional methods like Demons and a well-known deep learning method, VoxelMorph, on a public 3D brain MRI dataset (OASIS) and a local 2D brain MRI dataset with large deformations. Importantly, the image alignment accuracies are significantly improved at local regions guided by segmentation masks. Github link:https://github.com/ruizhe-l/MrRegNet.

Towards a More Reliable Interpretation of Machine Learning Outputs for Safety-Critical Systems using Feature Importance Fusion

When machine learning supports decision-making in safety-critical systems, it is important to verify and understand the reasons why a particular output is produced. Although feature importance calculation approaches assist in interpretation, there is a lack of consensus regarding how features' importance is quantified, which makes the explanations offered for the outcomes mostly unreliable. A possible solution to address the lack of agreement is to combine the results from multiple feature importance quantifiers to reduce the variance of estimates. Our hypothesis is that this will lead to more robust and trustworthy interpretations of the contribution of each feature to machine learning predictions. To assist test this hypothesis, we propose an extensible Framework divided in four main parts: (i) traditional data pre-processing and preparation for predictive machine learning models; (ii) predictive machine learning; (iii) feature importance quantification and (iv) feature importance decision fusion using an ensemble strategy. We also introduce a novel fusion metric and compare it to the state-of-the-art. Our approach is tested on synthetic data, where the ground truth is known. We compare different fusion approaches and their results for both training and test sets. We also investigate how different characteristics within the datasets affect the feature importance ensembles studied. Results show that our feature importance ensemble Framework overall produces 15% less feature importance error compared to existing methods. Additionally, results reveal that different levels of noise in the datasets do not affect the feature importance ensembles' ability to accurately quantify feature importance, whereas the feature importance quantification error increases with the number of features and number of orthogonal informative features.