Multi-task learning for classification, segmentation, reconstruction, and detection on chest CT scans

Lung cancer and covid-19 have one of the highest morbidity and mortality rates in the world. For physicians, the identification of lesions is difficult in the early stages of the disease and time-consuming. Therefore, multi-task learning is an approach to extracting important features, such as lesions, from small amounts of medical data because it learns to generalize better. We propose a novel multi-task framework for classification, segmentation, reconstruction, and detection. To the best of our knowledge, we are the first ones who added detection to the multi-task solution. Additionally, we checked the possibility of using two different backbones and different loss functions in the segmentation task.

The Effect of Balancing Methods on Model Behavior in Imbalanced Classification Problems

Imbalanced data poses a significant challenge in classification as model performance is affected by insufficient learning from minority classes. Balancing methods are often used to address this problem. However, such techniques can lead to problems such as overfitting or loss of information. This study addresses a more challenging aspect of balancing methods - their impact on model behavior. To capture these changes, Explainable Artificial Intelligence tools are used to compare models trained on datasets before and after balancing. In addition to the variable importance method, this study uses the partial dependence profile and accumulated local effects techniques. Real and simulated datasets are tested, and an open-source Python package edgaro is developed to facilitate this analysis. The results obtained show significant changes in model behavior due to balancing methods, which can lead to biased models toward a balanced distribution. These findings confirm that balancing analysis should go beyond model performance comparisons to achieve higher reliability of machine learning models. Therefore, we propose a new method performance gain plot for informed data balancing strategy to make an optimal selection of balancing method by analyzing the measure of change in model behavior versus performance gain.

SeFNet: Bridging Tabular Datasets with Semantic Feature Nets

Machine learning applications cover a wide range of predictive tasks in which tabular datasets play a significant role. However, although they often address similar problems, tabular datasets are typically treated as standalone tasks. The possibilities of using previously solved problems are limited due to the lack of structured contextual information about their features and the lack of understanding of the relations between them. To overcome this limitation, we propose a new approach called Semantic Feature Net (SeFNet), capturing the semantic meaning of the analyzed tabular features. By leveraging existing ontologies and domain knowledge, SeFNet opens up new opportunities for sharing insights between diverse predictive tasks. One such opportunity is the Dataset Ontology-based Semantic Similarity (DOSS) measure, which quantifies the similarity between datasets using relations across their features. In this paper, we present an example of SeFNet prepared for a collection of predictive tasks in healthcare, with the features' relations derived from the SNOMED-CT ontology. The proposed SeFNet framework and the accompanying DOSS measure address the issue of limited contextual information in tabular datasets. By incorporating domain knowledge and establishing semantic relations between features, we enhance the potential for meta-learning and enable valuable insights to be shared across different predictive tasks.

Prevention is better than cure: a case study of the abnormalities detection in the chest

Prevention is better than cure. This old truth applies not only to the prevention of diseases but also to the prevention of issues with AI models used in medicine. The source of malfunctioning of predictive models often lies not in the training process but reaches the data acquisition phase or design of the experiment phase. In this paper, we analyze in detail a single use case - a Kaggle competition related to the detection of abnormalities in X-ray lung images. We demonstrate how a series of simple tests for data imbalance exposes faults in the data acquisition and annotation process. Complex models are able to learn such artifacts and it is difficult to remove this bias during or after the training. Errors made at the data collection stage make it difficult to validate the model correctly. Based on this use case, we show how to monitor data and model balance (fairness) throughout the life cycle of a predictive model, from data acquisition to parity analysis of model scores.

Towards Evaluating Explanations of Vision Transformers for Medical Imaging

As deep learning models increasingly find applications in critical domains such as medical imaging, the need for transparent and trustworthy decision-making becomes paramount. Many explainability methods provide insights into how these models make predictions by attributing importance to input features. As Vision Transformer (ViT) becomes a promising alternative to convolutional neural networks for image classification, its interpretability remains an open research question. This paper investigates the performance of various interpretation methods on a ViT applied to classify chest X-ray images. We introduce the notion of evaluating faithfulness, sensitivity, and complexity of ViT explanations. The obtained results indicate that Layerwise relevance propagation for transformers outperforms Local interpretable model-agnostic explanations and Attention visualization, providing a more accurate and reliable representation of what a ViT has actually learned. Our findings provide insights into the applicability of ViT explanations in medical imaging and highlight the importance of using appropriate evaluation criteria for comparing them.

Hospital Length of Stay Prediction Based on Multi-modal Data towards Trustworthy Human-AI Collaboration in Radiomics

To what extent can the patient's length of stay in a hospital be predicted using only an X-ray image? We answer this question by comparing the performance of machine learning survival models on a novel multi-modal dataset created from 1235 images with textual radiology reports annotated by humans. Although black-box models predict better on average than interpretable ones, like Cox proportional hazards, they are not inherently understandable. To overcome this trust issue, we introduce time-dependent model explanations into the human-AI decision making process. Explaining models built on both: human-annotated and algorithm-extracted radiomics features provides valuable insights for physicians working in a hospital. We believe the presented approach to be general and widely applicable to other time-to-event medical use cases. For reproducibility, we open-source code and the TLOS dataset at https://github.com/mi2datalab/xlungs-trustworthy-los-prediction.

HADES: Homologous Automated Document Exploration and Summarization

This paper introduces HADES, a novel tool for automatic comparative documents with similar structures. HADES is designed to streamline the work of professionals dealing with large volumes of documents, such as policy documents, legal acts, and scientific papers. The tool employs a multi-step pipeline that begins with processing PDF documents using topic modeling, summarization, and analysis of the most important words for each topic. The process concludes with an interactive web app with visualizations that facilitate the comparison of the documents. HADES has the potential to significantly improve the productivity of professionals dealing with high volumes of documents, reducing the time and effort required to complete tasks related to comparative document analysis. Our package is publically available on GitHub.

Climate Policy Tracker: Pipeline for automated analysis of public climate policies

The number of standardized policy documents regarding climate policy and their publication frequency is significantly increasing. The documents are long and tedious for manual analysis, especially for policy experts, lawmakers, and citizens who lack access or domain expertise to utilize data analytics tools. Potential consequences of such a situation include reduced citizen governance and involvement in climate policies and an overall surge in analytics costs, rendering less accessibility for the public. In this work, we use a Latent Dirichlet Allocation-based pipeline for the automatic summarization and analysis of 10-years of national energy and climate plans (NECPs) for the period from 2021 to 2030, established by 27 Member States of the European Union. We focus on analyzing policy framing, the language used to describe specific issues, to detect essential nuances in the way governments frame their climate policies and achieve climate goals. The methods leverage topic modeling and clustering for the comparative analysis of policy documents across different countries. It allows for easier integration in potential user-friendly applications for the development of theories and processes of climate policy. This would further lead to better citizen governance and engagement over climate policies and public policy research.

SurvSHAP(t): Time-dependent explanations of machine learning survival models

Machine and deep learning survival models demonstrate similar or even improved time-to-event prediction capabilities compared to classical statistical learning methods yet are too complex to be interpreted by humans. Several model-agnostic explanations are available to overcome this issue; however, none directly explain the survival function prediction. In this paper, we introduce SurvSHAP(t), the first time-dependent explanation that allows for interpreting survival black-box models. It is based on SHapley Additive exPlanations with solid theoretical foundations and a broad adoption among machine learning practitioners. The proposed methods aim to enhance precision diagnostics and support domain experts in making decisions. Experiments on synthetic and medical data confirm that SurvSHAP(t) can detect variables with a time-dependent effect, and its aggregation is a better determinant of the importance of variables for a prediction than SurvLIME. SurvSHAP(t) is model-agnostic and can be applied to all models with functional output. We provide an accessible implementation of time-dependent explanations in Python at http://github.com/MI2DataLab/survshap .

Explainable expected goal models for performance analysis in football analytics

The expected goal provides a more representative measure of the team and player performance which also suit the low-scoring nature of football instead of score in modern football. The score of a match involves randomness and often may not represent the performance of the teams and players, therefore it has been popular to use the alternative statistics in recent years such as shots on target, ball possessions, and drills. To measure the probability of a shot being a goal by the expected goal, several features are used to train an expected goal model which is based on the event and tracking football data. The selection of these features, the size and date of the data, and the model which are used as the parameters that may affect the performance of the model. Using black-box machine learning models for increasing the predictive performance of the model decreases its interpretability that causes the loss of information that can be gathered from the model. This paper proposes an accurate expected goal model trained consisting of 315,430 shots from seven seasons between 2014-15 and 2020-21 of the top-five European football leagues. Moreover, this model is explained by using explainable artificial intelligence tool to obtain an explainable expected goal model for evaluating a team or player performance. To best of our knowledge, this is the first paper that demonstrates a practical application of an explainable artificial intelligence tool aggregated profiles to explain a group of observations on an accurate expected goal model for monitoring the team and player performance. Moreover, these methods can be generalized to other sports branches.