Roberto A. Lotufo

Diedre S. Carmo, Rosarie A. Tudas, Alejandro P. Comellas et al.

Automated segmentation of lung abnormalities in computed tomography is an important step for diagnosing and characterizing lung disease. In this work, we improve upon a previous method and propose S-MEDSeg, a deep learning based approach for accurate segmentation of lung lesions in chest CT images. S-MEDSeg combines a pre-trained EfficientNet backbone, bidirectional feature pyramid network, and modern network advancements to achieve improved segmentation performance. A comprehensive ablation study was performed to evaluate the contribution of the proposed network modifications. The results demonstrate modifications introduced in S-MEDSeg significantly improves segmentation performance compared to the baseline approach. The proposed method is applied to an independent dataset of long COVID inpatients to study the effect of post-acute infection vaccination on extent of lung findings. Open-source code, graphical user interface and pip package are available at https://github.com/MICLab-Unicamp/medseg.

Diedre S. Carmo, Jean A. Ribeiro, Alejandro P. Comellas et al.

The COVID-19 pandemic response highlighted the potential of deep learning methods in facilitating the diagnosis, prognosis and understanding of lung diseases through automated segmentation of pulmonary structures and lesions in chest computed tomography (CT). Automated separation of lung lesion into ground-glass opacity (GGO) and consolidation is hindered due to the labor-intensive and subjective nature of this task, resulting in scarce availability of ground truth for supervised learning. To tackle this problem, we propose MEDPSeg. MEDPSeg learns from heterogeneous chest CT targets through hierarchical polymorphic multitask learning (HPML). HPML explores the hierarchical nature of GGO and consolidation, lung lesions, and the lungs, with further benefits achieved through multitasking airway and pulmonary artery segmentation. Over 6000 volumetric CT scans from different partially labeled sources were used for training and testing. Experiments show PML enabling new state-of-the-art performance for GGO and consolidation segmentation tasks. In addition, MEDPSeg simultaneously performs segmentation of the lung parenchyma, airways, pulmonary artery, and lung lesions, all in a single forward prediction, with performance comparable to state-of-the-art methods specialized in each of those targets. Finally, we provide an open-source implementation with a graphical user interface at https://github.com/MICLab-Unicamp/medpseg.

Ramon Pires, Fábio C. de Souza, Guilherme Rosa et al.

A typical information extraction pipeline consists of token- or span-level classification models coupled with a series of pre- and post-processing scripts. In a production pipeline, requirements often change, with classes being added and removed, which leads to nontrivial modifications to the source code and the possible introduction of bugs. In this work, we evaluate sequence-to-sequence models as an alternative to token-level classification methods for information extraction of legal and registration documents. We finetune models that jointly extract the information and generate the output already in a structured format. Post-processing steps are learned during training, thus eliminating the need for rule-based methods and simplifying the pipeline. Furthermore, we propose a novel method to align the output with the input text, thus facilitating system inspection and auditing. Our experiments on four real-world datasets show that the proposed method is an alternative to classical pipelines.