Dataset Information

Encoder-decoder models for chest X-ray report generation perform no better than unconditioned baselines.

ABSTRACT: High quality radiology reporting of chest X-ray images is of core importance for high-quality patient diagnosis and care. Automatically generated reports can assist radiologists by reducing their workload and even may prevent errors. Machine Learning (ML) models for this task take an X-ray image as input and output a sequence of words. In this work, we show that ML models for this task based on the popular encoder-decoder approach, like 'Show, Attend and Tell' (SA&T) have similar or worse performance than models that do not use the input image, called unconditioned baseline. An unconditioned model achieved diagnostic accuracy of 0.91 on the IU chest X-ray dataset, and significantly outperformed SA&T (0.877) and other popular ML models (p-value < 0.001). This unconditioned model also outperformed SA&T and similar ML methods on the BLEU-4 and METEOR metrics. Also, an unconditioned version of SA&T obtained by permuting the reports generated from images of the test set, achieved diagnostic accuracy of 0.862, comparable to that of SA&T (p-value ≥ 0.05).

SUBMITTER: Babar Z

PROVIDER: S-EPMC8629217 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Encoder-decoder models for chest X-ray report generation perform no better than unconditioned baselines.

Babar Zaheer Z van Laarhoven Twan T Marchiori Elena E

PloS one 20211129 11

High quality radiology reporting of chest X-ray images is of core importance for high-quality patient diagnosis and care. Automatically generated reports can assist radiologists by reducing their workload and even may prevent errors. Machine Learning (ML) models for this task take an X-ray image as input and output a sequence of words. In this work, we show that ML models for this task based on the popular encoder-decoder approach, like 'Show, Attend and Tell' (SA&T) have similar or worse perfor ...[more]

PMID: 34843509

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Project description:Automatic lung lesion segmentation of chest computer tomography (CT) scans is considered a pivotal stage toward accurate diagnosis and severity measurement of COVID-19. Traditional U-shaped encoder-decoder architecture and its variants suffer from diminutions of contextual information in pooling/upsampling operations with increased semantic gaps among encoded and decoded feature maps as well as instigate vanishing gradient problems for its sequential gradient propagation that result in suboptimal performance. Moreover, operating with 3-D CT volume poses further limitations due to the exponential increase of computational complexity making the optimization difficult. In this article, an automated COVID-19 lesion segmentation scheme is proposed utilizing a highly efficient neural network architecture, namely CovSegNet, to overcome these limitations. Additionally, a two-phase training scheme is introduced where a deeper 2-D network is employed for generating region-of-interest (ROI)-enhanced CT volume followed by a shallower 3-D network for further enhancement with more contextual information without increasing computational burden. Along with the traditional vertical expansion of Unet, we have introduced horizontal expansion with multistage encoder-decoder modules for achieving optimum performance. Additionally, multiscale feature maps are integrated into the scale transition process to overcome the loss of contextual information. Moreover, a multiscale fusion module is introduced with a pyramid fusion scheme to reduce the semantic gaps between subsequent encoder/decoder modules while facilitating the parallel optimization for efficient gradient propagation. Outstanding performances have been achieved in three publicly available datasets that largely outperform other state-of-the-art approaches. The proposed scheme can be easily extended for achieving optimum segmentation performances in a wide variety of applications. Impact Statement-With lower sensitivity (60-70%), elongated testing time, and a dire shortage of testing kits, traditional RTPCR based COVID-19 diagnostic scheme heavily relies on postCT based manual inspection for further investigation. Hence, automating the process of infected lesions extraction from chestCT volumes will be major progress for faster accurate diagnosis of COVID-19. However, in challenging conditions with diffused, blurred, and varying shaped edges of COVID-19 lesions, conventional approaches fail to provide precise segmentation of lesions that can be deleterious for false estimation and loss of information. The proposed scheme incorporating an efficient neural network architecture (CovSegNet) overcomes the limitations of traditional approaches that provide significant improvement of performance (8.4% in averaged dice measurement scale) over two datasets. Therefore, this scheme can be an effective, economical tool for the physicians for faster infection analysis to greatly reduce the spread and massive death toll of this deadly virus through mass-screening.

Project description:BackgroundRNA secondary structural alignment serves as a foundational procedure in identifying conserved structural motifs among RNA sequences, crucially advancing our understanding of novel RNAs via comparative genomic analysis. While various computational strategies for RNA structural alignment exist, they often come with high computational complexity. Specifically, when addressing a set of RNAs with unknown structures, the task of simultaneously predicting their consensus secondary structure and determining the optimal sequence alignment requires an overwhelming computational effort of O(L6) for each RNA pair. Such an extremely high computational complexity makes these methods impractical for large-scale analysis despite their accurate alignment capabilities.ResultsIn this paper, we introduce REDalign, an innovative approach based on deep learning for RNA secondary structural alignment. By utilizing a residual encoder-decoder network, REDalign can efficiently capture consensus structures and optimize structural alignments. In this learning model, the encoder network leverages a hierarchical pyramid to assimilate high-level structural features. Concurrently, the decoder network, enhanced with residual skip connections, integrates multi-level encoded features to learn detailed feature hierarchies with fewer parameter sets. REDalign significantly reduces computational complexity compared to Sankoff-style algorithms and effectively handles non-nested structures, including pseudoknots, which are challenging for traditional alignment methods. Extensive evaluations demonstrate that REDalign provides superior accuracy and substantial computational efficiency.ConclusionREDalign presents a significant advancement in RNA secondary structural alignment, balancing high alignment accuracy with lower computational demands. Its ability to handle complex RNA structures, including pseudoknots, makes it an effective tool for large-scale RNA analysis, with potential implications for accelerating discoveries in RNA research and comparative genomics.

Dataset Information

Encoder-decoder models for chest X-ray report generation perform no better than unconditioned baselines.

Publications

Encoder-decoder models for chest X-ray report generation perform no better than unconditioned baselines.

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