Dataset Information

From explanation to intervention: Interactive knowledge extraction from Convolutional Neural Networks used in radiology.

ABSTRACT: Deep Learning models such as Convolutional Neural Networks (CNNs) are very effective at extracting complex image features from medical X-rays. However, the limited interpretability of CNNs has hampered their deployment in medical settings as they failed to gain trust among clinicians. In this work, we propose an interactive framework to allow clinicians to ask what-if questions and intervene in the decisions of a CNN, with the aim of increasing trust in the system. The framework translates a layer of a trained CNN into a measurable and compact set of symbolic rules. Expert interactions with visualizations of the rules promote the use of clinically-relevant CNN kernels and attach meaning to the rules. The definition and relevance of the kernels are supported by radiomics analyses and permutation evaluations, respectively. CNN kernels that do not have a clinically-meaningful interpretation are removed without affecting model performance. By allowing clinicians to evaluate the impact of adding or removing kernels from the rule set, our approach produces an interpretable refinement of the data-driven CNN in alignment with medical best practice.

SUBMITTER: Ngan KH

PROVIDER: S-EPMC11006149 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

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From explanation to intervention: Interactive knowledge extraction from Convolutional Neural Networks used in radiology.

Ngan Kwun Ho KH Mansouri-Benssassi Esma E Phelan James J Townsend Joseph J Garcez Artur d'Avila AD

PloS one 20240410 4

Deep Learning models such as Convolutional Neural Networks (CNNs) are very effective at extracting complex image features from medical X-rays. However, the limited interpretability of CNNs has hampered their deployment in medical settings as they failed to gain trust among clinicians. In this work, we propose an interactive framework to allow clinicians to ask what-if questions and intervene in the decisions of a CNN, with the aim of increasing trust in the system. The framework translates a lay ...[more]

PMID: 38598468

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Project description:As an essential task in protein structure and function prediction, protein fold recognition has attracted increasing attention. The majority of the existing machine learning-based protein fold recognition approaches strongly rely on handcrafted features, which depict the characteristics of different protein folds; however, effective feature extraction methods still represent the bottleneck for further performance improvement of protein fold recognition. As a powerful feature extractor, deep convolutional neural network (DCNN) can automatically extract discriminative features for fold recognition without human intervention, which has demonstrated an impressive performance on protein fold recognition. Despite the encouraging progress, DCNN often acts as a black box, and as such, it is challenging for users to understand what really happens in DCNN and why it works well for protein fold recognition. In this study, we explore the intrinsic mechanism of DCNN and explain why it works for protein fold recognition using a visual explanation technique. More specifically, we first trained a VGGNet-based DCNN model, termed VGGNet-FE, which can extract fold-specific features from the predicted protein residue-residue contact map for protein fold recognition. Subsequently, based on the trained VGGNet-FE, we implemented a new contact-assisted predictor, termed VGGfold, for protein fold recognition; we then visualized what features were extracted by each of the convolutional layers in VGGNet-FE using a deconvolution technique. Furthermore, we visualized the high-level semantic information, termed fold-discriminative region, of a predicted contact map from the localization map obtained from the last convolutional layer of VGGNet-FE. It is visually confirmed that VGGNet-FE could effectively extract distinct fold-discriminative regions for different types of protein folds, thereby accounting for the improved performance of VGGfold for protein fold recognition. In summary, this study is of great significance for both understanding the working principle of DCNNs in protein fold recognition and exploring the relationship between the predicted protein contact map and protein tertiary structure. This proposed visualization method is flexible and applicable to address other DCNN-based bioinformatics and computational biology questions. The online web server of VGGfold is freely available at http://csbio.njust.edu.cn/bioinf/vggfold/.

Dataset Information

From explanation to intervention: Interactive knowledge extraction from Convolutional Neural Networks used in radiology.

Publications

From explanation to intervention: Interactive knowledge extraction from Convolutional Neural Networks used in radiology.

Similar Datasets

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