BIODICA: a computational environment for Independent Component Analysis of omics data.

SUMMARY: We developed BIODICA, an integrated computational environment for application of independent component analysis (ICA) to bulk and single-cell molecular profiles, interpretation of the results in terms of biological functions and correlation with metadata. The computational core is the novel Python package stabilized-ica which provides interface to several ICA algorithms, a stabilization procedure, meta-analysis and component interpretation tools. BIODICA is equipped with a user-friendly graphical user interface, allowing non-experienced users to perform the ICA-based omics data analysis. The results are provided in interactive ways, thus facilitating communication with biology experts. AVAILABILITY AND IMPLEMENTATION: BIODICA is implemented in Java, Python and JavaScript. The source code is freely available on GitHub under the MIT and the GNU LGPL licenses. BIODICA is supported on all major operating systems. URL: https://sysbio-curie.github.io/biodica-environment/.

RadShap: An Explanation Tool for Highlighting the Contributions of Multiple Regions of Interest to the Prediction of Radiomic Models.

Explaining the decisions made by a radiomic model is of significant interest, as it can provide valuable insights into the information learned by complex models and foster trust in well-performing ones, thereby facilitating their clinical adoption. Promising radiomic approaches that aggregate information from multiple regions within an image currently lack suitable explanation tools that could identify the regions that most significantly influence their decisions. Here we present a model- and modality-agnostic tool (RadShap, https://github.com/ncaptier/radshap), based on Shapley values, that explains the predictions of multiregion radiomic models by highlighting the contribution of each individual region. Methods: The explanation tool leverages Shapley values to distribute the aggregative radiomic model's output among all the regions of interest of an image, highlighting their individual contribution. RadShap was validated using a retrospective cohort of 130 patients with advanced non-small cell lung cancer undergoing first-line immunotherapy. Their baseline PET scans were used to build 1,000 synthetic tasks to evaluate the degree of alignment between the tool's explanations and our data generation process. RadShap's potential was then illustrated through 2 real case studies by aggregating information from all segmented tumors: the prediction of the progression-free survival of the non-small cell lung cancer patients and the classification of the histologic tumor subtype. Results: RadShap demonstrated strong alignment with the ground truth, with a median frequency of 94% for consistently explained predictions in the synthetic tasks. In both real-case studies, the aggregative models yielded superior performance to the single-lesion models (average [±SD] time-dependent area under the receiver operating characteristic curve was 0.66 ± 0.02 for the aggregative survival model vs. 0.55 ± 0.04 for the primary tumor survival model). The tool's explanations provided relevant insights into the behavior of the aggregative models, highlighting that for the classification of the histologic subtype, the aggregative model used information beyond the biopsy site to correctly classify patients who were initially misclassified by a model focusing only on the biopsied tumor. Conclusion: RadShap aligned with ground truth explanations and provided valuable insights into radiomic models' behaviors. It is implemented as a user-friendly Python package with documentation and tutorials, facilitating its smooth integration into radiomic pipelines.

Promising Candidate Prognostic Biomarkers in [18F]FDG PET Images: Evaluation in Independent Cohorts of Non-Small Cell Lung Cancer Patients.

The normalized distances from the hot spot of radiotracer uptake (SUVmax) to the tumor centroid (NHOC) and to the tumor perimeter (NHOP) have recently been suggested as novel PET features reflecting tumor aggressiveness. These biomarkers characterizing the shift of SUVmax toward the lesion edge during tumor progression have been shown to be prognostic factors in breast and non-small cell lung cancer (NSCLC) patients. We assessed the impact of imaging parameters on NHOC and NHOP, their complementarity to conventional PET features, and their prognostic value for advanced-NSCLC patients. Methods: This retrospective study investigated baseline [18F]FDG PET scans: cohort 1 included 99 NSCLC patients with no treatment-related inclusion criteria (robustness study); cohort 2 included 244 NSCLC patients (survival analysis) treated with targeted therapy (93), immunotherapy (63), or immunochemotherapy (88). Although 98% of patients had metastases, radiomic features including SUVs were extracted from the primary tumor only. NHOCs and NHOPs were computed using 2 approaches: the normalized distance from the localization of SUVmax or SUVpeak to the tumor centroid or perimeter. Bland-Altman analyses were performed to investigate the impact of both spatial resolution (comparing PET images with and without gaussian postfiltering) and image sampling (comparing 2 voxel sizes) on feature values. The correlation of NHOCs and NHOPs with other features was studied using Spearman correlation coefficients (r). The ability of NHOCs and NHOPs to predict overall survival (OS) was estimated using the Kaplan-Meier method. Results: In cohort 1, NHOC and NHOP features were more robust to image filtering and to resampling than were SUVs. The correlations were weak between NHOCs and NHOPs (r ≤ 0.45) and between NHOCs or NHOPs and any other radiomic features (r ≤ 0.60). In cohort 2, the patients with short OS demonstrated higher NHOCs and lower NHOPs than those with long OS. NHOCs significantly distinguished 2 survival profiles in patients treated with immunotherapy (log-rank test, P < 0.01), whereas NHOPs stratified patients regarding OS in the targeted therapy (P = 0.02) and immunotherapy (P < 0.01) subcohorts. Conclusion: Our findings suggest that even in advanced NSCLC patients, NHOC and NHOP features pertaining to the primary tumor have prognostic potential. Moreover, these features appeared to be robust with respect to imaging protocol parameters and complementary to other radiomic features and are now available in LIFEx software to be independently tested by others.