Dataset Information

Prediction of Lung Nodule Progression with an Uncertainty-Aware Hierarchical Probabilistic Network.

ABSTRACT: Predicting whether a lung nodule will grow, remain stable or regress over time, especially early in its follow-up, would help doctors prescribe personalized treatments and better surgical planning. However, the multifactorial nature of lung tumour progression hampers the identification of growth patterns. In this work, we propose a deep hierarchical generative and probabilistic network that, given an initial image of the nodule, predicts whether it will grow, quantifies its future size and provides its expected semantic appearance at a future time. Unlike previous solutions, our approach also estimates the uncertainty in the predictions from the intrinsic noise in medical images and the inter-observer variability in the annotations. The evaluation of this method on an independent test set reported a future tumour growth size mean absolute error of 1.74 mm, a nodule segmentation Dice's coefficient of 78% and a tumour growth accuracy of 84% on predictions made up to 24 months ahead. Due to the lack of similar methods for providing future lung tumour growth predictions, along with their associated uncertainty, we adapted equivalent deterministic and alternative generative networks (i.e., probabilistic U-Net, Bayesian test dropout and Pix2Pix). Our method outperformed all these methods, corroborating the adequacy of our approach.

SUBMITTER: Rafael-Palou X

PROVIDER: S-EPMC9689366 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Prediction of Lung Nodule Progression with an Uncertainty-Aware Hierarchical Probabilistic Network.

Rafael-Palou Xavier X Aubanell Anton A Ceresa Mario M Ribas Vicent V Piella Gemma G Ballester Miguel A González MAG

Diagnostics (Basel, Switzerland) 20221031 11

Predicting whether a lung nodule will grow, remain stable or regress over time, especially early in its follow-up, would help doctors prescribe personalized treatments and better surgical planning. However, the multifactorial nature of lung tumour progression hampers the identification of growth patterns. In this work, we propose a deep hierarchical generative and probabilistic network that, given an initial image of the nodule, predicts whether it will grow, quantifies its future size and provi ...[more]

PMID: 36359482

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Project description:Accumulation of gene mutations in cells is known to be responsible for tumor progression, driving it from benign states to malignant states. However, previous studies have shown that the detailed sequence of gene mutations, or the steps in tumor progression, may vary from tumor to tumor, making it difficult to infer the exact path that a given type of tumor may have taken.In this paper, we propose an effective probabilistic algorithm for reconstructing the tumor progression process based on partial knowledge of the underlying gene regulatory network and the steady state distribution of the gene expression values in a given tumor. We take the BNp (Boolean networks with pertubation) framework to model the gene regulatory networks. We assume that the true network is not exactly known but we are given an uncertainty class of networks that contains the true network. This network uncertainty class arises from our partial knowledge of the true network, typically represented as a set of local pathways that are embedded in the global network. Given the SSD of the cancerous network, we aim to simultaneously identify the true normal (healthy) network and the set of gene mutations that drove the network into the cancerous state. This is achieved by analyzing the effect of gene mutation on the SSD of a gene regulatory network. At each step, the proposed algorithm reduces the uncertainty class by keeping only those networks whose SSDs get close enough to the cancerous SSD as a result of additional gene mutation. These steps are repeated until we can find the best candidate for the true network and the most probable path of tumor progression.Simulation results based on both synthetic networks and networks constructed from actual pathway knowledge show that the proposed algorithm can identify the normal network and the actual path of tumor progression with high probability. The algorithm is also robust to model mismatch and allows us to control the trade-off between efficiency and accuracy.

Project description:IntroductionMachine learning models have shown promising potential in individual-level outcome prediction for patients with psychosis, but also have several limitations. To address some of these limitations, we present a model that predicts multiple outcomes, based on longitudinal patient data, while integrating prediction uncertainty to facilitate more reliable clinical decision-making.Material and methodsWe devised a recurrent neural network architecture incorporating long short-term memory (LSTM) units to facilitate outcome prediction by leveraging multimodal baseline variables and clinical data collected at multiple time points. To account for model uncertainty, we employed a novel fuzzy logic approach to integrate the level of uncertainty into individual predictions. We predicted antipsychotic treatment outcomes in 446 first-episode psychosis patients in the OPTiMiSE study, for six different clinical scenarios. The treatment outcome measures assessed at both week 4 and week 10 encompassed symptomatic remission, clinical global remission, and functional remission.ResultsUsing only baseline predictors to predict different outcomes at week 4, leave-one-site-out validation AUC ranged from 0.62 to 0.66; performance improved when clinical data from week 1 was added (AUC = 0.66-0.71). For outcome at week 10, using only baseline variables, the models achieved AUC = 0.56-0.64; using data from more time points (weeks 1, 4, and 6) improved the performance to AUC = 0.72-0.74. After incorporating prediction uncertainties and stratifying the model decisions based on model confidence, we could achieve accuracies above 0.8 for ~50% of patients in five out of the six clinical scenarios.ConclusionWe constructed prediction models utilizing a recurrent neural network architecture tailored to clinical scenarios derived from a time series dataset. One crucial aspect we incorporated was the consideration of uncertainty in individual predictions, which enhances the reliability of decision-making based on the model's output. We provided evidence showcasing the significance of leveraging time series data for achieving more accurate treatment outcome prediction in the field of psychiatry.

Dataset Information

Prediction of Lung Nodule Progression with an Uncertainty-Aware Hierarchical Probabilistic Network.

Publications

Prediction of Lung Nodule Progression with an Uncertainty-Aware Hierarchical Probabilistic Network.

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