Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling

Current treatment planning of patients diagnosed with brain tumor could significantly benefit by accessing the spatial distribution of tumor cell concentration. Existing diagnostic modalities, such as magnetic-resonance imaging (MRI), contrast sufficiently well areas of high cell density. However, they do not portray areas of low concentration, which can often serve as a source for the secondary appearance of the tumor after treatment. Numerical simulations of tumor growth could complement imaging information by providing estimates of full spatial distributions of tumor cells. Over recent years a corpus of literature on medical image-based tumor modeling was published. It includes different mathematical formalisms describing the forward tumor growth model. Alongside, various parametric inference schemes were developed to perform an efficient tumor model personalization, i.e. solving the inverse problem. However, the unifying drawback of all existing approaches is the time complexity of the model personalization that prohibits a potential integration of the modeling into clinical settings. In this work, we introduce a methodology for inferring patient-specific spatial distribution of brain tumor from T1Gd and FLAIR MRI medical scans. Coined as \textit{Learn-Morph-Infer} the method achieves real-time performance in the order of minutes on widely available hardware and the compute time is stable across tumor models of different complexity, such as reaction-diffusion and reaction-advection-diffusion models. We believe the proposed inverse solution approach not only bridges the way for clinical translation of brain tumor personalization but can also be adopted to other scientific and engineering domains.

NAS-Bench-301 and the Case for Surrogate Benchmarks for Neural Architecture Search

Neural Architecture Search (NAS) is a logical next step in the automatic learning of representations, but the development of NAS methods is slowed by high computational demands. As a remedy, several tabular NAS benchmarks were proposed to simulate runs of NAS methods in seconds. However, all existing NAS benchmarks are limited to extremely small architectural spaces since they rely on exhaustive evaluations of the space. This leads to unrealistic results, such as a strong performance of local search and random search, that do not transfer to larger search spaces. To overcome this fundamental limitation, we propose NAS-Bench-301, the first model-based surrogate NAS benchmark, using a search space containing $10^{18}$ architectures, orders of magnitude larger than any previous NAS benchmark. We first motivate the benefits of using such a surrogate benchmark compared to a tabular one by smoothing out the noise stemming from the stochasticity of single SGD runs in a tabular benchmark. Then, we analyze our new dataset consisting of architecture evaluations and comprehensively evaluate various regression models as surrogates to demonstrate their capability to model the architecture space, also using deep ensembles to model uncertainty. Finally, we benchmark a wide range of NAS algorithms using NAS-Bench-301 allowing us to obtain comparable results to the true benchmark at a fraction of the cost.

Auto-PyTorch Tabular: Multi-Fidelity MetaLearning for Efficient and Robust AutoDL

While early AutoML frameworks focused on optimizing traditional ML pipelines and their hyperparameters, a recent trend in AutoML is to focus on neural architecture search. In this paper, we introduce Auto-PyTorch, which brings the best of these two worlds together by jointly and robustly optimizing the architecture of networks and the training hyperparameters to enable fully automated deep learning (AutoDL). Auto-PyTorch achieves state-of-the-art performance on several tabular benchmarks by combining multi-fidelity optimization with portfolio construction for warmstarting and ensembling of deep neural networks (DNNs) and common baselines for tabular data. To thoroughly study our assumptions on how to design such an AutoDL system, we additionally introduce a new benchmark on learning curves for DNNs, dubbed LCBench, and run extensive ablation studies of the full Auto-PyTorch on typical AutoML benchmarks, eventually showing that Auto-PyTorch performs better than several state-of-the-art competitors on average.