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Register a new userSafety and Robustness in Decision Making: Deep Bayesian Recurrent Neural Networks for Somatic Variant Calling in Cancer
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The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology. This involves next generation sequencing of a tumor sample and the subsequent identification of genomic aberrations, such as somatic mutations, to provide potential candidates of targeted therapy. The identification of these aberrations from sequencing noise and germline variant background poses a classic classification-style problem. This has been previously broached with many different supervised machine learning methods, including deep-learning neural networks. However, these neural networks have thus far not been tailored to give any indication of confidence in the mutation call, meaning an oncologist could be targeting a mutation with a low probability of being true. To address this, we present here a deep bayesian recurrent neural network for cancer variant calling, which shows no degradation in performance compared to standard neural networks. This approach enables greater flexibility through different priors to avoid overfitting to a single dataset. We will be incorporating this approach into software for oncologists to obtain safe, robust, and statistically confident somatic mutation calls for precision oncology treatment choices.
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The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application of next generation sequencing technologies to a tumor sample, followed by the identification of mutations in the DNA known as somatic variants. The differentiation of these variants from sequencing error poses a classic classification problem, which has traditionally been approached with Bayesian statistics, and more recently with supervised machine learning methods such as neural networks. Although these methods provide greater accuracy, classic neural networks lack the ability to indicate the confidence of a variant call. In this paper, we explore the performance of deep Bayesian neural networks on next generation sequencing data, and their ability to give probability estimates for somatic variant calls. In addition to demonstrating similar performance in comparison to standard neural networks, we show that the resultant output probabilities make these better suited to the disparate and highly-variable sequencing data-sets these models are likely to encounter in the real world. We aim to deliver algorithms to oncologists for which model certainty better reflects accuracy, for improved clinical application. By moving away from point estimates to reliable confidence intervals, we expect the resultant clinical and treatment decisions to be more robust and more informed by the underlying reality of the tumor molecular profile.
We study probabilistic safety for Bayesian Neural Networks (BNNs) under adversarial input perturbations. Given a compact set of input points, $T subseteq mathbb{R}^m$, we study the probability w.r.t. the BNN posterior that all the points in $T$ are mapped to the same region $S$ in the output space. In particular, this can be used to evaluate the probability that a network sampled from the BNN is vulnerable to adversarial attacks. We rely on relaxation techniques from non-convex optimization to develop a method for computing a lower bound on probabilistic safety for BNNs, deriving explicit procedures for the case of interval and linear function propagation techniques. We apply our methods to BNNs trained on a regression task, airborne collision avoidance, and MNIST, empirically showing that our approach allows one to certify probabilistic safety of BNNs with millions of parameters.
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we show that the error rate can be reduced by improving the base calling process. Results: We present the first open-source DNA base caller for the MinION sequencing platform by Oxford Nanopore. By employing carefully crafted recurrent neural networks, our tool improves the base calling accuracy compared to the default base caller supplied by the manufacturer. This advance may further enhance applicability of MinION for genome sequencing and various clinical applications. Availability: DeepNano can be downloaded at http://compbio.fmph.uniba.sk/deepnano/. Contact: [email protected]
Great advancement in deep neural networks (DNNs) has led to state-of-the-art performance on a wide range of tasks. However, recent studies have shown that DNNs are vulnerable to adversarial attacks, which have brought great concerns when deploying these models to safety-critical applications such as autonomous driving. Different defense approaches have been proposed against adversarial attacks, including: 1) empirical defenses, which can be adaptively attacked again without providing robustness certification; and 2) certifiably robust approaches, which consist of robustness verification providing the lower bound of robust accuracy against any attacks under certain conditions and corresponding robust training approaches. In this paper, we focus on these certifiably robust approaches and provide the first work to perform large-scale systematic analysis of different robustness verification and training approaches. In particular, we 1) provide a taxonomy for the robustness verification and training approaches, as well as discuss the detailed methodologies for representative algorithms, 2) reveal the fundamental connections among these approaches, 3) discuss current research progresses, theoretical barriers, main challenges, and several promising future directions for certified defenses for DNNs, and 4) provide an open-sourced unified platform to evaluate 20+ representative verification and corresponding robust training approaches on a wide range of DNNs.
Existing neural network-based autonomous systems are shown to be vulnerable against adversarial attacks, therefore sophisticated evaluation on their robustness is of great importance. However, evaluating the robustness only under the worst-case scenarios based on known attacks is not comprehensive, not to mention that some of them even rarely occur in the real world. In addition, the distribution of safety-critical data is usually multimodal, while most traditional attacks and evaluation methods focus on a single modality. To solve the above challenges, we propose a flow-based multimodal safety-critical scenario generator for evaluating decisionmaking algorithms. The proposed generative model is optimized with weighted likelihood maximization and a gradient-based sampling procedure is integrated to improve the sampling efficiency. The safety-critical scenarios are generated by querying the task algorithms and the log-likelihood of the generated scenarios is in proportion to the risk level. Experiments on a self-driving task demonstrate our advantages in terms of testing efficiency and multimodal modeling capability. We evaluate six Reinforcement Learning algorithms with our generated traffic scenarios and provide empirical conclusions about their robustness.
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