Consider a collection of datasets generated by unknown interventions on an unknown structural causal model $G$. Recently, Bengio et al. (2020) conjectured that among all candidate models, $G$ is the fastest to adapt from one dataset to another, along with promising experiments. Indeed, intuitively $G$ has less mechanisms to adapt, but this justification is incomplete. Our contribution is a more thorough analysis of this hypothesis. We investigate the adaptation speed of cause-effect SCMs. Using convergence rates from stochastic optimization, we justify that a relevant proxy for adaptation speed is distance in parameter space after intervention. Applying this proxy to categorical and normal cause-effect models, we show two results. When the intervention is on the cause variable, the SCM with the correct causal direction is advantaged by a large factor. When the intervention is on the effect variable, we characterize the relative adaptation speed. Surprisingly, we find situations where the anticausal model is advantaged, falsifying the initial hypothesis.

Distributional shift is one of the major obstacles when transferring machine learning prediction systems from the lab to the real world. To tackle this problem, we assume that variation across training domains is representative of the variation we might encounter at test time, but also that shifts at test time may be more extreme in magnitude. In particular, we show that reducing differences in risk across training domains can reduce a model’s sensitivity to a wide range of extreme distributional shifts, including the challenging setting where the input contains both causal and anti-causal elements. We motivate this approach, Risk Extrapolation (REx), as a form of robust optimization over a perturbation set of extrapolated domains (MM-REx), and propose a penalty on the variance of training risks (V-REx) as a simpler variant. We prove that variants of REx can recover the causal mechanisms of the targets, while also providing robustness to changes in the input distribution (“covariate shift”). By appropriately trading-off robustness to causally induced distributional shifts and covariate shift, REx is able to outperform alternative methods such as Invariant Risk Minimization in situations where these types of shift co-occur.

Games generalize the single-objective optimization paradigm by introducing different objective functions for different players. Differentiable games often proceed by simultaneous or alternating gradient updates. In machine learning, games are gaining new importance through formulations like generative adversarial networks (GANs) and actor-critic systems. However, compared to single-objective optimization, game dynamics is more complex and less understood. In this paper, we analyze gradient-based methods with momentum on simple games. We prove that alternating updates are more stable than simultaneous updates. Next, we show both theoretically and empirically that alternating gradient updates with a negative momentum term achieves convergence in a difficult toy adversarial problem, but also on the notoriously difficult to train saturating GANs.

This paper presents a joint effort between a group of computer scientists and bioinformaticians to take an important step towards a general big data platform for genome analysis pipelines. The key goals of this study are to develop a thorough understanding of the strengths and limitations of big data technology for genomic data analysis, and to identify the key questions that the research community could address to realize the vision of personalized genomic medicine. Our platform, called Gesall, is based on the new "Wrapper Technology" that supports existing genomic data analysis programs in their native forms, without having to rewrite them. To do so, our system provides several layers of software, including a new Genome Data Parallel Toolkit (GDPT), which can be used to "wrap" existing data analysis programs. This platform offers a concrete context for evaluating big data technology for genomics: we report on super-linear speedup and sublinear speedup for various tasks, as well as the reasons why a parallel program could produce different results from those of a serial program. These results lead to key research questions that require a synergy between genomics scientists and computer scientists to find solutions.