No abstract

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools.

Federated Learning is a distributed learning paradigm with two key challenges that differentiate it from traditional distributed optimization: (1) significant variability in terms of the systems characteristics on each device in the network (systems heterogeneity), and (2) non-identically distributed data across the network (statistical heterogeneity). In this work, we introduce a framework, FedProx, to tackle heterogeneity in federated networks. FedProx can be viewed as a generalization and re-parametrization of FedAvg, the current state-of-the-art method for federated learning. While FedProx makes only minor algorithmic modifications to FedAvg, these modifications have important ramifications both in theory and in practice. Theoretically, we provide convergence guarantees for our framework when learning over data from non-identical distributions (statistical heterogeneity), and while adhering to device-level systems constraints by allowing each participating device to perform a variable amount of work (systems heterogeneity). Practically, we demonstrate that FedProx allows for more robust convergence than FedAvg across a suite of federated datasets. In particular, in highly heterogeneous settings, FedProx demonstrates significantly more stable and accurate convergence behavior relative to FedAvg-improving absolute test accuracy by 22% on average.1 Privacy is a third key challenge in the federated setting. While not the focus of this work, standard privacy-preserving approaches such as differential privacy and secure multiparty communication can naturally be combined with the methods proposed herein-particularly since our framework proposes only lightweight algorithmic modifications to prior work.

Modern federated networks, such as those comprised of wearable devices, mobile phones, or autonomous vehicles, generate massive amounts of data each day. This wealth of data can help to learn models that can improve the user experience on each device. However, learning in federated settings presents new challenges at all stages of the machine learning pipeline. As the machine learning community begins to tackle these challenges, we are at a critical time to ensure that developments made in this area are grounded in real-world assumptions. To this end, we propose LEAF, a modular benchmarking framework for learning in federated settings. LEAF includes a suite of open-source federated datasets, a rigorous evaluation framework, and a set of reference implementations, all geared towards capturing the obstacles and intricacies of practical federated environments.

Federated learning aims to jointly learn statistical models over massively distributed remote devices. In this work, we propose FedDANE, an optimization method that we adapt from DANE [9, 10], a method for classical distributed optimization, to handle the practical constraints of federated learning. We provide convergence guarantees for this method when learning over both convex and non-convex functions. Despite encouraging theoretical results, we find that the method has underwhelming performance empirically. In particular, through empirical simulations on both synthetic and real-world datasets, FedDANE consistently underperforms baselines of FedAvg [8] and FedProx [6] in realistic federated settings. We identify low device participation and statistical device heterogeneity as two underlying causes of this underwhelming performance, and conclude by suggesting several directions of future work.