We consider the prediction of interfaces between proteins, a challenging problem with important applications in drug discovery and design, and examine the performance of existing and newly proposed spatial graph convolution operators for this task. By performing convolution over a local neighborhood of a node of interest, we are able to stack multiple layers of convolution and learn effective latent representations that integrate information across the graph that represent the three dimensional structure of a protein of interest. An architecture that combines the learned features across pairs of proteins is then used to classify pairs of amino acid residues as part of an interface or not. In our experiments, several graph convolution operators yielded accuracy that is better than the state-of-the-art SVM method in this task.

The Euclidean k-means problem is arguably the most widely-studied clustering problem in machine learning. While the k-means objective is NP-hard in the worst-case, practitioners have enjoyed remarkable success in applying heuristics like Lloyd's algorithm for this problem. To address this disconnect, we study the following question: what properties of real-world instances will enable us to design efficient algorithms and prove guarantees for finding the optimal clustering? We consider a natural notion called additive perturbation stability that we believe captures many practical instances of Euclidean k-means clustering. Stable instances have unique optimal k-means solutions that does not change even when each point is perturbed a little (in Euclidean distance). This captures the property that k-means optimal solution should be tolerant to measurement errors and uncertainty in the points. We design efficient algorithms that provably recover the optimal clustering for instances that are additive perturbation stable. When the instance has some additional separation, we can design a simple, efficient algorithm with provable guarantees that is also robust to outliers. We also complement these results by studying the amount of stability in real datasets, and demonstrating that our algorithm performs well on these benchmark datasets.

Source coding is the canonical problem of data compression in information theory. In a locally encodable source coding, each compressed bit depends on only few bits of the input. In this paper, we show that a recently popular model of semisupervised clustering is equivalent to locally encodable source coding. In this model, the task is to perform multiclass labeling of unlabeled elements. At the beginning, we can ask in parallel a set of simple queries to an oracle who provides (possibly erroneous) binary answers to the queries. The queries cannot involve more than two (or a fixed constant number $\Delta$ of) elements. Now the labeling of all the elements (or clustering) must be performed based on the (noisy) query answers. The goal is to recover all the correct labelings while minimizing the number of such queries. The equivalence to locally encodable source codes leads us to find lower bounds on the number of queries required in variety of scenarios. We are also able to show fundamental limitations of pairwise `same cluster' queries - and propose pairwise AND queries, that provably performs better in many situations.

We present a novel parallelisation scheme that simplifies the adaptation of learning algorithms to growing amounts of data as well as growing needs for accurate and confident predictions in critical applications. In contrast to other parallelisation techniques, it can be applied to a broad class of learning algorithms without further mathematical derivations and without writing dedicated code, while at the same time maintaining theoretical performance guarantees. Moreover, our parallelisation scheme is able to reduce the runtime of many learning algorithms to polylogarithmic time on quasi-polynomially many processing units. This is a significant step towards a general answer to an open question on efficient parallelisation of machine learning algorithms in the sense of Nick's Class (NC). The cost of this parallelisation is in the form of a larger sample complexity. Our empirical study confirms the potential of our parallelisation scheme with fixed numbers of processors and instances in realistic application scenarios.

One major obstacle towards AI is the poor ability of models to solve new problems quicker, and without forgetting previously acquired knowledge. To better understand this issue, we study the problem of continual learning, where the model observes, once and one by one, examples concerning a sequence of tasks. First, we propose a set of metrics to evaluate models learning over a continuum of data. These metrics characterize models not only by their test accuracy, but also in terms of their ability to transfer knowledge across tasks. Second, we propose a model for continual learning, called Gradient Episodic Memory (GEM) that alleviates forgetting, while allowing beneficial transfer of knowledge to previous tasks. Our experiments on variants of the MNIST and CIFAR-100 datasets demonstrate the strong performance of GEM when compared to the state-of-the-art.

Deep neural networks (NNs) are powerful black box predictors that have recently achieved impressive performance on a wide spectrum of tasks. Quantifying predictive uncertainty in NNs is a challenging and yet unsolved problem. Bayesian NNs, which learn a distribution over weights, are currently the state-of-the-art for estimating predictive uncertainty; however these require significant modifications to the training procedure and are computationally expensive compared to standard (non-Bayesian) NNs. We propose an alternative to Bayesian NNs that is simple to implement, readily parallelizable, requires very little hyperparameter tuning, and yields high quality predictive uncertainty estimates. Through a series of experiments on classification and regression benchmarks, we demonstrate that our method produces well-calibrated uncertainty estimates which are as good or better than approximate Bayesian NNs. To assess robustness to dataset shift, we evaluate the predictive uncertainty on test examples from known and unknown distributions, and show that our method is able to express higher uncertainty on out-of-distribution examples. We demonstrate the scalability of our method by evaluating predictive uncertainty estimates on ImageNet.

We initiate a systematic investigation of distribution learning (density estimation) when the data is distributed across multiple servers. The servers must communicate with a referee and the goal is to estimate the underlying distribution with as few bits of communication as possible. We focus on non-parametric density estimation of discrete distributions with respect to the l1 and l2 norms. We provide the first non-trivial upper and lower bounds on the communication complexity of this basic estimation task in various settings of interest. Specifically, our results include the following: 1. When the unknown discrete distribution is unstructured and each server has only one sample, we show that any blackboard protocol (i.e., any protocol in which servers interact arbitrarily using public messages) that learns the distribution must essentially communicate the entire sample. 2. For the case of structured distributions, such as k-histograms and monotone distributions, we design distributed learning algorithms that achieve significantly better communication guarantees than the naive ones, and obtain tight upper and lower bounds in several regimes. Our distributed learning algorithms run in near-linear time and are robust to model misspecification. Our results provide insights on the interplay between structure and communication efficiency for a range of fundamental distribution estimation tasks.

The design of good heuristics or approximation algorithms for NP-hard combinatorial optimization problems often requires significant specialized knowledge and trial-and-error. Can we automate this challenging, tedious process, and learn the algorithms instead? In many real-world applications, it is typically the case that the same optimization problem is solved again and again on a regular basis, maintaining the same problem structure but differing in the data. This provides an opportunity for learning heuristic algorithms that exploit the structure of such recurring problems. In this paper, we propose a unique combination of reinforcement learning and graph embedding to address this challenge. The learned greedy policy behaves like a meta-algorithm that incrementally constructs a solution, and the action is determined by the output of a graph embedding network capturing the current state of the solution. We show that our framework can be applied to a diverse range of optimization problems over graphs, and learns effective algorithms for the Minimum Vertex Cover, Maximum Cut and Traveling Salesman problems.

This paper presents a margin-based multiclass generalization bound for neural networks that scales with their margin-normalized "spectral complexity": their Lipschitz constant, meaning the product of the spectral norms of the weight matrices, times a certain correction factor. This bound is empirically investigated for a standard AlexNet network trained with SGD on the MNIST and CIFAR10 datasets, with both original and random labels; the bound, the Lipschitz constants, and the excess risks are all in direct correlation, suggesting both that SGD selects predictors whose complexity scales with the difficulty of the learning task, and secondly that the presented bound is sensitive to this complexity.

Hiererachical clustering, that is computing a recursive partitioning of a dataset to obtain clusters at increasingly finer granularity is a fundamental problem in data analysis. Although hierarchical clustering has mostly been studied through procedures such as linkage algorithms, or top-down heuristics, rather than as optimization problems, recently Dasgupta [1] proposed an objective function for hierarchical clustering and initiated a line of work developing algorithms that explicitly optimize an objective (see also [2, 3, 4]). In this paper, we consider a fairly general random graph model for hierarchical clustering, called the hierarchical stochastic blockmodel (HSBM), and show that in certain regimes the SVD approach of McSherry [5] combined with specific linkage methods results in a clustering that give an O(1)-approximation to Dasgupta’s cost function. We also show that an approach based on SDP relaxations for balanced cuts based on the work of Makarychev et al. [6], combined with the recursive sparsest cut algorithm of Dasgupta, yields an O(1) approximation in slightly larger regimes and also in the semi-random setting, where an adversary may remove edges from the random graph generated according to an HSBM. Finally, we report empirical evaluation on synthetic and real-world data showing that our proposed SVD-based method does indeed achieve a better cost than other widely-used heurstics and also results in a better classification accuracy when the underlying problem was that of multi-class classification.