NeurIPS 2020 Papers

Haplotype assembly and viral quasispecies reconstruction are challenging tasks concerned with analysis of genomic mixtures using sequencing data. High-throughput sequencing technologies generate enormous amounts of short fragments (reads) which essentially oversample components of a mixture; the representation redundancy enables reconstruction of the components (haplotypes, viral strains). The reconstruction problem, known to be NP-hard, boils down to grouping together reads originating from the same component in a mixture. Existing methods struggle to solve this problem with required level of accuracy and low runtimes; the problem is becoming increasingly more challenging as the number and length of the components increase. This paper proposes a read clustering method based on a convolutional auto-encoder designed to first project sequenced fragments to a low-dimensional space and then estimate the probability of the read origin using learned embedded features. The components are reconstructed by finding consensus sequences that agglomerate reads from the same origin. Mini-batch stochastic gradient descent and dimension reduction of reads allow the proposed method to efficiently deal with massive numbers of long reads. Experiments on simulated, semi-experimental and experimental data demonstrate the ability of the proposed method to accurately reconstruct haplotypes and viral quasispecies, often demonstrating superior performance compared to state-of-the-art methods. Source codes are available at https://github.com/WuLoli/CAECseq.

We propose an adaptively weighted stochastic gradient Langevin dynamics algorithm (SGLD), so-called contour stochastic gradient Langevin dynamics (CSGLD), for Bayesian learning in big data statistics. The proposed algorithm is essentially a scalable dynamic importance sampler, which automatically flattens the target distribution such that the simulation for a multi-modal distribution can be greatly facilitated. Theoretically, we prove a stability condition and establish the asymptotic convergence of the self-adapting parameter to a unique fixed-point, regardless of the non-convexity of the original energy function; we also present an error analysis for the weighted averaging estimators. Empirically, the CSGLD algorithm is tested on multiple benchmark datasets including CIFAR10 and CIFAR100. The numerical results indicate its superiority over the existing state-of-the-art algorithms in training deep neural networks.

We analyze continuous-time mirror descent applied to sparse phase retrieval, which is the problem of recovering sparse signals from a set of magnitude-only measurements. We apply mirror descent to the unconstrained empirical risk minimization problem (batch setting), using the square loss and square measurements. We provide a full convergence analysis of the algorithm in this non-convex setting and prove that, with the hypentropy mirror map, mirror descent recovers any $k$-sparse vector $\mathbf{x}^\star\in\mathbb{R}^n$ with minimum (in modulus) non-zero entry on the order of $\| \mathbf{x}^\star \|_2/\sqrt{k}$ from $k^2$ Gaussian measurements, modulo logarithmic terms. This yields a simple algorithm which, unlike most existing approaches to sparse phase retrieval, adapts to the sparsity level, without including thresholding steps or adding regularization terms. Our results also provide a principled theoretical understanding for Hadamard Wirtinger flow [54], as Euclidean gradient descent applied to the empirical risk problem with Hadamard parametrization can be recovered as a first-order approximation to mirror descent in discrete time.

A recent line of work has shown a qualitative equivalence between differentially private PAC learning and online learning: A concept class is privately learnable if and only if it is online learnable with a finite mistake bound. However, both directions of this equivalence incur significant losses in both sample and computational efficiency. Studying a special case of this connection, Gonen, Hazan, and Moran (NeurIPS 2019) showed that uniform or highly sample-efficient pure-private learners can be time-efficiently compiled into online learners. We show that, assuming the existence of one-way functions, such an efficient conversion is impossible even for general pure-private learners with polynomial sample complexity. This resolves a question of Neel, Roth, and Wu (FOCS 2019).

Human intelligence is characterized not only by the capacity to learn complex skills, but the ability to rapidly adapt and acquire new skills within an ever-changing environment. In this work we study how the learning of modular solutions can allow for effective generalization to both unseen and potentially differently distributed data. Our main postulate is that the combination of task segmentation, modular learning and memory-based ensembling can give rise to generalization on an exponentially growing number of unseen tasks. We provide a concrete instantiation of this idea using a combination of: (1) the Forget-Me-Not Process, for task segmentation and memory based ensembling; and (2) Gated Linear Networks, which in contrast to contemporary deep learning techniques use a modular and local learning mechanism. We demonstrate that this system exhibits a number of desirable continual learning properties: robustness to catastrophic forgetting, no negative transfer and increasing levels of positive transfer as more tasks are seen. We show competitive performance against both offline and online methods on standard continual learning benchmarks.

The support/query (S/Q) episodic training strategy has been widely used in modern meta-learning algorithms and is believed to improve their generalization ability to test environments. This paper conducts a theoretical investigation of this training strategy on generalization. From a stability perspective, we analyze the generalization error bound of generic meta-learning algorithms trained with such strategy. We show that the S/Q episodic training strategy naturally leads to a counterintuitive generalization bound of $O(1/\sqrt{n})$, which only depends on the task number $n$ but independent of the inner-task sample size $m$. Under the common assumption $m<

Current methods for training robust networks lead to a drop in test accuracy, which has led prior works to posit that a robustness-accuracy tradeoff may be inevitable in deep learning. We take a closer look at this phenomenon and first show that real image datasets are actually separated. With this property in mind, we then prove that robustness and accuracy should both be achievable for benchmark datasets through locally Lipschitz functions, and hence, there should be no inherent tradeoff between robustness and accuracy. Through extensive experiments with robustness methods, we argue that the gap between theory and practice arises from two limitations of current methods: either they fail to impose local Lipschitzness or they are insufficiently generalized. We explore combining dropout with robust training methods and obtain better generalization. We conclude that achieving robustness and accuracy in practice may require using methods that impose local Lipschitzness and augmenting them with deep learning generalization techniques.

Causal treatment effect estimation is a key problem that arises in a variety of real-world settings, from personalized medicine to governmental policy making. There has been a flurry of recent work in machine learning on estimating causal effects when one has access to an instrument. However, to achieve identifiability, they in general require one-size-fits-all assumptions such as an additive error model for the outcome. An alternative is partial identification, which provides bounds on the causal effect. Little exists in terms of bounding methods that can deal with the most general case, where the treatment itself can be continuous. Moreover, bounding methods generally do not allow for a continuum of assumptions on the shape of the causal effect that can smoothly trade off stronger background knowledge for more informative bounds. In this work, we provide a method for causal effect bounding in continuous distributions, leveraging recent advances in gradient-based methods for the optimization of computationally intractable objective functions. We demonstrate on a set of synthetic and real-world data that our bounds capture the causal effect when additive methods fail, providing a useful range of answers compatible with observation as opposed to relying on unwarranted structural assumptions.

We present a causal view on the robustness of neural networks against input manipulations, which applies not only to traditional classification tasks but also to general measurement data. Based on this view, we design a deep causal manipulation augmented model (deep CAMA) which explicitly models possible manipulations on certain causes leading to changes in the observed effect. We further develop data augmentation and test-time fine-tuning methods to improve deep CAMA's robustness. When compared with discriminative deep neural networks, our proposed model shows superior robustness against unseen manipulations. As a by-product, our model achieves disentangled representation which separates the representation of manipulations from those of other latent causes.

We introduce a generic \emph{two-loop} scheme for smooth minimax optimization with strongly-convex-concave objectives. Our approach applies the accelerated proximal point framework (or Catalyst) to the associated \emph{dual problem} and takes full advantage of existing gradient-based algorithms to solve a sequence of well-balanced strongly-convex-strongly-concave minimax problems. Despite its simplicity, this leads to a family of near-optimal algorithms with improved complexity over all existing methods designed for strongly-convex-concave minimax problems. Additionally, we obtain the first variance-reduced algorithms for this class of minimax problems with finite-sum structure and establish even faster convergence rate. Furthermore, when extended to the nonconvex-concave minimax optimization, our algorithm again achieves the state-of-the-art complexity for finding a stationary point. We carry out several numerical experiments showcasing the superiority of the Catalyst framework in practice.

The ability to compose learned skills to solve new tasks is an important property for lifelong-learning agents. In this work we formalise the logical composition of tasks as a Boolean algebra. This allows us to formulate new tasks in terms of the negation, disjunction and conjunction of a set of base tasks. We then show that by learning goal-oriented value functions and restricting the transition dynamics of the tasks, an agent can solve these new tasks with no further learning. We prove that by composing these value functions in specific ways, we immediately recover the optimal policies for all tasks expressible under the Boolean algebra. We verify our approach in two domains---including a high-dimensional video game environment requiring function approximation---where an agent first learns a set of base skills, and then composes them to solve a super-exponential number of new tasks.

Learning latent features from time series data is an important problem in both machine learning and brain function. One approach, called Slow Feature Analysis (SFA), leverages the slowness of many salient features relative to the rapidly varying input signals. Furthermore, when trained on naturalistic stimuli, SFA reproduces interesting properties of cells in the primary visual cortex and hippocampus, suggesting that the brain uses temporal slowness as a computational principle for learning latent features. However, despite the potential relevance of SFA for modeling brain function, there is currently no SFA algorithm with a biologically plausible neural network implementation, by which we mean an algorithm operates in the online setting and can be mapped onto a neural network with local synaptic updates. In this work, starting from an SFA objective, we derive an SFA algorithm, called Bio-SFA, with a biologically plausible neural network implementation. We validate Bio-SFA on naturalistic stimuli.

Humans easily interpret expressions that describe unfamiliar situations composed from familiar parts ("greet the pink brontosaurus by the ferris wheel"). Modern neural networks, by contrast, struggle to interpret novel compositions. In this paper, we introduce a new benchmark, gSCAN, for evaluating compositional generalization in situated language understanding. Going beyond a related benchmark that focused on syntactic aspects of generalization, gSCAN defines a language grounded in the states of a grid world, facilitating novel evaluations of acquiring linguistically motivated rules. For example, agents must understand how adjectives such as 'small' are interpreted relative to the current world state or how adverbs such as 'cautiously' combine with new verbs. We test a strong multi-modal baseline model and a state-of-the-art compositional method finding that, in most cases, they fail dramatically when generalization requires systematic compositional rules.

We take a Bayesian perspective to illustrate a connection between training speed and the marginal likelihood in linear models. This provides two major insights: first, that a measure of a model's training speed can be used to estimate its marginal likelihood. Second, that this measure, under certain conditions, predicts the relative weighting of models in linear model combinations trained to minimize a regression loss. We verify our results in model selection tasks for linear models and for the infinite-width limit of deep neural networks. We further provide encouraging empirical evidence that the intuition developed in these settings also holds for deep neural networks trained with stochastic gradient descent. Our results suggest a promising new direction towards explaining why neural networks trained with stochastic gradient descent are biased towards functions that generalize well.

We investigate neural network representations from a probabilistic perspective. Specifically, we leverage Bayesian nonparametrics to construct models of neural activations in Convolutional Neural Networks (CNNs) and latent representations in Variational Autoencoders (VAEs). This allows us to formulate a tractable complexity measure for distributions of neural activations and to explore global structure of latent spaces learned by VAEs. We use this machinery to uncover how memorization and two common forms of regularization, i.e. dropout and input augmentation, influence representational complexity in CNNs. We demonstrate that networks that can exploit patterns in data learn vastly less complex representations than networks forced to memorize. We also show marked differences between effects of input augmentation and dropout, with the latter strongly depending on network width. Next, we investigate latent representations learned by standard $\beta$-VAEs and Maximum Mean Discrepancy (MMD) $\beta$-VAEs. We show that aggregated posterior in standard VAEs quickly collapses to the diagonal prior when regularization strength increases. MMD-VAEs, on the other hand, learn more complex posterior distributions, even with strong regularization. While this gives a richer sample space, MMD-VAEs do not exhibit independence of latent dimensions. Finally, we leverage our probabilistic models as an effective sampling strategy for latent codes, improving quality of samples in VAEs with rich posteriors.

We consider online bandit learning in which at every time step, an algorithm has to make a decision and then observe only its reward. The goal is to design efficient (polynomial-time) algorithms that achieve a total reward approximately close to that of the best fixed decision in hindsight. In this paper, we introduce a new notion of $(\lambda,\mu)$-concave functions and present a bandit learning algorithm that achieves a performance guarantee which is characterized as a function of the concavity parameters $\lambda$ and $\mu$. The algorithm is based on the mirror descent algorithm in which the update directions follow the gradient of the multilinear extensions of the reward functions. The regret bound induced by our algorithm is $\widetilde{O}(\sqrt{T})$ which is nearly optimal. We apply our algorithm to auction design, specifically to welfare maximization, revenue maximization, and no-envy learning in auctions. In welfare maximization, we show that a version of fictitious play in smooth auctions guarantees a competitive regret bound which is determined by the smooth parameters. In revenue maximization, we consider the simultaneous second-price auctions with reserve prices in multi-parameter environments. We give a bandit algorithm which achieves the total revenue at least $1/2$ times that of the best fixed reserve prices in hindsight. In no-envy learning, we study the bandit item selection problem where the player valuation is submodular and provide an efficient $1/2$-approximation no-envy algorithm.

When a toddler is presented a new toy, their instinctual behaviour is to pick it up and inspect it with their hand and eyes in tandem, clearly searching over its surface to properly understand what they are playing with. At any instance here, touch provides high fidelity localized information while vision provides complementary global context. However, in 3D shape reconstruction, the complementary fusion of visual and haptic modalities remains largely unexplored. In this paper, we study this problem and present an effective chart-based approach to multi-modal shape understanding which encourages a similar fusion vision and touch information. To do so, we introduce a dataset of simulated touch and vision signals from the interaction between a robotic hand and a large array of 3D objects. Our results show that (1) leveraging both vision and touch signals consistently improves single- modality baselines; (2) our approach outperforms alternative modality fusion methods and strongly benefits from the proposed chart-based structure; (3) the reconstruction quality increases with the number of grasps provided; and (4) the touch information not only enhances the reconstruction at the touch site but also extrapolates to its local neighborhood.

Self-supervised learning methods have witnessed a recent surge of interest after proving successful in multiple application fields. In this work, we leverage these techniques, and we propose 3D versions for five different self-supervised methods, in the form of proxy tasks. Our methods facilitate neural network feature learning from unlabeled 3D images, aiming to reduce the required cost for expert annotation. The developed algorithms are 3D Contrastive Predictive Coding, 3D Rotation prediction, 3D Jigsaw puzzles, Relative 3D patch location, and 3D Exemplar networks. Our experiments show that pretraining models with our 3D tasks yields more powerful semantic representations, and enables solving downstream tasks more accurately and efficiently, compared to training the models from scratch and to pretraining them on 2D slices. We demonstrate the effectiveness of our methods on three downstream tasks from the medical imaging domain: i) Brain Tumor Segmentation from 3D MRI, ii) Pancreas Tumor Segmentation from 3D CT, and iii) Diabetic Retinopathy Detection from 2D Fundus images. In each task, we assess the gains in data-efficiency, performance, and speed of convergence. Interestingly, we also find gains when transferring the learned representations, by our methods, from a large unlabeled 3D corpus to a small downstream-specific dataset. We achieve results competitive to state-of-the-art solutions at a fraction of the computational expense. We publish our implementations for the developed algorithms (both 3D and 2D versions) as an open-source library, in an effort to allow other researchers to apply and extend our methods on their datasets.

We consider the problem of obtaining dense 3D reconstructions of deformable objects from single and partially occluded views. In such cases, the visual evidence is usually insufficient to identify a 3D reconstruction uniquely, so we aim at recovering several plausible reconstructions compatible with the input data. We suggest that ambiguities can be modeled more effectively by parametrizing the possible body shapes and poses via a suitable 3D model, such as SMPL for humans. We propose to learn a multi-hypothesis neural network regressor using a best-of-M loss, where each of the M hypotheses is constrained to lie on a manifold of plausible human poses by means of a generative model. We show that our method outperforms alternative approaches in ambiguous pose recovery on standard benchmarks for 3D humans, and in heavily occluded versions of these benchmarks.