NeurIPS 2022 Papers

Illuminating interactions between proteins and small drug molecules is a long-standing challenge in the field of drug discovery. Despite the importance of understanding these interactions, most previous works are limited by hand-designed scoring functions and insufficient conformation sampling. The recently-proposed graph neural network-based methods provides alternatives to predict protein-ligand complex conformation in a one-shot manner. However, these methods neglect the geometric constraints of the complex structure and weaken the role of local functional regions. As a result, they might produce unreasonable conformations for challenging targets and generalize poorly to novel proteins. In this paper, we propose Trigonometry-Aware Neural networKs for binding structure prediction, TANKBind, that builds trigonometry constraint as a vigorous inductive bias into the model and explicitly attends to all possible binding sites for each protein by segmenting the whole protein into functional blocks. We construct novel contrastive losses with local region negative sampling to jointly optimize the binding interaction and affinity. Extensive experiments show substantial performance gains in comparison to state-of-the-art physics-based and deep learning-based methods on commonly-used benchmark datasets for both binding structure and affinity predictions with variant settings.

We study the task of efficiently sampling from a Gibbs distribution $d \pi^* = e^{-h} d {\text{vol}}_g$ over a Riemannian manifold $M$ via (geometric) Langevin MCMC; this algorithm involves computing exponential maps in random Gaussian directions and is efficiently implementable in practice. The key to our analysis of Langevin MCMC is a bound on the discretization error of the geometric Euler-Murayama scheme, assuming $\nabla h$ is Lipschitz and $M$ has bounded sectional curvature. Our error bound matches the error of Euclidean Euler-Murayama in terms of its stepsize dependence. Combined with a contraction guarantee for the geometric Langevin Diffusion under Kendall-Cranston coupling, we prove that the Langevin MCMC iterates lie within $\epsilon$-Wasserstein distance of $\pi^*$ after $\tilde{O}(\epsilon^{-2})$ steps, which matches the iteration complexity for Euclidean Langevin MCMC. Our results apply in general settings where $h$ can be nonconvex and $M$ can have negative Ricci curvature. Under additional assumptions that the Riemannian curvature tensor has bounded derivatives, and that $\pi^*$ satisfies a $CD(\cdot,\infty)$ condition, we analyze the stochastic gradient version of Langevin MCMC, and bound its iteration complexity by $\tilde{O}(\epsilon^{-2})$ as well.

The Differentiable ARchiTecture Search (DARTS) has dominated the neural architecture search community due to its search efficiency and simplicity. DARTS leverages continuous relaxation to convert the intractable operation selection problem into a continuous magnitude optimization problem which can be easily handled with gradient-descent, while it poses an additional challenge in measuring the operation importance or selecting an architecture from the optimized magnitudes. The vanilla DARTS assumes the optimized magnitudes reflect the importance of operations, while more recent works find this naive assumption leads to poor generalization and is without any theoretical guarantees. In this work, we leverage influence functions, the functional derivatives of the loss function, to theoretically reveal the operation selection part in DARTS and estimate the candidate operation importance by approximating its influence on the supernet with Taylor expansions. We show the operation strength is not only related to the magnitude but also second-order information, leading to a fundamentally new criterion for operation selection in DARTS, named Influential Magnitude. Empirical studies across different tasks on several spaces show that vanilla DARTS and its variants can avoid most failures by leveraging the proposed theory-driven operation selection criterion.

Constrained reinforcement learning (RL) is an area of RL whose objective is to find an optimal policy that maximizes expected cumulative return while satisfying a given constraint. Most of the previous constrained RL works consider expected cumulative sum cost as the constraint. However, optimization with this constraint cannot guarantee a target probability of outage event that the cumulative sum cost exceeds a given threshold. This paper proposes a framework, named Quantile Constrained RL (QCRL), to constrain the quantile of the distribution of the cumulative sum cost that is a necessary and sufficient condition to satisfy the outage constraint. This is the first work that tackles the issue of applying the policy gradient theorem to the quantile and provides theoretical results for approximating the gradient of the quantile. Based on the derived theoretical results and the technique of the Lagrange multiplier, we construct a constrained RL algorithm named Quantile Constrained Policy Optimization (QCPO). We use distributional RL with the Large Deviation Principle (LDP) to estimate quantiles and tail probability of the cumulative sum cost for the implementation of QCPO. The implemented algorithm satisfies the outage probability constraint after the training period.

In the last years, neural networks (NN) have evolved from laboratory environments to the state-of-the-art for many real-world problems. It was shown that NN models (i.e., their weights and biases) evolve on unique trajectories in weight space during training. Following, a population of such neural network models (referred to as model zoo) would form structures in weight space. We think that the geometry, curvature and smoothness of these structures contain information about the state of training and can reveal latent properties of individual models. With such model zoos, one could investigate novel approaches for (i) model analysis, (ii) discover unknown learning dynamics, (iii) learn rich representations of such populations, or (iv) exploit the model zoos for generative modelling of NN weights and biases. Unfortunately, the lack of standardized model zoos and available benchmarks significantly increases the friction for further research about populations of NNs. With this work, we publish a novel dataset of model zoos containing systematically generated and diverse populations of NN models for further research. In total the proposed model zoo dataset is based on eight image datasets, consists of 27 model zoos trained with varying hyperparameter combinations and includes 50’360 unique NN models as well as their sparsified twins, resulting in over 3’844’360 collected model states. Additionally, to the model zoo data we provide an in-depth analysis of the zoos and provide benchmarks for multiple downstream tasks. The dataset can be found at www.modelzoos.cc.

Learning functions with high-dimensional outputs is critical in many applications, such as physical simulation and engineering design. However, collecting training examples for these applications is often costly, e.g., by running numerical solvers. The recent work (Li et al., 2022) proposes the first multi-fidelity active learning approach for high-dimensional outputs, which can acquire examples at different fidelities to reduce the cost while improving the learning performance. However, this method only queries at one pair of fidelity and input at a time, and hence has a risk of bringing in strongly correlated examples to reduce the learning efficiency. In this paper, we propose Batch Multi-Fidelity Active Learning with Budget Constraints (BMFAL-BC), which can promote the diversity of training examples to improve the benefit-cost ratio, while respecting a given budget constraint for batch queries. Hence, our method can be more practically useful. Specifically, we propose a novel batch acquisition function that measures the mutual information between a batch of multi-fidelity queries and the target function, so as to penalize highly correlated queries and encourages diversity. The optimization of the batch acquisition function is challenging in that it involves a combinatorial search over many fidelities while subject to the budget constraint. To address this challenge, we develop a weighted greedy algorithm that can sequentially identify each (fidelity, input) pair, while achieving a near $(1 - 1/e)$-approximation of the optimum. We show the advantage of our method in several computational physics and engineering applications.

Transformer is a transformative framework for deep learning which models sequential data and has achieved remarkable performance on a wide range of tasks, but with high computational and energy cost. To improve its efficiency, a popular choice is to compress the models via binarization which constrains the floating-point values into binary ones to save resource consumption owing to cheap bitwise operations significantly. However, existing binarization methods only aim at minimizing the information loss for the input distribution statistically, while ignoring the pairwise similarity modeling at the core of the attention mechanism. To this end, we propose a new binarization paradigm customized to high-dimensional softmax attention via kernelized hashing, called EcoFormer, to map the original queries and keys into low-dimensional binary codes in Hamming space. The kernelized hash functions are learned to match the ground-truth similarity relations extracted from the attention map in a self-supervised way. Based on the equivalence between the inner product of binary codes and the Hamming distance as well as the associative property of matrix multiplication, we can approximate the attention in linear complexity by expressing it as a dot-product of binary codes. Moreover, the compact binary representations of queries and keys in EcoFormer enable us to replace most of the expensive multiply-accumulate operations in attention with simple accumulations to save considerable on-chip energy footprint on edge devices. Extensive experiments on both vision and language tasks show that EcoFormer consistently achieves comparable performance with standard attentions while consuming much fewer resources. For example, based on PVTv2-B0 and ImageNet-1K, EcoFormer achieves a 73% reduction in on-chip energy footprint with only a slight performance drop of 0.33% compared to the standard attention. Code is available at https://github.com/ziplab/EcoFormer.

A fundamental component of human vision is our ability to parse complex visual scenes and judge the relations between their constituent objects. AI benchmarks for visual reasoning have driven rapid progress in recent years with state-of-the-art systems now reaching human accuracy on some of these benchmarks. Yet, there remains a major gap between humans and AI systems in terms of the sample efficiency with which they learn new visual reasoning tasks. Humans' remarkable efficiency at learning has been at least partially attributed to their ability to harness compositionality -- allowing them to efficiently take advantage of previously gained knowledge when learning new tasks. Here, we introduce a novel visual reasoning benchmark, Compositional Visual Relations (CVR), to drive progress towards the development of more data-efficient learning algorithms. We take inspiration from fluidic intelligence and non-verbal reasoning tests and describe a novel method for creating compositions of abstract rules and generating image datasets corresponding to these rules at scale. Our proposed benchmark includes measures of sample efficiency, generalization, compositionality, and transfer across task rules. We systematically evaluate modern neural architectures and find that convolutional architectures surpass transformer-based architectures across all performance measures in most data regimes. However, all computational models are much less data efficient than humans, even after learning informative visual representations using self-supervision. Overall, we hope our challenge will spur interest in developing neural architectures that can learn to harness compositionality for more efficient learning.

As an important framework for safe Reinforcement Learning, the Constrained Markov Decision Process (CMDP) has been extensively studied in the recent literature. However, despite the rich results under various on-policy learning settings, there still lacks some essential understanding of the offline CMDP problems, in terms of both the algorithm design and the information theoretic sample complexity lower bound. In this paper, we focus on solving the CMDP problems where only offline data are available. By adopting the concept of the single-policy concentrability coefficient $C^*$, we establish an $\Omega\left(\frac{\min\left\{|\mathcal{S}||\mathcal{A}|,|\mathcal{S}|+I\right\} C^*}{(1-\gamma)^3\epsilon^2}\right)$ sample complexity lower bound for the offline CMDP problem, where $I$ stands for the number of constraints. By introducing a simple but novel deviation control mechanism, we propose a near-optimal primal-dual learning algorithm called DPDL. This algorithm provably guarantees zero constraint violation and its sample complexity matches the above lower bound except for an $\tilde{\mathcal{O}}((1-\gamma)^{-1})$ factor. Comprehensive discussion on how to deal with the unknown constant $C^*$ and the potential asynchronous structure on the offline dataset are also included.

Existing gradient-based optimization methods update parameters locally, in a direction that minimizes the loss function. We study a different approach, symmetry teleportation, that allows parameters to travel a large distance on the loss level set, in order to improve the convergence speed in subsequent steps. Teleportation exploits symmetries in the loss landscape of optimization problems. We derive loss-invariant group actions for test functions in optimization and multi-layer neural networks, and prove a necessary condition for teleportation to improve convergence rate. We also show that our algorithm is closely related to second order methods. Experimentally, we show that teleportation improves the convergence speed of gradient descent and AdaGrad for several optimization problems including test functions, multi-layer regressions, and MNIST classification.

Computer simulations have proven a valuable tool for understanding complex phenomena across the sciences. However, the utility of simulators for modelling and forecasting purposes is often restricted by low data quality, as well as practical limits to model fidelity. In order to circumvent these difficulties, we argue that modellers must treat simulators as idealistic representations of the true data generating process, and consequently should thoughtfully consider the risk of model misspecification. In this work we revisit neural posterior estimation (NPE), a class of algorithms that enable black-box parameter inference in simulation models, and consider the implication of a simulation-to-reality gap. While recent works have demonstrated reliable performance of these methods, the analyses have been performed using synthetic data generated by the simulator model itself, and have therefore only addressed the well-specified case. In this paper, we find that the presence of misspecification, in contrast, leads to unreliable inference when NPE is used naïvely. As a remedy we argue that principled scientific inquiry with simulators should incorporate a model criticism component, to facilitate interpretable identification of misspecification and a robust inference component, to fit ‘wrong but useful’ models. We propose robust neural posterior estimation (RNPE), an extension of NPE to simultaneously achieve both these aims, through explicitly modelling the discrepancies between simulations and the observed data. We assess the approach on a range of artificially misspecified examples, and find RNPE performs well across the tasks, whereas naïvely using NPE leads to misleading and erratic posteriors.

This paper studies a simple extension of image-based Masked Autoencoders (MAE) to self-supervised representation learning from audio spectrograms. Following the Transformer encoder-decoder design in MAE, our Audio-MAE first encodes audio spectrogram patches with a high masking ratio, feeding only the non-masked tokens through encoder layers. The decoder then re-orders and decodes the encoded context padded with mask tokens, in order to reconstruct the input spectrogram. We find it beneficial to incorporate local window attention in the decoder, as audio spectrograms are highly correlated in local time and frequency bands. We then fine-tune the encoder with a lower masking ratio on target datasets. Empirically, Audio-MAE sets new state-of-the-art performance on six audio and speech classification tasks, outperforming other recent models that use external supervised pre-training. Our code and models is available at https://github.com/facebookresearch/AudioMAE.

State-of-the-art Mixed Integer Linear Programming (MILP) solvers combine systematic tree search with a plethora of hard-coded heuristics, such as branching rules. While approaches to learn branching strategies have received increasing attention and have shown very promising results, most of the literature focuses on learning fast approximations of the \emph{strong branching} rule. Instead, we propose to learn branching rules from scratch with Reinforcement Learning (RL). We revisit the work of Etheve et al. (2020) and propose a generalization of Markov Decisions Processes (MDP), which we call \emph{tree MDP}, that provides a more suitable formulation of the branching problem. We derive a policy gradient theorem for tree MDPs that exhibits a better credit assignment compared to its temporal counterpart. We demonstrate through computational experiments that this new framework is suitable to tackle the learning-to-branch problem in MILP, and improves the learning convergence.

Groundbreaking language-vision architectures like CLIP and DALL-E proved the utility of training on large amounts of noisy image-text data, without relying on expensive accurate labels used in standard vision unimodal supervised learning. The resulting models showed capabilities of strong text-guided image generation and transfer to downstream tasks, while performing remarkably at zero-shot classification with noteworthy out-of-distribution robustness. Since then, large-scale language-vision models like ALIGN, BASIC, GLIDE, Flamingo and Imagen made further improvements. Studying the training and capabilities of such models requires datasets containing billions of image-text pairs. Until now, no datasets of this size have been made openly available for the broader research community. To address this problem and democratize research on large-scale multi-modal models, we present LAION-5B - a dataset consisting of 5.85 billion CLIP-filtered image-text pairs, of which 2.32B contain English language. We show successful replication and fine-tuning of foundational models like CLIP, GLIDE and Stable Diffusion using the dataset, and discuss further experiments enabled with an openly available dataset of this scale. Additionally we provide several nearest neighbor indices, an improved web-interface for dataset exploration and subset generation, and detection scores for watermark, NSFW, and toxic content detection.

Bayesian coresets approximate a posterior distribution by building a small weighted subset of the data points. Any inference procedure that is too computationally expensive to be run on the full posterior can instead be run inexpensively on the coreset, with results that approximate those on the full data. However, current approaches are limited by either a significant run-time or the need for the user to specify a low-cost approximation to the full posterior. We propose a Bayesian coreset construction algorithm that first selects a uniformly random subset of data, and then optimizes the weights using a novel quasi-Newton method. Our algorithm is a simple to implement, black-box method, that does not require the user to specify a low-cost posterior approximation. It is the first to come with a general high-probability bound on the KL divergence of the output coreset posterior. Experiments demonstrate that our method provides significant improvements in coreset quality against alternatives with comparable construction times, with far less storage cost and user input required.

Distillation with unlabeled examples is a popular and powerful method for training deep neural networks in settings where the amount of labeled data is limited: A large “teacher” neural network is trained on the labeled data available, and then it is used to generate labels on an unlabeled dataset (typically much larger in size). These labels are then utilized to train the smaller “student” model which will actually be deployed. Naturally, the success of the approach depends on the quality of the teacher’s labels, since the student could be confused if trained on inaccurate data. This paper proposes a principled approach for addressing this issue based on a “debiasing" reweighting of the student’s loss function tailored to the distillation training paradigm. Our method is hyper-parameter free, data-agnostic, and simple to implement. We demonstrate significant improvements on popular academic datasets and we accompany our results with a theoretical analysis which rigorously justifies the performance of our method in certain settings.

An influential framework within systems neuroscience posits that neural computations can be understood in terms of low-dimensional dynamics in recurrent circuits. A number of methods have thus been developed to extract latent dynamical systems from neural recordings, but inferring models that are both predictive and interpretable remains a difficult challenge. Here we propose a new method called Low-rank Inference from Neural Trajectories (LINT), based on a class of low-rank recurrent neural networks (lrRNNs) for which a link between connectivity and dynamics has been previously demonstrated. By fitting such networks to trajectories of neural activity, LINT yields a mechanistic model of latent dynamics, as well as a set of axes for dimensionality reduction and verifiable predictions for inactivations of specific populations of neurons. Here, we first demonstrate the consistency of our method and apply it to two use cases: (i) we reverse-engineer "black-box" vanilla RNNs trained to perform cognitive tasks, and (ii) we infer latent dynamics and neural contributions from electrophysiological recordings of nonhuman primates performing a similar task.

Successful applications of InfoNCE (Information Noise-Contrastive Estimation) and its variants have popularized the use of contrastive variational mutual information (MI) estimators in machine learning . While featuring superior stability, these estimators crucially depend on costly large-batch training, and they sacrifice bound tightness for variance reduction. To overcome these limitations, we revisit the mathematics of popular variational MI bounds from the lens of unnormalized statistical modeling and convex optimization. Our investigation yields a new unified theoretical framework encompassing popular variational MI bounds, and leads to a novel, simple, and powerful contrastive MI estimator we name FLO. Theoretically, we show that the FLO estimator is tight, and it converges under stochastic gradient descent. Empirically, the proposed FLO estimator overcomes the limitations of its predecessors and learns more efficiently. The utility of FLO is verified using extensive benchmarks, and we further inspire the community with novel applications in meta-learning. Our presentation underscores the foundational importance of variational MI estimation in data-efficient learning.

There has been a significant research effort focused on explaining predictive models, for example through post-hoc explainability and recourse methods. Most of the proposed techniques operate upon a single, fixed, predictive model. However, it is well-known that given a dataset and a predictive task, there may be a multiplicity of models that solve the problem (nearly) equally well. In this work, we investigate the implications of this kind of model indeterminacy on the post-hoc explanations of predictive models. We show how it can lead to explanatory multiplicity, and we explore the underlying drivers. We show how predictive multiplicity, and the related concept of epistemic uncertainty, are not reliable indicators of explanatory multiplicity. We further illustrate how a set of models showing very similar aggregate performance on a test dataset may show large variations in their local explanations, i.e., for a specific input. We explore these effects for Shapley value based explanations on three risk assessment datasets. Our results indicate that model indeterminacy may have a substantial impact on explanations in practice, leading to inconsistent and even contradicting explanations.