NeurIPS 2021 论文列表

Machine learning could enable an unprecedented level of control in protein engineering for therapeutic and industrial applications. Critical to its use in designing proteins with desired properties, machine learning models must capture the protein sequence-function relationship, often termed fitness landscape. Existing benchmarks like CASP or CAFA assess structure and function predictions of proteins, respectively, yet they do not target metrics relevant for protein engineering. In this work, we introduce Fitness Landscape Inference for Proteins (FLIP), a benchmark for function prediction to encourage rapid scoring of representation learning for protein engineering. Our curated splits, baselines, and metrics probe model generalization in settings relevant for protein engineering, e.g. low-resource and extrapolative. Currently, FLIP encompasses experimental data across adeno-associated virus stability for gene therapy, protein domain B1 stability and immunoglobulin binding, and thermostability from multiple protein families. In order to enable ease of use and future expansion to new splits, all data are presented in a standard format. FLIP scripts and data are freely accessible at https://benchmark.protein.properties.

Most existing methods for conditional average treatment effect estimation are designed to estimate the effect of a single cause - only one variable can be intervened on at one time. However, many applications involve simultaneous intervention on multiple variables, which leads to multi-cause treatment effect problems. The multi-cause problem is challenging because one needs to overcome the confounding bias for a large number of treatment groups, each with a different cause combination. The combinatorial nature of the problem also leads to severe data scarcity - we only observe one factual outcome out of many potential outcomes. In this work, we propose Single-cause Perturbation (SCP), a novel two-step procedure to estimate the multi-cause treatment effect. SCP starts by augmenting the observational dataset with the estimated potential outcomes under single-cause interventions. It then performs covariate adjustment on the augmented dataset to obtain the estimator. SCP is agnostic to the exact choice of algorithm in either step. We show formally that the procedure is valid under standard assumptions in causal inference. We demonstrate the performance gain of SCP on extensive synthetic and semi-synthetic experiments.

Truncated linear regression is a classical challenge in Statistics, wherein a label, $y = w^T x + \varepsilon$, and its corresponding feature vector, $x \in \mathbb{R}^k$, are only observed if the label falls in some subset $S \subseteq \mathbb{R}$; otherwise the existence of the pair $(x, y)$ is hidden from observation. Linear regression with truncated observations has remained a challenge, in its general form, since the early works of [Tobin'58, Amemiya '73]. When the distribution of the error is normal with known variance, recent work of [Daskalakis et al. '19] provides computationally and statistically efficient estimators of the linear model, $w$. In this paper, we provide the first computationally and statistically efficient estimators for truncated linear regression when the noise variance is unknown, estimating both the linear model and the variance of the noise. Our estimator is based on an efficient implementation of Projected Stochastic Gradient Descent on the negative log-likelihood of the truncated sample. Importantly, we show that the error of our estimates is asymptotically normal, and we use this to provide explicit confidence regions for our estimates.

We propose a novel training method that integrates rules into deep learning, in a way the strengths of the rules are controllable at inference. Deep Neural Networks with Controllable Rule Representations (DeepCTRL) incorporates a rule encoder into the model coupled with a rule-based objective, enabling a shared representation for decision making. DeepCTRL is agnostic to data type and model architecture. It can be applied to any kind of rule defined for inputs and outputs. The key aspect of DeepCTRL is that it does not require retraining to adapt the rule strength -- at inference, the user can adjust it based on the desired operation point on accuracy vs. rule verification ratio. In real-world domains where incorporating rules is critical -- such as Physics, Retail and Healthcare -- we show the effectiveness of DeepCTRL in teaching rules for deep learning. DeepCTRL improves the trust and reliability of the trained models by significantly increasing their rule verification ratio, while also providing accuracy gains at downstream tasks. Additionally, DeepCTRL enables novel use cases such as hypothesis testing of the rules on data samples, and unsupervised adaptation based on shared rules between datasets.

A number of recent studies of continuous variational autoencoder (VAE) models have noted, either directly or indirectly, the tendency of various parameter gradients to drift towards infinity during training. Because such gradients could potentially contribute to numerical instabilities, and are often framed as a problematic phenomena to be avoided, it may be tempting to shift to alternative energy functions that guarantee bounded gradients. But it remains an open question: What might the unintended consequences of such a restriction be? To address this issue, we examine how unbounded gradients relate to the regularization of a broad class of autoencoder-based architectures, including VAE models, as applied to data lying on or near a low-dimensional manifold (e.g., natural images). Our main finding is that, if the ultimate goal is to simultaneously avoid over-regularization (high reconstruction errors, sometimes referred to as posterior collapse) and under-regularization (excessive latent dimensions are not pruned from the model), then an autoencoder-based energy function with infinite gradients around optimal representations is provably required per a certain technical sense which we carefully detail. Given that both over- and under-regularization can directly lead to poor generated sample quality or suboptimal feature selection, this result suggests that heuristic modifications to or constraints on the VAE energy function may at times be ill-advised, and large gradients should be accommodated to the extent possible.

The Hessian of a neural network captures parameter interactions through second-order derivatives of the loss. It is a fundamental object of study, closely tied to various problems in deep learning, including model design, optimization, and generalization. Most prior work has been empirical, typically focusing on low-rank approximations and heuristics that are blind to the network structure. In contrast, we develop theoretical tools to analyze the range of the Hessian map, which provide us with a precise understanding of its rank deficiency and the structural reasons behind it. This yields exact formulas and tight upper bounds for the Hessian rank of deep linear networks --- allowing for an elegant interpretation in terms of rank deficiency. Moreover, we demonstrate that our bounds remain faithful as an estimate of the numerical Hessian rank, for a larger class of models such as rectified and hyperbolic tangent networks. Further, we also investigate the implications of model architecture (e.g.~width, depth, bias) on the rank deficiency. Overall, our work provides novel insights into the source and extent of redundancy in overparameterized neural networks.

Transformers with linearised attention (''linear Transformers'') have demonstrated the practical scalability and effectiveness of outer product-based Fast Weight Programmers (FWPs) from the '90s. However, the original FWP formulation is more general than the one of linear Transformers: a slow neural network (NN) continually reprograms the weights of a fast NN with arbitrary architecture. In existing linear Transformers, both NNs are feedforward and consist of a single layer. Here we explore new variations by adding recurrence to the slow and fast nets. We evaluate our novel recurrent FWPs (RFWPs) on two synthetic algorithmic tasks (code execution and sequential ListOps), Wikitext-103 language models, and on the Atari 2600 2D game environment. Our models exhibit properties of Transformers and RNNs. In the reinforcement learning setting, we report large improvements over LSTM in several Atari games. Our code is public.

The growing literature of Federated Learning (FL) has recently inspired Federated Reinforcement Learning (FRL) to encourage multiple agents to federatively build a better decision-making policy without sharing raw trajectories. Despite its promising applications, existing works on FRL fail to I) provide theoretical analysis on its convergence, and II) account for random system failures and adversarial attacks. Towards this end, we propose the first FRL framework the convergence of which is guaranteed and tolerant to less than half of the participating agents being random system failures or adversarial attackers. We prove that the sample efficiency of the proposed framework is guaranteed to improve with the number of agents and is able to account for such potential failures or attacks. All theoretical results are empirically verified on various RL benchmark tasks.

Most existing temporal action localization (TAL) methods rely on a transfer learning pipeline: by first optimizing a video encoder on a large action classification dataset (i.e., source domain), followed by freezing the encoder and training a TAL head on the action localization dataset (i.e., target domain). This results in a task discrepancy problem for the video encoder – trained for action classification, but used for TAL. Intuitively, joint optimization with both the video encoder and TAL head is a strong baseline solution to this discrepancy. However, this is not operable for TAL subject to the GPU memory constraints, due to the prohibitive computational cost in processing long untrimmed videos. In this paper, we resolve this challenge by introducing a novel low-fidelity (LoFi) video encoder optimization method. Instead of always using the full training configurations in TAL learning, we propose to reduce the mini-batch composition in terms of temporal, spatial, or spatio-temporal resolution so that jointly optimizing the video encoder and TAL head becomes operable under the same memory conditions of a mid-range hardware budget. Crucially, this enables the gradients to flow backwards through the video encoder conditioned on a TAL supervision loss, favourably solving the task discrepancy problem and providing more effective feature representations. Extensive experiments show that the proposed LoFi optimization approach can significantly enhance the performance of existing TAL methods. Encouragingly, even with a lightweight ResNet18 based video encoder in a single RGB stream, our method surpasses two-stream (RGB + optical-flow) ResNet50 based alternatives, often by a good margin. Our code is publicly available at https://github.com/saic-fi/lofi_action_localization.

We introduce implicit Deep Adaptive Design (iDAD), a new method for performing adaptive experiments in real-time with implicit models. iDAD amortizes the cost of Bayesian optimal experimental design (BOED) by learning a design policy network upfront, which can then be deployed quickly at the time of the experiment. The iDAD network can be trained on any model which simulates differentiable samples, unlike previous design policy work that requires a closed form likelihood and conditionally independent experiments. At deployment, iDAD allows design decisions to be made in milliseconds, in contrast to traditional BOED approaches that require heavy computation during the experiment itself. We illustrate the applicability of iDAD on a number of experiments, and show that it provides a fast and effective mechanism for performing adaptive design with implicit models.

The reliable identification of the “best” arm while keeping the sample complexity as low as possible is a common task in the field of multi-armed bandits. In the multi-dueling variant of multi-armed bandits, where feedback is provided in the form of a winning arm among as set of k chosen ones, a reasonable notion of best arm is the generalized Condorcet winner (GCW). The latter is an the arm that has the greatest probability of being the winner in each subset containing it. In this paper, we derive lower bounds on the sample complexity for the task of identifying the GCW under various assumptions. As a by-product, our lower bound results provide new insights for the special case of dueling bandits (k = 2). We propose the Dvoretzky–Kiefer–Wolfowitz tournament (DKWT) algorithm, which we prove to be nearly optimal. In a numerical study, we show that DKWT empirically outperforms current state-of-the-art algorithms, even in the special case of dueling bandits or under a Plackett-Luce assumption on the feedback mechanism.

Learning binary representations of instances and classes is a classical problem with several high potential applications. In modern settings, the compression of high-dimensional neural representations to low-dimensional binary codes is a challenging task and often require large bit-codes to be accurate. In this work, we propose a novel method for $\textbf{L}$earning $\textbf{L}$ow-dimensional binary $\textbf{C}$odes $(\textbf{LLC})$ for instances as well as classes. Our method does ${\textit{not}}$ require any side-information, like annotated attributes or label meta-data, and learns extremely low-dimensional binary codes ($\approx 20$ bits for ImageNet-1K). The learnt codes are super-efficient while still ensuring $\textit{nearly optimal}$ classification accuracy for ResNet50 on ImageNet-1K. We demonstrate that the learnt codes capture intrinsically important features in the data, by discovering an intuitive taxonomy over classes. We further quantitatively measure the quality of our codes by applying it to the efficient image retrieval as well as out-of-distribution (OOD) detection problems. For ImageNet-100 retrieval problem, our learnt binary codes outperform $16$ bit HashNet using only $10$ bits and also are as accurate as $10$ dimensional real representations. Finally, our learnt binary codes can perform OOD detection, out-of-the-box, as accurately as a baseline that needs $\approx3000$ samples to tune its threshold, while we require ${\textit{none}}$. Code is open-sourced at https://github.com/RAIVNLab/LLC.

Neuropixels (NP) probes are dense linear multi-electrode arrays that have rapidly become essential tools for studying the electrophysiology of large neural populations. Unfortunately, a number of challenges remain in analyzing the large datasets output by these probes. Here we introduce several new methods for extracting useful spiking information from NP probes. First, we use a simple point neuron model, together with a neural-network denoiser, to efficiently map spikes detected on the probe into three-dimensional localizations. Previous methods localized spikes in two dimensions only; we show that the new localization approach is significantly more robust and provides an improved feature set for clustering spikes according to neural identity (``spike sorting"). Next, we apply a Poisson denoising method to the resulting three-dimensional point-cloud representation of the data, and show that the resulting 3D images can be accurately registered over time, leading to improved tracking of time-varying neural activity over the probe, and in turn, crisper estimates of neural clusters over time. The code to reproduce our results and an example neuropixels dataset is provided in the supplementary material.

Image classifiers are typically scored on their test set accuracy, but high accuracy can mask a subtle type of model failure. We find that high scoring convolutional neural networks (CNNs) on popular benchmarks exhibit troubling pathologies that allow them to display high accuracy even in the absence of semantically salient features. When a model provides a high-confidence decision without salient supporting input features, we say the classifier has overinterpreted its input, finding too much class-evidence in patterns that appear nonsensical to humans. Here, we demonstrate that neural networks trained on CIFAR-10 and ImageNet suffer from overinterpretation, and we find models on CIFAR-10 make confident predictions even when 95% of input images are masked and humans cannot discern salient features in the remaining pixel-subsets. We introduce Batched Gradient SIS, a new method for discovering sufficient input subsets for complex datasets, and use this method to show the sufficiency of border pixels in ImageNet for training and testing. Although these patterns portend potential model fragility in real-world deployment, they are in fact valid statistical patterns of the benchmark that alone suffice to attain high test accuracy. Unlike adversarial examples, overinterpretation relies upon unmodified image pixels. We find ensembling and input dropout can each help mitigate overinterpretation.

We introduce a new kind of linear transform named Deformable Butterfly (DeBut) that generalizes the conventional butterfly matrices and can be adapted to various input-output dimensions. It inherits the fine-to-coarse-grained learnable hierarchy of traditional butterflies and when deployed to neural networks, the prominent structures and sparsity in a DeBut layer constitutes a new way for network compression. We apply DeBut as a drop-in replacement of standard fully connected and convolutional layers, and demonstrate its superiority in homogenizing a neural network and rendering it favorable properties such as light weight and low inference complexity, without compromising accuracy. The natural complexity-accuracy tradeoff arising from the myriad deformations of a DeBut layer also opens up new rooms for analytical and practical research. The codes and Appendix are publicly available at: https://github.com/ruilin0212/DeBut.

Explainable Natural Language Processing (ExNLP) has increasingly focused on collecting human-annotated textual explanations. These explanations are used downstream in three ways: as data augmentation to improve performance on a predictive task, as supervision to train models to produce explanations for their predictions, and as a ground-truth to evaluate model-generated explanations. In this review, we identify 65 datasets with three predominant classes of textual explanations (highlights, free-text, and structured), organize the literature on annotating each type, identify strengths and shortcomings of existing collection methodologies, and give recommendations for collecting ExNLP datasets in the future.

Deep Reinforcement Learning (RL) is successful in solving many complex Markov Decision Processes (MDPs) problems. However, agents often face unanticipated environmental changes after deployment in the real world. These changes are often spurious and unrelated to the underlying problem, such as background shifts for visual input agents. Unfortunately, deep RL policies are usually sensitive to these changes and fail to act robustly against them. This resembles the problem of domain generalization in supervised learning. In this work, we study this problem for goal-conditioned RL agents. We propose a theoretical framework in the Block MDP setting that characterizes the generalizability of goal-conditioned policies to new environments. Under this framework, we develop a practical method PA-SkewFit that enhances domain generalization. The empirical evaluation shows that our goal-conditioned RL agent can perform well in various unseen test environments, improving by 50\% over baselines.

Recurrent neural networks (RNNs) are powerful models for processing time-series data, but it remains challenging to understand how they function. Improving this understanding is of substantial interest to both the machine learning and neuroscience communities. The framework of reverse engineering a trained RNN by linearizing around its fixed points has provided insight, but the approach has significant challenges. These include difficulty choosing which fixed point to expand around when studying RNN dynamics and error accumulation when reconstructing the nonlinear dynamics with the linearized dynamics. We present a new model that overcomes these limitations by co-training an RNN with a novel switching linear dynamical system (SLDS) formulation. A first-order Taylor series expansion of the co-trained RNN and an auxiliary function trained to pick out the RNN's fixed points govern the SLDS dynamics. The results are a trained SLDS variant that closely approximates the RNN, an auxiliary function that can produce a fixed point for each point in state-space, and a trained nonlinear RNN whose dynamics have been regularized such that its first-order terms perform the computation, if possible. This model removes the post-training fixed point optimization and allows us to unambiguously study the learned dynamics of the SLDS at any point in state-space. It also generalizes SLDS models to continuous manifolds of switching points while sharing parameters across switches. We validate the utility of the model on two synthetic tasks relevant to previous work reverse engineering RNNs. We then show that our model can be used as a drop-in in more complex architectures, such as LFADS, and apply this LFADS hybrid to analyze single-trial spiking activity from the motor system of a non-human primate.

One of the most commonly used methods for forming confidence intervals is the empirical bootstrap, which is especially expedient when the limiting distribution of the estimator is unknown. However, despite its ubiquitous role in machine learning, its theoretical properties are still not well understood. Recent developments in probability have provided new tools to study the bootstrap method. However, they have been applied only to specific applications and contexts, and it is unclear whether these techniques are applicable to the understanding of the consistency of the bootstrap in machine learning pipelines. In this paper, we derive general stability conditions under which the empirical bootstrap estimator is consistent and quantify the speed of convergence. Moreover, we propose alternative ways to use the bootstrap method to build confidence intervals with coverage guarantees. Finally, we illustrate the generality and tightness of our results by examples of interest for machine learning including for two-sample kernel tests after kernel selection and the empirical risk of stacked estimators.