OpenRaiser/Intern-Atlas huggingface dataset:
Hierarchical Generation of Molecular Graphs using Structural Motifs
Venue: Conference ICML 2020
Year: 2020

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to smaller molecules. Indeed, as we demonstrate, their performance degrades significantly for larger molecules. In this paper, we propose a new hierarchical graph encoder-decoder that employs significantly larger and more flexible graph motifs as basic building blocks. Our encoder produces a multi-resolution representation for each molecule in a fine-to-coarse fashion, from atoms to connected motifs. Each level integrates the encoding of constituents below with the graph at that level. Our autoregressive coarse-to-fine decoder adds one motif at a time, interleaving the decision of selecting a new motif with the process of resolving its attachments to the emerging molecule. We evaluate our model on multiple molecule generation tasks, including polymers, and show that our model significantly outperforms previous state-of-the-art baselines.
Multi-Objective Molecule Generation using Interpretable Substructures
Venue: Conference ICML 2020
Year: 2020

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes increasingly challenging when there are many property constraints. We propose to offset this complexity by composing molecules from a vocabulary of substructures that we call molecular rationales. These rationales are identified from molecules as substructures that are likely responsible for each property of interest. We then learn to expand rationales into a full molecule using graph generative models. Our final generative model composes molecules as mixtures of multiple rationale completions, and this mixture is fine-tuned to preserve the properties of interest. We evaluate our model on various drug design tasks and demonstrate significant improvements over state-of-the-art baselines in terms of accuracy, diversity, and novelty of generated compounds.
Reward-Free Exploration for Reinforcement Learning
Venue: Conference ICML 2020
Year: 2020

Exploration is widely regarded as one of the most challenging aspects of reinforcement learning (RL), with many naive approaches succumbing to exponential sample complexity. To isolate the challenges of exploration, we propose a new "reward-free RL" framework. In the exploration phase, the agent first collects trajectories from an MDP $\mathcal{M}$ without a pre-specified reward function. After exploration, it is tasked with computing near-optimal policies under for $\mathcal{M}$ for a collection of given reward functions. This framework is particularly suitable when there are many reward functions of interest, or when the reward function is shaped by an external agent to elicit desired behavior. We give an efficient algorithm that conducts $\tilde{\mathcal{O}}(S^2A\mathrm{poly}(H)/ε^2)$ episodes of exploration and returns $ε$-suboptimal policies for an arbitrary number of reward functions. We achieve this by finding exploratory policies that visit each "significant" state with probability proportional to its maximum visitation probability under any possible policy. Moreover, our planning procedure can be instantiated by any black-box approximate planner, such as value iteration or natural policy gradient. We also give a nearly-matching $Ω(S^2AH^2/ε^2)$ lower bound, demonstrating the near-optimality of our algorithm in this setting.
What is Local Optimality in Nonconvex-Nonconcave Minimax Optimization?
Venue: Conference ICML 2020
Year: 2020

Minimax optimization has found extensive applications in modern machine learning, in settings such as generative adversarial networks (GANs), adversarial training and multi-agent reinforcement learning. As most of these applications involve continuous nonconvex-nonconcave formulations, a very basic question arises---"what is a proper definition of local optima?" Most previous work answers this question using classical notions of equilibria from simultaneous games, where the min-player and the max-player act simultaneously. In contrast, most applications in machine learning, including GANs and adversarial training, correspond to sequential games, where the order of which player acts first is crucial (since minimax is in general not equal to maximin due to the nonconvex-nonconcave nature of the problems). The main contribution of this paper is to propose a proper mathematical definition of local optimality for this sequential setting---local minimax, as well as to present its properties and existence results. Finally, we establish a strong connection to a basic local search algorithm---gradient descent ascent (GDA): under mild conditions, all stable limit points of GDA are exactly local minimax points up to some degenerate points.
Efficiently Solving MDPs with Stochastic Mirror Descent
Venue: Conference ICML 2020
Year: 2020

We present a unified framework based on primal-dual stochastic mirror descent for approximately solving infinite-horizon Markov decision processes (MDPs) given a generative model. When applied to an average-reward MDP with $A_{tot}$ total state-action pairs and mixing time bound $t_{mix}$ our method computes an $ε$-optimal policy with an expected $\widetilde{O}(t_{mix}^2 A_{tot} ε^{-2})$ samples from the state-transition matrix, removing the ergodicity dependence of prior art. When applied to a $γ$-discounted MDP with $A_{tot}$ total state-action pairs our method computes an $ε$-optimal policy with an expected $\widetilde{O}((1-γ)^{-4} A_{tot} ε^{-2})$ samples, matching the previous state-of-the-art up to a $(1-γ)^{-1}$ factor. Both methods are model-free, update state values and policies simultaneously, and run in time linear in the number of samples taken. We achieve these results through a more general stochastic mirror descent framework for solving bilinear saddle-point problems with simplex and box domains and we demonstrate the flexibility of this framework by providing further applications to constrained MDPs.
Guided Learning of Nonconvex Models through Successive Functional Gradient Optimization
Venue: Conference ICML 2020
Year: 2020

This paper presents a framework of successive functional gradient optimization for training nonconvex models such as neural networks, where training is driven by mirror descent in a function space. We provide a theoretical analysis and empirical study of the training method derived from this framework. It is shown that the method leads to better performance than that of standard training techniques.
AdaScale SGD: A User-Friendly Algorithm for Distributed Training
Venue: Conference ICML 2020
Year: 2020

When using large-batch training to speed up stochastic gradient descent, learning rates must adapt to new batch sizes in order to maximize speed-ups and preserve model quality. Re-tuning learning rates is resource intensive, while fixed scaling rules often degrade model quality. We propose AdaScale SGD, an algorithm that reliably adapts learning rates to large-batch training. By continually adapting to the gradient's variance, AdaScale automatically achieves speed-ups for a wide range of batch sizes. We formally describe this quality with AdaScale's convergence bound, which maintains final objective values, even as batch sizes grow large and the number of iterations decreases. In empirical comparisons, AdaScale trains well beyond the batch size limits of popular "linear learning rate scaling" rules. This includes large-batch training with no model degradation for machine translation, image classification, object detection, and speech recognition tasks. AdaScale's qualitative behavior is similar to that of "warm-up" heuristics, but unlike warm-up, this behavior emerges naturally from a principled mechanism. The algorithm introduces negligible computational overhead and no new hyperparameters, making AdaScale an attractive choice for large-scale training in practice.
Being Bayesian about Categorical Probability
Venue: Conference ICML 2020
Year: 2020

Neural networks utilize the softmax as a building block in classification tasks, which contains an overconfidence problem and lacks an uncertainty representation ability. As a Bayesian alternative to the softmax, we consider a random variable of a categorical probability over class labels. In this framework, the prior distribution explicitly models the presumed noise inherent in the observed label, which provides consistent gains in generalization performance in multiple challenging tasks. The proposed method inherits advantages of Bayesian approaches that achieve better uncertainty estimation and model calibration. Our method can be implemented as a plug-and-play loss function with negligible computational overhead compared to the softmax with the cross-entropy loss function.
Evaluating the Performance of Reinforcement Learning Algorithms
Venue: Conference ICML 2020
Year: 2020

Performance evaluations are critical for quantifying algorithmic advances in reinforcement learning. Recent reproducibility analyses have shown that reported performance results are often inconsistent and difficult to replicate. In this work, we argue that the inconsistency of performance stems from the use of flawed evaluation metrics. Taking a step towards ensuring that reported results are consistent, we propose a new comprehensive evaluation methodology for reinforcement learning algorithms that produces reliable measurements of performance both on a single environment and when aggregated across environments. We demonstrate this method by evaluating a broad class of reinforcement learning algorithms on standard benchmark tasks.
Sub-Goal Trees a Framework for Goal-Based Reinforcement Learning
Venue: Conference ICML 2020
Year: 2020

Many AI problems, in robotics and other domains, are goal-based, essentially seeking trajectories leading to various goal states. Reinforcement learning (RL), building on Bellman's optimality equation, naturally optimizes for a single goal, yet can be made multi-goal by augmenting the state with the goal. Instead, we propose a new RL framework, derived from a dynamic programming equation for the all pairs shortest path (APSP) problem, which naturally solves multi-goal queries. We show that this approach has computational benefits for both standard and approximate dynamic programming. Interestingly, our formulation prescribes a novel protocol for computing a trajectory: instead of predicting the next state given its predecessor, as in standard RL, a goal-conditioned trajectory is constructed by first predicting an intermediate state between start and goal, partitioning the trajectory into two. Then, recursively, predicting intermediate points on each sub-segment, until a complete trajectory is obtained. We call this trajectory structure a sub-goal tree. Building on it, we additionally extend the policy gradient methodology to recursively predict sub-goals, resulting in novel goal-based algorithms. Finally, we apply our method to neural motion planning, where we demonstrate significant improvements compared to standard RL on navigating a 7-DoF robot arm between obstacles.
Partial Trace Regression and Low-Rank Kraus Decomposition
Venue: Conference ICML 2020
Year: 2020

The trace regression model, a direct extension of the well-studied linear regression model, allows one to map matrices to real-valued outputs. We here introduce an even more general model, namely the partial-trace regression model, a family of linear mappings from matrix-valued inputs to matrix-valued outputs; this model subsumes the trace regression model and thus the linear regression model. Borrowing tools from quantum information theory, where partial trace operators have been extensively studied, we propose a framework for learning partial trace regression models from data by taking advantage of the so-called low-rank Kraus representation of completely positive maps. We show the relevance of our framework with synthetic and real-world experiments conducted for both i) matrix-to-matrix regression and ii) positive semidefinite matrix completion, two tasks which can be formulated as partial trace regression problems.
Variational Autoencoders with Riemannian Brownian Motion Priors
Venue: Conference ICML 2020
Year: 2020

Variational Autoencoders (VAEs) represent the given data in a low-dimensional latent space, which is generally assumed to be Euclidean. This assumption naturally leads to the common choice of a standard Gaussian prior over continuous latent variables. Recent work has, however, shown that this prior has a detrimental effect on model capacity, leading to subpar performance. We propose that the Euclidean assumption lies at the heart of this failure mode. To counter this, we assume a Riemannian structure over the latent space, which constitutes a more principled geometric view of the latent codes, and replace the standard Gaussian prior with a Riemannian Brownian motion prior. We propose an efficient inference scheme that does not rely on the unknown normalizing factor of this prior. Finally, we demonstrate that this prior significantly increases model capacity using only one additional scalar parameter.
Learning and Evaluating Contextual Embedding of Source Code
Venue: Conference ICML 2020
Year: 2020

Recent research has achieved impressive results on understanding and improving source code by building up on machine-learning techniques developed for natural languages. A significant advancement in natural-language understanding has come with the development of pre-trained contextual embeddings, such as BERT, which can be fine-tuned for downstream tasks with less labeled data and training budget, while achieving better accuracies. However, there is no attempt yet to obtain a high-quality contextual embedding of source code, and to evaluate it on multiple program-understanding tasks simultaneously; that is the gap that this paper aims to mitigate. Specifically, first, we curate a massive, deduplicated corpus of 7.4M Python files from GitHub, which we use to pre-train CuBERT, an open-sourced code-understanding BERT model; and, second, we create an open-sourced benchmark that comprises five classification tasks and one program-repair task, akin to code-understanding tasks proposed in the literature before. We fine-tune CuBERT on our benchmark tasks, and compare the resulting models to different variants of Word2Vec token embeddings, BiLSTM and Transformer models, as well as published state-of-the-art models, showing that CuBERT outperforms them all, even with shorter training, and with fewer labeled examples. Future work on source-code embedding can benefit from reusing our benchmark, and from comparing against CuBERT models as a strong baseline.
Operation-Aware Soft Channel Pruning using Differentiable Masks
Venue: Conference ICML 2020
Year: 2020

We propose a simple but effective data-driven channel pruning algorithm, which compresses deep neural networks in a differentiable way by exploiting the characteristics of operations. The proposed approach makes a joint consideration of batch normalization (BN) and rectified linear unit (ReLU) for channel pruning; it estimates how likely the two successive operations deactivate each feature map and prunes the channels with high probabilities. To this end, we learn differentiable masks for individual channels and make soft decisions throughout the optimization procedure, which facilitates to explore larger search space and train more stable networks. The proposed framework enables us to identify compressed models via a joint learning of model parameters and channel pruning without an extra procedure of fine-tuning. We perform extensive experiments and achieve outstanding performance in terms of the accuracy of output networks given the same amount of resources when compared with the state-of-the-art methods.
Non-autoregressive Machine Translation with Disentangled Context Transformer
Venue: Conference ICML 2020
Year: 2020

State-of-the-art neural machine translation models generate a translation from left to right and every step is conditioned on the previously generated tokens. The sequential nature of this generation process causes fundamental latency in inference since we cannot generate multiple tokens in each sentence in parallel. We propose an attention-masking based model, called Disentangled Context (DisCo) transformer, that simultaneously generates all tokens given different contexts. The DisCo transformer is trained to predict every output token given an arbitrary subset of the other reference tokens. We also develop the parallel easy-first inference algorithm, which iteratively refines every token in parallel and reduces the number of required iterations. Our extensive experiments on 7 translation directions with varying data sizes demonstrate that our model achieves competitive, if not better, performance compared to the state of the art in non-autoregressive machine translation while significantly reducing decoding time on average. Our code is available at https://github.com/facebookresearch/DisCo.
Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention
Venue: Conference ICML 2020
Year: 2020

Transformers achieve remarkable performance in several tasks but due to their quadratic complexity, with respect to the input's length, they are prohibitively slow for very long sequences. To address this limitation, we express the self-attention as a linear dot-product of kernel feature maps and make use of the associativity property of matrix products to reduce the complexity from $\mathcal{O}\left(N^2\right)$ to $\mathcal{O}\left(N\right)$, where $N$ is the sequence length. We show that this formulation permits an iterative implementation that dramatically accelerates autoregressive transformers and reveals their relationship to recurrent neural networks. Our linear transformers achieve similar performance to vanilla transformers and they are up to 4000x faster on autoregressive prediction of very long sequences.
Rate-distortion optimization guided autoencoder for isometric embedding in Euclidean latent space
Venue: Conference ICML 2020
Year: 2020

To analyze high-dimensional and complex data in the real world, deep generative models, such as variational autoencoder (VAE) embed data in a low-dimensional space (latent space) and learn a probabilistic model in the latent space. However, they struggle to accurately reproduce the probability distribution function (PDF) in the input space from that in the latent space. If the embedding were isometric, this issue can be solved, because the relation of PDFs can become tractable. To achieve isometric property, we propose Rate- Distortion Optimization guided autoencoder inspired by orthonormal transform coding. We show our method has the following properties: (i) the Jacobian matrix between the input space and a Euclidean latent space forms a constantlyscaled orthonormal system and enables isometric data embedding; (ii) the relation of PDFs in both spaces can become tractable one such as proportional relation. Furthermore, our method outperforms state-of-the-art methods in unsupervised anomaly detection with four public datasets.
Feature Noise Induces Loss Discrepancy Across Groups
Venue: Conference ICML 2020
Year: 2020

The performance of standard learning procedures has been observed to differ widely across groups. Recent studies usually attribute this loss discrepancy to an information deficiency for one group (e.g., one group has less data). In this work, we point to a more subtle source of loss discrepancy---feature noise. Our main result is that even when there is no information deficiency specific to one group (e.g., both groups have infinite data), adding the same amount of feature noise to all individuals leads to loss discrepancy. For linear regression, we thoroughly characterize the effect of feature noise on loss discrepancy in terms of the amount of noise, the difference between moments of the two groups, and whether group information is used or not. We then show this loss discrepancy does not vanish immediately if a shift in distribution causes the groups to have similar moments. On three real-world datasets, we show feature noise increases the loss discrepancy if groups have different distributions, while it does not affect the loss discrepancy on datasets where groups have similar distributions.
Entropy Minimization In Emergent Languages
Venue: Conference ICML 2020
Year: 2020

There is growing interest in studying the languages that emerge when neural agents are jointly trained to solve tasks requiring communication through a discrete channel. We investigate here the information-theoretic complexity of such languages, focusing on the basic two-agent, one-exchange setup. We find that, under common training procedures, the emergent languages are subject to an entropy minimization pressure that has also been detected in human language, whereby the mutual information between the communicating agent's inputs and the messages is minimized, within the range afforded by the need for successful communication. That is, emergent languages are (nearly) as simple as the task they are developed for allow them to be. This pressure is amplified as we increase communication channel discreteness. Further, we observe that stronger discrete-channel-driven entropy minimization leads to representations with increased robustness to overfitting and adversarial attacks. We conclude by discussing the implications of our findings for the study of natural and artificial communication systems.
Private Outsourced Bayesian Optimization
Venue: Conference ICML 2020
Year: 2020

This paper presents the private-outsourced-Gaussian process-upper confidence bound (PO-GP-UCB) algorithm, which is the first algorithm for privacy-preserving Bayesian optimization (BO) in the outsourced setting with a provable performance guarantee. We consider the outsourced setting where the entity holding the dataset and the entity performing BO are represented by different parties, and the dataset cannot be released non-privately. For example, a hospital holds a dataset of sensitive medical records and outsources the BO task on this dataset to an industrial AI company. The key idea of our approach is to make the BO performance of our algorithm similar to that of non-private GP-UCB run using the original dataset, which is achieved by using a random projection-based transformation that preserves both privacy and the pairwise distances between inputs. Our main theoretical contribution is to show that a regret bound similar to that of the standard GP-UCB algorithm can be established for our PO-GP-UCB algorithm. We empirically evaluate the performance of our PO-GP-UCB algorithm with synthetic and real-world datasets.
What can I do here? A Theory of Affordances in Reinforcement Learning
Venue: Conference ICML 2020
Year: 2020

Reinforcement learning algorithms usually assume that all actions are always available to an agent. However, both people and animals understand the general link between the features of their environment and the actions that are feasible. Gibson (1977) coined the term "affordances" to describe the fact that certain states enable an agent to do certain actions, in the context of embodied agents. In this paper, we develop a theory of affordances for agents who learn and plan in Markov Decision Processes. Affordances play a dual role in this case. On one hand, they allow faster planning, by reducing the number of actions available in any given situation. On the other hand, they facilitate more efficient and precise learning of transition models from data, especially when such models require function approximation. We establish these properties through theoretical results as well as illustrative examples. We also propose an approach to learn affordances and use it to estimate transition models that are simpler and generalize better.