huashen218/convxai-cia-dataset huggingface dataset:
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design
Keywords: Drug Discovery, Antibody Design, Generative Models, Graph Generation

Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this paper, we propose a generative model to automatically design the CDRs of antibodies with enhanced binding specificity or neutralization capabilities. Previous generative approaches formulate protein design as a structure-conditioned sequence generation task, assuming the desired 3D structure is given a priori. In contrast, we propose to co-design the sequence and 3D structure of CDRs as graphs. Our model unravels a sequence autoregressively while iteratively refining its predicted global structure. The inferred structure in turn guides subsequent residue choices. For efficiency, we model the conditional dependence between residues inside and outside of a CDR in a coarse-grained manner. Our method achieves superior log-likelihood on the test set and outperforms previous baselines in designing antibodies capable of neutralizing the SARS-CoV-2 virus.
Churn Reduction via Distillation
Keywords: distillation, churn, constraints

In real-world systems, models are frequently updated as more data becomes available, and in addition to achieving high accuracy, the goal is to also maintain a low difference in predictions compared to the base model (i.e. predictive churn). If model retraining results in vastly different behavior, then it could cause negative effects in downstream systems, especially if this churn can be avoided with limited impact on model accuracy. In this paper, we show an equivalence between training with distillation using the base model as the teacher and training with an explicit constraint on the predictive churn. We then show that distillation performs strongly for low churn training against a number of recent baselines on a wide range of datasets and model architectures, including fully-connected networks, convolutional networks, and transformers.
Learning Causal Models from Conditional Moment Restrictions by Importance Weighting
Keywords: Causal inference, Conditional moment restrictions

We consider learning causal relationships under conditional moment restrictions. Unlike causal inference under unconditional moment restrictions, conditional moment restrictions pose serious challenges for causal inference. To address this issue, we propose a method that transforms conditional moment restrictions to unconditional moment restrictions through importance weighting using a conditional density ratio estimator. Then, using this transformation, we propose a method that successfully estimate a parametric or nonparametric functions defined under the conditional moment restrictions. We analyze the estimation error and provide a bound on the structural function, providing theoretical support for our proposed method. In experiments, we confirm the soundness of our proposed method.
Scalable One-Pass Optimisation of High-Dimensional Weight-Update Hyperparameters by Implicit Differentiation
Keywords: Hyperparameter Optimisation

Machine learning training methods depend plentifully and intricately on hyperparameters, motivating automated strategies for their optimisation. Many existing algorithms restart training for each new hyperparameter choice, at considerable computational cost. Some hypergradient-based one-pass methods exist, but these either cannot be applied to arbitrary optimiser hyperparameters (such as learning rates and momenta) or take several times longer to train than their base models. We extend these existing methods to develop an approximate hypergradient-based hyperparameter optimiser which is applicable to any continuous hyperparameter appearing in a differentiable model weight update, yet requires only one training episode, with no restarts. We also provide a motivating argument for convergence to the true hypergradient, and perform tractable gradient-based optimisation of independent learning rates for each model parameter. Our method performs competitively from varied random hyperparameter initialisations on several UCI datasets and Fashion-MNIST (using a one-layer MLP), Penn Treebank (using an LSTM) and CIFAR-10 (using a ResNet-18), in time only 2-3x greater than vanilla training.
Sample Efficient Deep Reinforcement Learning via Uncertainty Estimation
Keywords: Deep reinforcement learning, uncertainty estimation, inverse-variance, heteroscedastic

In model-free deep reinforcement learning (RL) algorithms, using noisy value estimates to supervise policy evaluation and optimization is detrimental to the sample efficiency. As this noise is heteroscedastic, its effects can be mitigated using uncertainty-based weights in the optimization process. Previous methods rely on sampled ensembles, which do not capture all aspects of uncertainty. We provide a systematic analysis of the sources of uncertainty in the noisy supervision that occurs in RL, and introduce inverse-variance RL, a Bayesian framework which combines probabilistic ensembles and Batch Inverse Variance weighting. We propose a method whereby two complementary uncertainty estimation methods account for both the Q-value and the environment stochasticity to better mitigate the negative impacts of noisy supervision. Our results show significant improvement in terms of sample efficiency on discrete and continuous control tasks.
Learning Pruning-Friendly Networks via Frank-Wolfe: One-Shot, Any-Sparsity, And No Retraining
Keywords: Pruning, Frank-Wolfe

We present a novel framework to train a large deep neural network (DNN) for only $\textit{once}$, which can then be pruned to $\textit{any sparsity ratio}$ to preserve competitive accuracy $\textit{without any re-training}$. Conventional methods often require (iterative) pruning followed by re-training, which not only incurs large overhead beyond the original DNN training but also can be sensitive to retraining hyperparameters. Our core idea is to re-cast the DNN training as an explicit $\textit{pruning-aware}$ process: that is formulated with an auxiliary $K$-sparse polytope constraint, to encourage network weights to lie in a convex hull spanned by $K$-sparse vectors, potentially resulting in more sparse weight matrices. We then leverage a stochastic Frank-Wolfe (SFW) algorithm to solve this new constrained optimization, which naturally leads to sparse weight updates each time. We further note an overlooked fact that existing DNN initializations were derived to enhance SGD training (e.g., avoid gradient explosion or collapse), but was unaligned with the challenges of training with SFW. We hence also present the first learning-based initialization scheme specifically for boosting SFW-based DNN training. Experiments on CIFAR-10 and Tiny-ImageNet datasets demonstrate that our new framework named $\textbf{SFW-pruning}$ consistently achieves the state-of-the-art performance on various benchmark DNNs over a wide range of pruning ratios. Moreover, SFW-pruning only needs to train once on the same model and dataset, for obtaining arbitrary ratios, while requiring neither iterative pruning nor retraining. All codes will be released to the public.
Learning transferable motor skills with hierarchical latent mixture policies
Keywords: Robotics, Reinforcement Learning, Hierarchical, Latent Variable Models, Skills, Transfer

For robots operating in the real world, it is desirable to learn reusable abstract behaviours that can effectively be transferred across numerous tasks and scenarios.
        We propose an approach to learn skills from data using a hierarchical mixture latent variable model.
        Our method exploits a multi-level hierarchy of both discrete and continuous latent variables, to model a discrete set of abstract high-level behaviours while allowing for variance in how they are executed.
        We demonstrate in manipulation domains that the method can effectively cluster offline data into distinct, executable behaviours, while retaining the flexibility of a continuous latent variable model.
        The resulting skills can be transferred to new tasks, unseen objects, and from state to vision-based policies, yielding significantly better sample efficiency and asymptotic performance compared to existing skill- and imitation-based methods.
        We also perform further analysis showing how and when the skills are most beneficial: they encourage directed exploration to cover large regions of the state space relevant to the task, making them most effective in challenging sparse-reward settings.
Compositional Training for End-to-End Deep AUC Maximization
Keywords: Compositional Training, Imbalanced Losses, AUC optimization, Deep Learning

Recently, deep AUC maximization (DAM) has achieved great success in different domains (e.g., medical image classification). However, the end-to-end training for deep AUC maximization still remains a challenging problem. Previous studies employ an ad-hoc  two-stage approach that first trains the network by optimizing a traditional  loss (e.g., cross-entropy loss) and then finetunes the network by optimizing an AUC loss. This is because that training a deep neural network from scratch by maximizing an AUC loss usually does not yield a satisfactory performance. This phenomenon can be attributed to the degraded feature representations learned by maximizing the AUC loss from scratch. To address this issue, we propose a novel compositional training framework for end-to-end DAM, namely compositional DAM. The key idea of compositional training is to minimize a compositional objective function, where the outer function corresponds to an AUC loss and the inner function represents  a gradient descent step for minimizing a traditional loss, e.g., the cross-entropy (CE) loss. To optimize the non-standard compositional objective, we propose an efficient and provable stochastic optimization algorithm. The proposed algorithm enhances the capabilities  of  both robust feature learning and robust classifier learning  by alternatively taking a gradient descent step for the CE loss and for the AUC loss in a systematic way.  We conduct extensive empirical studies on imbalanced benchmark and medical image datasets, which unanimously verify the effectiveness of the proposed method.  Our results show that the compositional training approach dramatically improves both the feature representations and the testing AUC score compared with traditional deep learning approaches, and yields better performance than the two-stage approaches for DAM as well. The proposed method is implemented in our open-sourced library LibAUC (https://www.libauc.org) and code is available at https://github.com/Optimization-AI/LibAUC.
Explanations of Black-Box Models based on Directional Feature Interactions
Keywords: Explainability, Shapley values, Interpretability, Directional interaction, feature interaction

As machine learning algorithms are deployed ubiquitously to a variety of domains, it is imperative to make these often black-box models transparent.  Several recent works explain black-box models by capturing the most influential features for prediction per instance; such explanation methods are univariate, as they characterize importance per feature.  We extend univariate explanation to a higher-order; this enhances explainability, as bivariate methods can capture feature interactions in black-box models, represented as a directed graph.  Analyzing this graph enables us to discover groups of features that are equally important (i.e., interchangeable), while the notion of directionality allows us to identify the most influential features.  We apply our bivariate method on Shapley value explanations, and experimentally demonstrate the ability of directional explanations to discover feature interactions. We show the superiority of our method against state-of-the-art on CIFAR10, IMDB, Census, Divorce, Drug, and gene data.
On Lottery Tickets and Minimal Task Representations in Deep Reinforcement Learning
Keywords: Reinforcement Learning, Sparsity, Pruning, Lottery Ticket Hypothesis

The lottery ticket hypothesis questions the role of overparameterization in supervised deep learning. But how is the performance of winning lottery tickets affected by the distributional shift inherent to reinforcement learning problems? In this work, we address this question by comparing sparse agents who have to address the non-stationarity of the exploration-exploitation problem with supervised agents trained to imitate an expert. We show that feed-forward networks trained with behavioural cloning compared to reinforcement learning can be pruned to higher levels of sparsity without performance degradation. This suggests that in order to solve the RL-specific distributional shift agents require more degrees of freedom. Using a set of carefully designed baseline conditions, we find that the majority of the lottery ticket effect in both learning paradigms can be attributed to the identified mask rather than the weight initialization. The input layer mask selectively prunes entire input dimensions that turn out to be irrelevant for the task at hand. At a moderate level of sparsity the mask identified by iterative magnitude pruning yields minimal task-relevant representations, i.e., an interpretable inductive bias. Finally, we propose a simple initialization rescaling which promotes the robust identification of sparse task representations in low-dimensional control tasks.
Self-supervised Learning is More Robust to Dataset Imbalance
Keywords: self-supervised learning, dataset imbalance, representation learning, long-tailed recognition

Self-supervised learning (SSL) is a scalable way to learn general visual representations since it learns without labels. However, large-scale unlabeled datasets in the wild often have long-tailed label distributions, where we know little about the behavior of SSL. In this work, we systematically investigate self-supervised learning under dataset imbalance. First, we find via extensive experiments that off-the-shelf self-supervised representations are already more robust to class imbalance than supervised representations. The performance gap between balanced and imbalanced pre-training with SSL is significantly smaller than the gap with supervised learning, across sample sizes, for both in-domain and, especially, out-of-domain evaluation. Second, towards understanding the robustness of SSL, we hypothesize that SSL learns richer features from frequent data: it may learn label-irrelevant-but-transferable features that help classify the rare classes and downstream tasks. In contrast, supervised learning has no incentive to learn features irrelevant to the labels from frequent examples. We validate this hypothesis with semi-synthetic experiments as well as rigorous mathematical analyses on a simplified setting. Third, inspired by the theoretical insights, we devise a re-weighted regularization technique that  consistently improves the SSL representation quality on imbalanced datasets with several evaluation criteria, closing the small gap between balanced and imbalanced datasets with the same number of examples.
Ab-Initio Potential Energy Surfaces by Pairing GNNs with Neural Wave Functions
Keywords: Graph Neural Networks, Computational Physics, Self-Generative Learning, Machine Learning for Science

Solving the Schrödinger equation is key to many quantum mechanical properties. However, an analytical solution is only tractable for single-electron systems. Recently, neural networks succeeded at modelling wave functions of many-electron systems. Together with the variational Monte-Carlo (VMC) framework, this led to solutions on par with the best known classical methods. Still, these neural methods require tremendous amounts of computational resources as one has to train a separate model for each molecular geometry. In this work, we combine a Graph Neural Network (GNN) with a neural wave function to simultaneously solve the Schrödinger equation for multiple geometries via VMC. This enables us to model continuous subsets of the potential energy surface with a single training pass. Compared to existing state-of-the-art networks, our Potential Energy Surface Network (PESNet) speeds up training for multiple geometries by up to 40 times while matching or surpassing their accuracy. This may open the path to accurate and orders of magnitude cheaper quantum mechanical calculations.
Near-Optimal Reward-Free Exploration for Linear Mixture MDPs with Plug-in Solver
Keywords: reward-free exploration, model-based reinforcement learning, learning theory

Although model-based reinforcement learning (RL) approaches are considered more sample efficient, existing algorithms are usually relying on sophisticated planning algorithm to couple tightly with the model-learning procedure. Hence the learned models may lack the ability of being re-used with more specialized planners. In this paper we address this issue and provide approaches to learn an RL model efficiently without the guidance of a reward signal. In particular, we take a plug-in solver approach, where we focus on learning a model in the exploration phase and demand that \emph{any planning algorithm} on the learned model can give a near-optimal policy. Specicially, we focus on the linear mixture MDP setting, where the probability transition matrix is a (unknown) convex combination of a set of existing models. We show that, by establishing a novel exploration algorithm, the plug-in approach learns a model by taking $\tilde{O}(d^2H^3/\epsilon^2)$ interactions with the environment and \emph{any} $\epsilon$-optimal planner on the model gives an $O(\epsilon)$-optimal policy on the original model. This sample complexity matches lower bounds for non-plug-in approaches and is \emph{statistically optimal}. We achieve this result by leveraging a careful maximum total-variance bound using Bernstein inequality and properties specified to linear mixture MDP.
Meta Discovery: Learning to Discover Novel Classes given Very Limited Data

In novel class discovery (NCD), we are given labeled data from seen classes and unlabeled data from unseen classes, and we train clustering models for the unseen classes. However, the implicit assumptions behind NCD are still unclear. In this paper, we demystify assumptions behind NCD and find that high-level semantic features should be shared among the seen and unseen classes. Based on this finding, NCD is theoretically solvable under certain assumptions and can be naturally linked to meta-learning that has exactly the same assumption as NCD. Thus, we can empirically solve the NCD problem by meta-learning algorithms after slight modifications. This meta-learning-based methodology significantly reduces the amount of unlabeled data needed for training and makes it more practical, as demonstrated in experiments. The use of very limited data is also justified by the application scenario of NCD: since it is unnatural to label only seen-class data, NCD is sampling instead of labeling in causality. Therefore, unseen-class data should be collected on the way of collecting seen-class data, which is why they are novel and first need to be clustered.
Constrained Policy Optimization via Bayesian World Models
Keywords: Reinforcement learning, Constrained Markov decision processes, Constrained policy optimization, Bayesian model-based RL

Improving sample-efficiency and safety are crucial challenges when deploying reinforcement learning in high-stakes real world applications. We propose LAMBDA, a novel model-based approach for policy optimization in safety critical tasks modeled via constrained Markov decision processes. Our approach utilizes Bayesian world models, and harnesses the resulting uncertainty to maximize optimistic upper bounds on the task objective, as well as pessimistic upper bounds on the safety constraints. We demonstrate LAMBDA's state of the art performance on the Safety-Gym benchmark suite in terms of sample efficiency and constraint violation.
VAE Approximation Error: ELBO and Exponential Families

The importance of Variational Autoencoders reaches far beyond standalone generative models -- the approach is also used for learning latent representations and can be generalized to semi-supervised learning. This requires a thorough analysis of their commonly known shortcomings: posterior collapse and approximation errors. This paper analyzes VAE approximation errors caused by the combination of the ELBO objective and encoder models from conditional exponential families, including, but not limited to, commonly used conditionally independent discrete and continuous models.
        We characterize subclasses of generative models consistent with these encoder families. We show that the ELBO optimizer is pulled away from the likelihood optimizer towards the consistent subset and study this effect experimentally. Importantly, this subset can not be enlarged, and the respective error cannot be decreased, by considering deeper encoder/decoder networks.
Generalized Decision Transformer for Offline Hindsight Information Matching
Keywords: Hindsight Information Matching, Decision Transformer, State-Marginal Matching, Hindsight Experience Replay, Reinforcement Learning

How to extract as much learning signal from each trajectory data has been a key problem in reinforcement learning (RL), where sample inefficiency has posed serious challenges for practical applications. Recent works have shown that using expressive policy function approximators and conditioning on future trajectory information -- such as future states in hindsight experience replay (HER) or returns-to-go in Decision Transformer (DT) -- enables efficient learning of multi-task policies, where at times online RL is fully replaced by offline behavioral cloning (BC), e.g. sequence modeling. We demonstrate that all these approaches are doing hindsight information matching (HIM) -- training policies that can output the rest of trajectory that matches some statistics of future state information. We present Generalized Decision Transformer (GDT) for solving any HIM problem, and show how different choices for the feature function and the anti-causal aggregator not only recover DT as a special case, but also lead to novel Categorical DT (CDT) and Bi-directional DT (BDT) for matching different statistics of the future. For evaluating CDT and BDT, we define offline multi-task state-marginal matching (SMM) and imitation learning (IL) as two generic HIM problems, propose a Wasserstein distance loss as a metric for both, and empirically study them on MuJoCo continuous control benchmarks. Categorical DT, which simply replaces anti-causal summation with anti-causal binning in DT, enables arguably the first effective offline multi-task SMM algorithm that generalizes well to unseen (and even synthetic) multi-modal reward or state-feature distributions. Bi-directional DT, which uses an anti-causal second transformer as the aggregator, can learn to model any statistics of the future and outperforms DT variants in offline multi-task IL, i.e. one-shot IL. Our generalized formulations from HIM and GDT greatly expand the role of powerful sequence modeling architectures in modern RL.
Unifying Likelihood-free Inference with Black-box Optimization and Beyond
Keywords: biological sequence design, black-box optimization, likelihood-free inference, Bayesian inference

Black-box optimization formulations for biological sequence design have drawn recent attention due to their promising potential impact on the pharmaceutical industry. In this work, we propose to unify two seemingly distinct worlds: likelihood-free inference and black-box optimization, under one probabilistic framework. In tandem, we provide a recipe for constructing various sequence design methods based on this framework. We show how previous optimization approaches can be "reinvented" in our framework, and further propose new probabilistic black-box optimization algorithms. Extensive experiments on sequence design application illustrate the benefits of the proposed methodology.