NeurIPS 2022 Papers

Conference on Neural Information Processing Systems

Decision breakdown

2,901papers

Counted from the official paper list; may differ slightly from the number the conference announced.

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Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

Leon Hetzel, Simon Boehm, Niki Kilbertus, Stephan Günnemann, Mohammad Lotfollahi, Fabian J Theis

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Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

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Size and depth of monotone neural networks: interpolation and approximation

Dan Mikulincer, Daniel Reichman

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Monotone functions and data sets arise in a variety of applications. We study the interpolation problem for monotone data sets: The input is a monotone data set with $n$ points, and the goal is to find a size and depth efficient monotone neural network with \emph{non negative parameters} and threshold units that interpolates the data set. We show that there are monotone data sets that cannot be interpolated by a monotone network of depth $2$. On the other hand, we prove that for every monotone data set with $n$ points in $\mathbb{R}^d$, there exists an interpolating monotone network of depth $4$ and size $O(nd)$. Our interpolation result implies that every monotone function over $[0,1]^d$ can be approximated arbitrarily well by a depth-4 monotone network, improving the previous best-known construction of depth $d+1$. Finally, building on results from Boolean circuit complexity, we show that the inductive bias of having positive parameters can lead to a super-polynomial blow-up in the number of neurons when approximating monotone functions.

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VF-PS: How to Select Important Participants in Vertical Federated Learning, Efficiently and Securely?

Jiawei Jiang, Lukas Burkhalter, Fangcheng Fu, Bolin Ding, Bo Du, Anwar Hithnawi, Bo Li, Ce Zhang

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Vertical Federated Learning (VFL), that trains federated models over vertically partitioned data, has emerged as an important learning paradigm. However, existing VFL methods are facing two challenges: (1) scalability when # participants grows to even modest scale and (2) diminishing return w.r.t. # participants: not all participants are equally important and many will not introduce quality improvement in a large consortium. Inspired by these two challenges, in this paper, we ask: How can we select l out of m participants, where l ≪ m, that are most important? We call this problem Vertically Federated Participant Selection, and model it with a principled mutual information-based view. Our first technical contribution is VF-MINE—a Vertically Federated Mutual INformation Estimator—that uses one of the most celebrated algorithms in database theory—Fagin’s algorithm as a building block. Our second contribution is to further optimize VF-MINE to enable VF-PS, a group testing-based participant selection framework. We empirically show that vertically federated participation selection can be orders of magnitude faster than training a full-fledged VFL model, while being able to identify the most important subset of participants that often lead to a VFL model of similar quality.

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Out-of-Distribution Detection with An Adaptive Likelihood Ratio on Informative Hierarchical VAE

Yewen Li, Chaojie Wang, Xiaobo Xia, Tongliang Liu, Xin Miao, Bo An

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Unsupervised out-of-distribution (OOD) detection is essential for the reliability of machine learning. In the literature, existing work has shown that higher-level semantics captured by hierarchical VAEs can be used to detect OOD instances. However, we empirically show that, the inherent issue of hierarchical VAEs, i.e., ``posterior collapse'', would seriously limit their capacity for OOD detection. Based on a thorough analysis for `posterior collapse'', we propose a novel informative hierarchical VAE to alleviate this issue through enhancing the connections between the data sample and its multi-layer stochastic latent representations during training. Furthermore, we propose a novel score function for unsupervised OOD detection, referred to as Adaptive Likelihood Ratio. With this score function, one can selectively aggregate the semantic information on multiple hidden layers of hierarchical VAEs, leading to a strong separability between in-distribution and OOD samples. Experimental results demonstrate that our method can significantly outperform existing state-of-the-art unsupervised OOD detection approaches.

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The Pitfalls of Regularization in Off-Policy TD Learning

Gaurav Manek, J Zico Kolter

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Temporal Difference (TD) learning is ubiquitous in reinforcement learning, where it is often combined with off-policy sampling and function approximation. Unfortunately learning with this combination (known as the deadly triad), exhibits instability and unbounded error. To account for this, modern Reinforcement Learning methods often implicitly (or sometimes explicitly) assume that regularization is sufficient to mitigate the problem in practice; indeed, the standard deadly triad examples from the literature can be ``fixed'' via proper regularization. In this paper, we introduce a series of new counterexamples to show that the instability and unbounded error of TD methods is not solved by regularization. We demonstrate that, in the off-policy setting with linear function approximation, TD methods can fail to learn a non-trivial value function under any amount of regularization; we further show that regularization can induce divergence under common conditions; and we show that one of the most promising methods to mitigate this divergence (Emphatic TD algorithms) may also diverge under regularization. We further demonstrate such divergence when using neural networks as function approximators. Thus, we argue that the role of regularization in TD methods needs to be reconsidered, given that it is insufficient to prevent divergence and may itself introduce instability. There needs to be much more care in the practical and theoretical application of regularization to Reinforcement Learning methods.

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Contrastive Learning as Goal-Conditioned Reinforcement Learning

Benjamin Eysenbach, Tianjun Zhang, Sergey Levine, Ruslan Salakhutdinov

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In reinforcement learning (RL), it is easier to solve a task if given a good representation. While deep RL should automatically acquire such good representations, prior work often finds that learning representations in an end-to-end fashion is unstable and instead equip RL algorithms with additional representation learning parts (e.g., auxiliary losses, data augmentation). How can we design RL algorithms that directly acquire good representations? In this paper, instead of adding representation learning parts to an existing RL algorithm, we show (contrastive) representation learning methods are already RL algorithms in their own right. To do this, we build upon prior work and apply contrastive representation learning to action-labeled trajectories, in such a way that the (inner product of) learned representations exactly corresponds to a goal-conditioned value function. We use this idea to reinterpret a prior RL method as performing contrastive learning, and then use the idea to propose a much simpler method that achieves similar performance. Across a range of goal-conditioned RL tasks, we demonstrate that contrastive RL methods achieve higher success rates than prior non-contrastive methods. We also show that contrastive RL outperforms prior methods on image-based tasks, without using data augmentation or auxiliary objectives

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Deep Differentiable Logic Gate Networks

Felix Petersen, Christian Borgelt, Hilde Kuehne, Oliver Deussen

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Recently, research has increasingly focused on developing efficient neural network architectures. In this work, we explore logic gate networks for machine learning tasks by learning combinations of logic gates. These networks comprise logic gates such as "AND" and "XOR", which allow for very fast execution. The difficulty in learning logic gate networks is that they are conventionally non-differentiable and therefore do not allow training with gradient descent. Thus, to allow for effective training, we propose differentiable logic gate networks, an architecture that combines real-valued logics and a continuously parameterized relaxation of the network. The resulting discretized logic gate networks achieve fast inference speeds, e.g., beyond a million images of MNIST per second on a single CPU core.

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When Do Flat Minima Optimizers Work?

Jean Kaddour, Linqing Liu, Ricardo Silva, Matt Kusner

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Recently, flat-minima optimizers, which seek to find parameters in low-loss neighborhoods, have been shown to improve a neural network's generalization performance over stochastic and adaptive gradient-based optimizers. Two methods have received significant attention due to their scalability: 1. Stochastic Weight Averaging (SWA), and 2. Sharpness-Aware Minimization (SAM). However, there has been limited investigation into their properties and no systematic benchmarking of them across different domains. We fill this gap here by comparing the loss surfaces of the models trained with each method and through broad benchmarking across computer vision, natural language processing, and graph representation learning tasks. We discover several surprising findings from these results, which we hope will help researchers further improve deep learning optimizers, and practitioners identify the right optimizer for their problem.

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An In-depth Study of Stochastic Backpropagation

Jun Fang, Mingze Xu, Hao Chen, Bing Shuai, Zhuowen Tu, Joseph Tighe

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In this paper, we provide an in-depth study of Stochastic Backpropagation (SBP) when training deep neural networks for standard image classification and object detection tasks. During backward propagation, SBP calculates gradients by using only a subset of feature maps to save GPU memory and computational cost. We interpret SBP as an efficient way to implement stochastic gradient decent by performing backpropagation dropout, which leads to significant memory saving and training run-time reduction, with a minimal impact on the overall model accuracy. We offer best practices to apply SBP for training image recognition models, which can be adopted in learning a wide range of deep neural networks. Experiments on image classification and object detection show that SBP can save up to 40% of GPU memory with less than 1% accuracy degradation. Code is available at: https://github.com/amazon-research/stochastic-backpropagation

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The price of ignorance: how much does it cost to forget noise structure in low-rank matrix estimation?

jean barbier, TianQi Hou, Marco Mondelli, Manuel Saenz

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We consider the problem of estimating a rank-$1$ signal corrupted by structured rotationally invariant noise, and address the following question: \emph{how well do inference algorithms perform when the noise statistics is unknown and hence Gaussian noise is assumed?} While the matched Bayes-optimal setting with unstructured noise is well understood, the analysis of this mismatched problem is only at its premises. In this paper, we make a step towards understanding the effect of the strong source of mismatch which is the noise statistics. Our main technical contribution is the rigorous analysis of a Bayes estimator and of an approximate message passing (AMP) algorithm, both of which incorrectly assume a Gaussian setup. The first result exploits the theory of spherical integrals and of low-rank matrix perturbations; the idea behind the second one is to design and analyze an artificial AMP which, by taking advantage of the flexibility in the denoisers, is able to "correct" the mismatch. Armed with these sharp asymptotic characterizations, we unveil a rich and often unexpected phenomenology. For example, despite AMP is in principle designed to efficiently compute the Bayes estimator, the former is \emph{outperformed} by the latter in terms of mean-square error. We show that this performance gap is due to an incorrect estimation of the signal norm. In fact, when the SNR is large enough, the overlaps of the AMP and the Bayes estimator coincide, and they even match those of optimal estimators taking into account the structure of the noise.

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Neural Estimation of Submodular Functions with Applications to Differentiable Subset Selection

Abir De, Soumen Chakrabarti

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Submodular functions and variants, through their ability to characterize diversity and coverage, have emerged as a key tool for data selection and summarization. Many recent approaches to learn submodular functions suffer from limited expressiveness. In this work, we propose FlexSubNet, a family of flexible neural models for both monotone and non-monotone submodular functions. To fit a latent submodular function from (set, value) observations, our method applies a concave function on modular functions in a recursive manner. We do not draw the concave function from a restricted family, but rather learn from data using a highly expressive neural network that implements a differentiable quadrature procedure. Such an expressive neural model for concave functions may be of independent interest. Next, we extend this setup to provide a novel characterization of monotone $\alpha$-submodular functions, a recently introduced notion of approximate submodular functions. We then use this characterization to design a novel neural model for such functions. Finally, we consider learning submodular set functions under distant supervision in the form of (perimeter, high-value-subset) pairs. This yields a novel subset selection method based on an order-invariant, yet greedy sampler built around the above neural set functions. Our experiments on synthetic and real data show that FlexSubNet outperforms several baselines.

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Nonparametric Uncertainty Quantification for Single Deterministic Neural Network

Nikita Yurevich Kotelevskii, Aleksandr Artemenkov, Kirill Fedyanin, Fedor Noskov, Alexander Fishkov, Artem Shelmanov, Artem Vazhentsev, Aleksandr Petiushko, Maxim Panov

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This paper proposes a fast and scalable method for uncertainty quantification of machine learning models' predictions. First, we show the principled way to measure the uncertainty of predictions for a classifier based on Nadaraya-Watson's nonparametric estimate of the conditional label distribution. Importantly, the approach allows to disentangle explicitly \textit{aleatoric} and \textit{epistemic} uncertainties. The resulting method works directly in the feature space. However, one can apply it to any neural network by considering an embedding of the data induced by the network. We demonstrate the strong performance of the method in uncertainty estimation tasks on text classification problems and a variety of real-world image datasets, such as MNIST, SVHN, CIFAR-100 and several versions of ImageNet.

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Instance-Based Uncertainty Estimation for Gradient-Boosted Regression Trees

Jonathan Brophy, Daniel Lowd

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Gradient-boosted regression trees (GBRTs) are hugely popular for solving tabular regression problems, but provide no estimate of uncertainty. We propose Instance-Based Uncertainty estimation for Gradient-boosted regression trees (IBUG), a simple method for extending any GBRT point predictor to produce probabilistic predictions. IBUG computes a non-parametric distribution around a prediction using the $k$-nearest training instances, where distance is measured with a tree-ensemble kernel. The runtime of IBUG depends on the number of training examples at each leaf in the ensemble, and can be improved by sampling trees or training instances. Empirically, we find that IBUG achieves similar or better performance than the previous state-of-the-art across 22 benchmark regression datasets. We also find that IBUG can achieve improved probabilistic performance by using different base GBRT models, and can more flexibly model the posterior distribution of a prediction than competing methods. We also find that previous methods suffer from poor probabilistic calibration on some datasets, which can be mitigated using a scalar factor tuned on the validation data. Source code is available at https://github.com/jjbrophy47/ibug.

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Finding Naturally Occurring Physical Backdoors in Image Datasets

Emily Wenger, Roma Bhattacharjee, Arjun Nitin Bhagoji, Josephine Passananti, Emilio Andere, Haitao Zheng, Ben Zhao

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Extensive literature on backdoor poison attacks has studied attacks and defenses for backdoors using “digital trigger patterns.” In contrast, “physical backdoors” use physical objects as triggers, have only recently been identified, and are qualitatively different enough to resist most defenses targeting digital trigger backdoors. Research on physical backdoors is limited by access to large datasets containing real images of physical objects co-located with misclassification targets. Building these datasets is time- and labor-intensive. This work seeks to address the challenge of accessibility for research on physical backdoor attacks. We hypothesize that there may be naturally occurring physically co-located objects already present in popular datasets such as ImageNet. Once identified, a careful relabeling of these data can transform them into training samples for physical backdoor attacks. We propose a method to scalably identify these subsets of potential triggers in existing datasets, along with the specific classes they can poison. We call these naturally occurring trigger-class subsets natural backdoor datasets. Our techniques successfully identify natural backdoors in widely-available datasets, and produce models behaviorally equivalent to those trained on manually curated datasets. We release our code to allow the research community to create their own datasets for research on physical backdoor attacks.

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SKFlow: Learning Optical Flow with Super Kernels

Shangkun Sun, Yuanqi Chen, Yu Zhu, Guodong Guo, Ge Li

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Optical flow estimation is a classical yet challenging task in computer vision. One of the essential factors in accurately predicting optical flow is to alleviate occlusions between frames. However, it is still a thorny problem for current top-performing optical flow estimation methods due to insufficient local evidence to model occluded areas. In this paper, we propose the Super Kernel Flow Network (SKFlow), a CNN architecture to ameliorate the impacts of occlusions on optical flow estimation. SKFlow benefits from the super kernels which bring enlarged receptive fields to complement the absent matching information and recover the occluded motions. We present efficient super kernel designs by utilizing conical connections and hybrid depth-wise convolutions. Extensive experiments demonstrate the effectiveness of SKFlow on multiple benchmarks, especially in the occluded areas. Without pre-trained backbones on ImageNet and with a modest increase in computation, SKFlow achieves compelling performance and ranks $\textbf{1st}$ among currently published methods on the Sintel benchmark. On the challenging Sintel clean and final passes (test), SKFlow surpasses the best-published result in the unmatched areas ($7.96$ and $12.50$) by $9.09\%$ and $7.92\%$. The code is available at https://github.com/littlespray/SKFlow.

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Learning interacting dynamical systems with latent Gaussian process ODEs

Cagatay Yildiz, Melih Kandemir, Barbara Rakitsch

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We study uncertainty-aware modeling of continuous-time dynamics of interacting objects. We introduce a new model that decomposes independent dynamics of single objects accurately from their interactions. By employing latent Gaussian process ordinary differential equations, our model infers both independent dynamics and their interactions with reliable uncertainty estimates. In our formulation, each object is represented as a graph node and interactions are modeled by accumulating the messages coming from neighboring objects. We show that efficient inference of such a complex network of variables is possible with modern variational sparse Gaussian process inference techniques. We empirically demonstrate that our model improves the reliability of long-term predictions over neural network based alternatives and it successfully handles missing dynamic or static information. Furthermore, we observe that only our model can successfully encapsulate independent dynamics and interaction information in distinct functions and show the benefit from this disentanglement in extrapolation scenarios.

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Unsupervised Learning under Latent Label Shift

Manley Roberts, Pranav Mani, Saurabh Garg, Zachary Chase Lipton

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What sorts of structure might enable a learner to discover classes from unlabeled data? Traditional approaches rely on feature-space similarity and heroic assumptions on the data. In this paper, we introduce unsupervised learning under Latent Label Shift (LLS), where the label marginals $p_d(y)$ shift but the class conditionals $p(x|y)$ do not. This work instantiates a new principle for identifying classes: elements that shift together group together. For finite input spaces, we establish an isomorphism between LLS and topic modeling: inputs correspond to words, domains to documents, and labels to topics. Addressing continuous data, we prove that when each label's support contains a separable region, analogous to an anchor word, oracle access to $p(d|x)$ suffices to identify $p_d(y)$ and $p_d(y|x)$ up to permutation. Thus motivated, we introduce a practical algorithm that leverages domain-discriminative models as follows: (i) push examples through domain discriminator $p(d|x)$; (ii) discretize the data by clustering examples in $p(d|x)$ space; (iii) perform non-negative matrix factorization on the discrete data; (iv) combine the recovered $p(y|d)$ with the discriminator outputs $p(d|x)$ to compute $p_d(y|x) \; \forall d$. With semisynthetic experiments, we show that our algorithm can leverage domain information to improve upon competitive unsupervised classification methods. We reveal a failure mode of standard unsupervised classification methods when data-space similarity does not indicate true groupings, and show empirically that our method better handles this case. Our results establish a deep connection between distribution shift and topic modeling, opening promising lines for future work.

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Expected Improvement for Contextual Bandits

Hung Tran-The, Sunil Gupta, Santu Rana, Tuan Truong, Long Tran-Thanh, Svetha Venkatesh

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The expected improvement (EI) is a popular technique to handle the tradeoff between exploration and exploitation under uncertainty. This technique has been widely used in Bayesian optimization but it is not applicable for the contextual bandit problem which is a generalization of the standard bandit and Bayesian optimization. In this paper, we initiate and study the EI technique for contextual bandits from both theoretical and practical perspectives. We propose two novel EI-based algorithms, one when the reward function is assumed to be linear and the other for more general reward functions. With linear reward functions, we demonstrate that our algorithm achieves a near-optimal regret. Notably, our regret improves that of LinTS \cite{agrawal13} by a factor $\sqrt{d}$ while avoiding to solve a NP-hard problem at each iteration as in LinUCB \cite{Abbasi11}. For more general reward functions which are modeled by deep neural networks, we prove that our algorithm achieves a $\tilde{\mathcal O} (\tilde{d}\sqrt{T})$ regret, where $\tilde{d}$ is the effective dimension of a neural tangent kernel (NTK) matrix, and $T$ is the number of iterations. Our experiments on various benchmark datasets show that both proposed algorithms work well and consistently outperform existing approaches, especially in high dimensions.

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Does GNN Pretraining Help Molecular Representation?

Ruoxi Sun, Hanjun Dai, Adams Wei Yu

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Extracting informative representations of molecules using Graph neural networks (GNNs) is crucial in AI-driven drug discovery. Recently, the graph research community has been trying to replicate the success of self-supervised pretraining in natural language processing, with several successes claimed. However, we find the benefit brought by self-supervised pretraining on small molecular data can be negligible in many cases. We conduct thorough ablation studies on the key components of GNN pretraining, including pretraining objectives, data splitting methods, input features, pretraining dataset scales, and GNN architectures, to see how they affect the accuracy of the downstream tasks. Our first important finding is, self-supervised graph pretraining do not always have statistically significant advantages over non-pretraining methods in many settings. Secondly, although noticeable improvement can be observed with additional supervised pretraining, the improvement may diminish with richer features or more balanced data splits. Thirdly, hyper-parameters could have larger impacts on accuracy of downstream tasks than the choice of pretraining tasks, especially when the scales of downstream tasks are small. Finally, we provide our conjectures where the complexity of some pretraining methods on small molecules might be insufficient, followed by empirical evidences on different pretraining datasets.

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Hyper-Representations as Generative Models: Sampling Unseen Neural Network Weights

Konstantin Schürholt, Boris Knyazev, Xavier Giró-i-Nieto, Damian Borth

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Learning representations of neural network weights given a model zoo is an emerg- ing and challenging area with many potential applications from model inspection, to neural architecture search or knowledge distillation. Recently, an autoencoder trained on a model zoo was able to learn a hyper-representation, which captures intrinsic and extrinsic properties of the models in the zoo. In this work, we ex- tend hyper-representations for generative use to sample new model weights. We propose layer-wise loss normalization which we demonstrate is key to generate high-performing models and several sampling methods based on the topology of hyper-representations. The models generated using our methods are diverse, per- formant and capable to outperform strong baselines as evaluated on several down- stream tasks: initialization, ensemble sampling and transfer learning. Our results indicate the potential of knowledge aggregation from model zoos to new models via hyper-representations thereby paving the avenue for novel research directions.

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