We investigate time-dependent data analysis from the perspective of recurrent kernel machines, from which models with hidden units and gated memory cells arise naturally. By considering dynamic gating of the memory cell, a model closely related to the long short-term memory (LSTM) recurrent neural network is derived. Extending this setup to $n$-gram filters, the convolutional neural network (CNN), Gated CNN, and recurrent additive network (RAN) are also recovered as special cases. Our analysis provides a new perspective on the LSTM, while also extending it to $n$-gram convolutional filters. Experiments are performed on natural language processing tasks and on analysis of local field potentials (neuroscience). We demonstrate that the variants we derive from kernels perform on par or even better than traditional neural methods. For the neuroscience application, the new models demonstrate significant improvements relative to the prior state of the art.

We study the average robustness notion in deep neural networks in (selected) wide and narrow, deep and shallow, as well as lazy and non-lazy training settings. We prove that in the under-parameterized setting, width has a negative effect while it improves robustness in the over-parameterized setting. The effect of depth closely depends on the initialization and the training mode. In particular, when initialized with LeCun initialization, depth helps robustness with the lazy training regime. In contrast, when initialized with Neural Tangent Kernel (NTK) and He-initialization, depth hurts the robustness. Moreover, under the non-lazy training regime, we demonstrate how the width of a two-layer ReLU network benefits robustness. Our theoretical developments improve the results by [Huang et al.

Computational lithography provides algorithmic and mathematical support for resolution enhancement in optical lithography, which is the critical step in semiconductor manufacturing. The time-consuming lithography simulation and mask optimization processes limit the practical application of inverse lithography technology (ILT), a promising solution to the challenges of advanced-node lithography. Although various machine learning methods for ILT have shown promise for reducing the computational burden, this field is in lack of a dataset that can train the models thoroughly and evaluate the performance comprehensively. To boost the development of AI-driven computational lithography, we present the LithoBench dataset, a collection of circuit layout tiles for deep-learning-based lithography simulation and mask optimization. LithoBench consists of more than 120k tiles that are cropped from real circuit designs or synthesized according to the layout topologies of famous ILT testcases. The ground truths are generated by a famous lithography model in academia and an advanced ILT method. Based on the data, we provide a framework to design and evaluate deep neural networks (DNNs) with the data. The framework is used to benchmark state-of-the-art models on lithography simulation and mask optimization. We hope LithoBench can promote the research and development of computational lithography.

Periodic graphs are graphs consisting of repetitive local structures, such as crystal nets and polygon mesh. Their generative modeling has great potential in real-world applications such as material design and graphics synthesis. Classical models either rely on domain-specific predefined generation principles (e.g., in crystal net design), or follow geometry-based prescribed rules. Recently, deep generative models have shown great promise in automatically generating general graphs. However, their advancement into periodic graphs has not been well explored due to several key challenges in 1) maintaining graph periodicity; 2) disentangling local and global patterns; and 3) efficiency in learning repetitive patterns.

Automatic optimization for tensor programs becomes increasingly important as we deploy deep learning in various environments, and efficient optimization relies on a rich search space and effective search. Most existing efforts adopt a search space which lacks the ability to efficiently enable domain experts to grow the search space. This paper introduces MetaSchedule, a domain-specific probabilistic programming language abstraction to construct a rich search space of tensor programs. Our abstraction allows domain experts to analyze the program, and easily propose stochastic choices in a modular way to compose program transformation accordingly. We also build an end-to-end learning-driven framework to find an optimized program for a given search space. Experimental results show that MetaSchedule can cover the search space used in the state-of-the-art tensor program optimization frameworks in a modular way. Additionally, it empowers domain experts to conveniently grow the search space and modularly enhance the system, which brings 48% speedup on end-to-end deep learning workloads.

Recurrent Neural Networks (RNNs) capture long dependencies and context, and 2 hence are the key component of typical sequential data based tasks. However, the sequential nature of RNNs dictates a large inference cost for long sequences even if the hardware supports parallelization. To induce long-term dependencies, and yet admit parallelization, we introduce novel shallow RNNs. In this architecture, the first layer splits the input sequence and runs several independent RNNs.

Color is a crucial visual cue readily exploited by Convolutional Neural Networks (CNNs) for object recognition. However, CNNs struggle if there is data imbalance between color variations introduced by accidental recording conditions. Color invariance addresses this issue but does so at the cost of removing all color information, which sacrifices discriminative power. In this paper, we propose Color Equivariant Convolutions (CEConvs), a novel deep learning building block that enables shape feature sharing across the color spectrum while retaining important color information. We extend the notion of equivariance from geometric to photometric transformations by incorporating parameter sharing over hue-shifts in a neural network. We demonstrate the benefits of CEConvs in terms of downstream performance to various tasks and improved robustness to color changes, including train-test distribution shifts. Our approach can be seamlessly integrated into existing architectures, such as ResNets, and offers a promising solution for addressing color-based domain shifts in CNNs.

We provide single-model estimates of aleatoric and epistemic uncertainty for deep neural networks. To estimate aleatoric uncertainty, we propose Simultaneous Quantile Regression (SQR), a loss function to learn all the conditional quantiles of a given target variable. These quantiles can be used to compute well-calibrated prediction intervals. To estimate epistemic uncertainty, we propose Orthonormal Certificates (OCs), a collection of diverse non-constant functions that map all training samples to zero. These certificates map out-of-distribution examples to non-zero values, signaling epistemic uncertainty. Our uncertainty estimators are computationally attractive, as they do not require ensembling or retraining deep models, and achieve state-of-the-art performance.

Advanced deep neural networks (DNNs), designed by either human or AutoML algorithms, are growing increasingly complex. Diverse operations are connected by complicated connectivity patterns, e.g., various types of skip connections. Those topological compositions are empirically effective and observed to smooth the loss landscape and facilitate the gradient flow in general. However, it remains elusive to derive any principled understanding of their effects on the DNN capacity or trainability, and to understand why or in which aspect one specific connectivity pattern is better than another. In this work, we theoretically characterize the impact of connectivity patterns on the convergence of DNNs under gradient descent training in fine granularity. By analyzing a wide network's Neural Network Gaussian Process (NNGP), we are able to depict how the spectrum of an NNGP kernel propagates through a particular connectivity pattern, and how that affects the bound of convergence rates. As one practical implication of our results, we show that by a simple filtration of unpromising connectivity patterns, we can trim down the number of models to evaluate, and significantly accelerate the large-scale neural architecture search without any overhead.

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark will be open-sourced soon.