Permutation Equivariant Neural Functionals

This work studies the design of neural networks that can process the weights or gradients of other neural networks, which we refer to as neural functional networks (NFNs). Despite a wide range of potential applications, including learned optimization, processing implicit neural representations, network editing, and policy evaluation, there are few unifying principles for designing effective architectures that process the weights of other networks. We approach the design of neural functionals through the lens of symmetry, in particular by focusing on the permutation symmetries that arise in the weights of deep feedforward networks because hidden layer neurons have no inherent order. We introduce a framework for building permutation equivariant neural functionals, whose architectures encode these symmetries as an inductive bias. The key building blocks of this framework are NF-Layers (neural functional layers) that we constrain to be permutation equivariant through an appropriate parameter sharing scheme. In our experiments, we find that permutation equivariant neural functionals are effective on a diverse set of tasks that require processing the weights of MLPs and CNNs, such as predicting classifier generalization, producing "winning ticket" sparsity masks for initializations, and classifying or editing implicit neural representations (INRs). In addition, we provide code for our models and experiments at https://github.com/AllanYangZhou/nfn.Comment: To appear in Neural Information Processing Systems (NeurIPS), 202

A Genetic Programming Approach to Designing Convolutional Neural Network Architectures

The convolutional neural network (CNN), which is one of the deep learning models, has seen much success in a variety of computer vision tasks. However, designing CNN architectures still requires expert knowledge and a lot of trial and error. In this paper, we attempt to automatically construct CNN architectures for an image classification task based on Cartesian genetic programming (CGP). In our method, we adopt highly functional modules, such as convolutional blocks and tensor concatenation, as the node functions in CGP. The CNN structure and connectivity represented by the CGP encoding method are optimized to maximize the validation accuracy. To evaluate the proposed method, we constructed a CNN architecture for the image classification task with the CIFAR-10 dataset. The experimental result shows that the proposed method can be used to automatically find the competitive CNN architecture compared with state-of-the-art models.Comment: This is the revised version of the GECCO 2017 paper. The code of our method is available at https://github.com/sg-nm/cgp-cn

Targeted sequence design within the coarse-grained polymer genome

The chemical design of polymers with target structural and/or functional properties represents a grand challenge in materials science. While data-driven design approaches are promising, success with polymers has been limited, largely due to limitations in data availability. Here, we demonstrate the targeted sequence design of single-chain structure in polymers by combining coarse-grained modeling, machine learning, and model optimization. Nearly 2000 unique coarse-grained polymers are simulated to construct and analyze machine learning models. We find that deep neural networks inexpensively and reliably predict structural properties with limited sequence information as input. By coupling trained ML models with sequential model-based optimization, polymer sequences are proposed to exhibit globular, swollen, or rod-like behaviors, which are verified by explicit simulations. This work highlights the promising integration of coarse-grained modeling with data-driven design and represents a necessary and crucial step toward more complex polymer design efforts

Machine learning-guided directed evolution for protein engineering

Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed evolution, we introduce the steps required to build ML sequence-function models and use them to guide engineering, making recommendations at each stage. This review covers basic concepts relevant to using ML for protein engineering as well as the current literature and applications of this new engineering paradigm. ML methods accelerate directed evolution by learning from information contained in all measured variants and using that information to select sequences that are likely to be improved. We then provide two case studies that demonstrate the ML-guided directed evolution process. We also look to future opportunities where ML will enable discovery of new protein functions and uncover the relationship between protein sequence and function.Comment: Made significant revisions to focus on aspects most relevant to applying machine learning to speed up directed evolutio

PowerPlanningDL: Reliability-Aware Framework for On-Chip Power Grid Design using Deep Learning

With the increase in the complexity of chip designs, VLSI physical design has become a time-consuming task, which is an iterative design process. Power planning is that part of the floorplanning in VLSI physical design where power grid networks are designed in order to provide adequate power to all the underlying functional blocks. Power planning also requires multiple iterative steps to create the power grid network while satisfying the allowed worst-case IR drop and Electromigration (EM) margin. For the first time, this paper introduces Deep learning (DL)-based framework to approximately predict the initial design of the power grid network, considering different reliability constraints. The proposed framework reduces many iterative design steps and speeds up the total design cycle. Neural Network-based multi-target regression technique is used to create the DL model. Feature extraction is done, and the training dataset is generated from the floorplans of some of the power grid designs extracted from the IBM processor. The DL model is trained using the generated dataset. The proposed DL-based framework is validated using a new set of power grid specifications (obtained by perturbing the designs used in the training phase). The results show that the predicted power grid design is closer to the original design with minimal prediction error (~2%). The proposed DL-based approach also improves the design cycle time with a speedup of ~6X for standard power grid benchmarks.Comment: Published in proceedings of IEEE/ACM Design, Automation and Test in Europe Conference (DATE) 2020, 6 page