DeepNLP/ICLR-2023-Accepted-Papers huggingface dataset:
Molecule Generation For Target Protein Binding with Structural Motifs
Authors: ZAIXI ZHANG,Yaosen Min,Shuxin Zheng,Qi Liu

Designing ligand molecules that bind to specific protein binding sites is a fundamental problem in structure-based drug design. Although deep generative models and geometric deep learning have made great progress in drug design, existing works either sample in the 2D graph space or fail to generate valid molecules with realistic substructures. To tackle these problems, we propose a Fragment-based LigAnd Generation framework (FLAG), to generate 3D molecules with valid and realistic substructures fragment-by-fragment. In FLAG, a motif vocabulary is constructed by extracting common molecular fragments (i.e., motif) in the dataset. At each generation step, a 3D graph neural network is first employed to encode the intermediate context information. Then, our model selects the focal motif, predicts the next motif type, and attaches the new motif. The bond lengths/angles can be quickly and accurately determined by cheminformatics tools. Finally, the molecular geometry is further adjusted according to the predicted rotation angle and the structure refinement. Our model not only achieves competitive performances on conventional metrics such as binding affinity, QED, and SA, but also outperforms baselines by a large margin in generating molecules with realistic substructures.
Towards Robustness Certification Against Universal Perturbations
Authors: Yi Zeng,Zhouxing Shi,Ming Jin,Feiyang Kang,Lingjuan Lyu,Cho-Jui Hsieh,Ruoxi Jia

In this paper, we investigate the problem of certifying neural network robustness against universal perturbations (UPs), which have been widely used in universal adversarial attacks and backdoor attacks. Existing robustness certification methods aim to provide robustness guarantees for each sample with respect to the worst-case perturbations given a neural network. However, those sample-wise bounds will be loose when considering the UP threat model as they overlook the important constraint that the perturbation should be shared across all samples. We propose a method based on a combination of linear relaxation-based perturbation analysis and Mixed Integer Linear Programming to establish the first robust certification method for UP. In addition, we develop a theoretical framework for computing error bounds on the entire population using the certification results from a randomly sampled batch. Aside from an extensive evaluation of the proposed certification, we further show how the certification facilitates efficient comparison of robustness among different models or efficacy among different universal adversarial attack defenses and enables accurate detection of backdoor target classes.
Deep Generative Modeling on Limited Data with Regularization by Nontransferable Pre-trained Models
Authors: Yong Zhong,Hongtao Liu,Xiaodong Liu,Fan Bao,Weiran Shen,Chongxuan Li

Deep generative models (DGMs) are data-eager because learning a complex model on limited data suffers from a large variance and easily overfits. Inspired by the classical perspective of the bias-variance tradeoff, we propose regularized deep generative model (Reg-DGM), which leverages a nontransferable pre-trained model to reduce the variance of generative modeling with limited data. Formally, Reg-DGM optimizes a weighted sum of a certain divergence and the expectation of an energy function, where the divergence is between the data and the model distributions, and the energy function is defined by the pre-trained model w.r.t. the model distribution. We analyze a simple yet representative Gaussian-fitting case to demonstrate how the weighting hyperparameter trades off the bias and the variance. Theoretically, we characterize the existence and the uniqueness of the global minimum of Reg-DGM in a non-parametric setting and prove its convergence with neural networks trained by gradient-based methods. Empirically, with various pre-trained feature extractors and a data-dependent energy function, Reg-DGM consistently improves the generation performance of strong DGMs with limited data and achieves competitive results to the state-of-the-art methods. Our implementation is available at https://github.com/ML-GSAI/Reg-ADA-APA.
Basic Binary Convolution Unit for Binarized Image Restoration Network
Authors: Bin Xia,Yulun Zhang,Yitong Wang,Yapeng Tian,Wenming Yang,Radu Timofte,Luc Van Gool

Lighter and faster image restoration (IR) models are crucial for the deployment on resource-limited devices. Binary neural network (BNN), one of the most promising model compression methods, can dramatically reduce the computations and parameters of full-precision convolutional neural networks (CNN). However, there are different properties between BNN and full-precision CNN, and we can hardly use the experience of designing CNN to develop BNN. In this study, we reconsider components in binary convolution, such as residual connection, BatchNorm, activation function, and structure, for IR tasks. We conduct systematic analyses to explain each component's role in binary convolution and discuss the pitfalls. Specifically, we find that residual connection can reduce the information loss caused by binarization; BatchNorm can solve the value range gap between residual connection and binary convolution; The position of the activation function dramatically affects the performance of BNN. Based on our findings and analyses, we design a simple yet efficient basic binary convolution unit (BBCU). Furthermore, we divide IR networks into four parts and specially design variants of BBCU for each part to explore the benefit of binarizing these parts. We conduct experiments on different IR tasks, and our BBCU significantly outperforms other BNNs and lightweight models, which shows that BBCU can serve as a basic unit for binarized IR networks. All codes and models will be released.
Multimodal Federated Learning via Contrastive Representation Ensemble
Authors: Qiying Yu,Yang Liu,Yimu Wang,Ke Xu,Jingjing Liu

With the increasing amount of multimedia data on modern mobile systems and IoT infrastructures, harnessing these rich multimodal data without breaching user privacy becomes a critical issue. Federated learning (FL) serves as a privacy-conscious alternative to centralized machine learning. However, existing FL methods extended to multimodal data all rely on model aggregation on single modality level, which restrains the server and clients to have identical model architecture for each modality. This limits the global model in terms of both model complexity and data capacity, not to mention task diversity. In this work, we propose \textit{Contrastive Representation Ensemble and Aggregation for Multimodal FL (CreamFL)}, a multimodal federated learning framework that enables training larger server models from clients with heterogeneous model architectures and data modalities, while only communicating knowledge on public dataset. To achieve better multimodal representation fusion, we design a global-local cross-modal ensemble strategy to aggregate client representations. To mitigate local model drift caused by two unprecedented heterogeneous factors stemming from multimodal discrepancy (\textit{modality gap} and \textit{task gap}), we further propose two inter-modal and intra-modal contrasts to regularize local training, which complements information of the absent modality for uni-modal clients and regularizes local clients to head towards global consensus. Thorough evaluations and ablation studies on image-text retrieval and visual question answering tasks showcase the superiority of CreamFL over state-of-the-art FL methods and its practical value.
Eva: Practical Second-order Optimization with Kronecker-vectorized Approximation
Authors: Lin Zhang,Shaohuai Shi,Bo Li

Second-order optimization algorithms exhibit excellent convergence properties for training deep learning models, but often incur significant computation and memory overheads. This can result in lower training efficiency than the first-order counterparts such as stochastic gradient descent (SGD). In this work, we present a memory- and time-efficient second-order algorithm named Eva with two novel techniques: 1) we construct the second-order information with the Kronecker factorization of small stochastic vectors over a mini-batch of training data to reduce memory consumption, and 2) we derive an efficient update formula without explicitly computing the inverse of matrices using the Sherman-Morrison formula. We further provide a theoretical interpretation of Eva from a trust-region optimization point of view to understand how it works. Extensive experimental results on different models and datasets show that Eva reduces the end-to-end training time up to $2.05\times$ and $2.42\times$ compared to first-order SGD and second-order algorithms (K-FAC and Shampoo), respectively.
Can CNNs Be More Robust Than Transformers?
Authors: Zeyu Wang,Yutong Bai,Yuyin Zhou,Cihang Xie

The recent success of Vision Transformers is shaking the long dominance of Convolutional Neural Networks (CNNs) in image recognition for a decade. Specifically, in terms of robustness on out-of-distribution samples, recent research finds that Transformers are inherently more robust than CNNs, regardless of different training setups. Moreover, it is believed that such superiority of Transformers should largely be credited to their \emph{self-attention-like architectures per se}. In this paper, we question that belief by closely examining the design of Transformers. Our findings lead to three highly effective architecture designs for boosting robustness, yet simple enough to be implemented in several lines of code, namely a) patchifying input images, b) enlarging kernel size, and c) reducing activation layers and normalization layers. Bringing these components together, we are able to build pure CNN architectures without any attention-like operations that are as robust as, or even more robust than, Transformers. We hope this work can help the community better understand the design of robust neural architectures. The code is publicly available at https://github.com/UCSC-VLAA/RobustCNN.
Risk-Aware Reinforcement Learning with Coherent Risk Measures and Non-linear Function Approximation
Authors: Thanh Lam,Arun Verma,Bryan Kian Hsiang Low,Patrick Jaillet

We study the risk-aware reinforcement learning (RL) problem in the episodic finite-horizon Markov decision process with unknown transition and reward functions. In contrast to the risk-neutral RL problem, we consider minimizing the risk of having low rewards, which arise due to the intrinsic randomness of the MDPs and imperfect knowledge of the model. Our work provides a unified framework to analyze the regret of risk-aware RL policy with coherent risk measures in conjunction with non-linear function approximation, which gives the first sub-linear regret bounds in the setting. Finally, we validate our theoretical results via empirical experiments on synthetic and real-world data.
Bi-level Physics-Informed Neural Networks for PDE Constrained Optimization using Broyden's Hypergradients
Authors: Zhongkai Hao,Chengyang Ying,Hang Su,Jun Zhu,Jian Song,Ze Cheng

Deep learning based approaches like Physics-informed neural networks (PINNs) and DeepONets have shown promise on solving PDE constrained optimization (PDECO) problems. 
However, existing methods are insufficient to handle those PDE constraints that have a complicated or nonlinear dependency on optimization targets. In this paper, we present a novel bi-level optimization framework to resolve the challenge by decoupling the optimization of the targets and constraints. For the inner loop optimization, we adopt PINNs to solve the PDE constraints only. For the outer loop, we design a novel method by using Broyden's method based on the Implicit Function Theorem (IFT), which is efficient and accurate for approximating hypergradients. We further present theoretical explanations and error analysis of the hypergradients computation. Extensive experiments on multiple large-scale and nonlinear PDE constrained optimization problems demonstrate that our method achieves state-of-the-art results compared with strong baselines.
On the Saturation Effect of Kernel Ridge Regression
Authors: Yicheng Li,Haobo Zhang,Qian Lin

The saturation effect refers to the  phenomenon that the kernel ridge regression (KRR) fails to achieve the information theoretical lower bound when the smoothness of the underground truth function exceeds certain level. The saturation effect  has been widely observed in practices and a saturation lower bound of KRR has been conjectured for decades. In this paper, we provide a proof of this long-standing conjecture.
Protein Representation Learning by Geometric Structure Pretraining
Authors: Zuobai Zhang,Minghao Xu,Arian Rokkum Jamasb,Vijil Chenthamarakshan,Aurelie Lozano,Payel Das,Jian Tang

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.
Trainable Weight Averaging: Efficient Training by Optimizing Historical Solutions
Authors: Tao Li,Zhehao Huang,Qinghua Tao,Yingwen Wu,Xiaolin Huang

Stochastic gradient descent (SGD) and its variants are considered as the de-facto methods to train deep neural networks (DNNs). While recent improvements to SGD mainly focus on the descent algorithm itself, few works pay attention to utilizing the historical solutions---as an iterative method, SGD has gone through substantial explorations before convergence. Recently, an interesting attempt is stochastic weight averaging (SWA), which significantly improves the generalization by simply averaging the solutions at the tail stage of training. In this paper, we realize that the averaging coefficients could be determined in a trainable manner and propose Trainable Weight Averaging (TWA), a novel optimization method in the reduced subspace spanned by historical solutions. TWA has much greater flexibility and can be applied to the head stage of training to achieve training efficiency while preserving good generalization capability. Further, we propose a distributed training scheme to resolve the memory burden of large-scale training with efficient parallel computation. In the extensive numerical experiments, (i) TWA achieves consistent improvements over SWA with less sensitivity to learning rate; (ii) applying TWA in the head stage of training largely speeds up the convergence, resulting in over $40\%$ time saving on CIFAR and $30\%$ on ImageNet with improved generalization compared with regular training.
Deep Declarative Dynamic Time Warping for End-to-End Learning of Alignment Paths
Authors: Ming Xu,Sourav Garg,Michael Milford,Stephen Gould

This paper addresses learning end-to-end models for time series data that include a temporal alignment step via dynamic time warping (DTW). Existing approaches to differentiable DTW either differentiate through a fixed warping path or apply a differentiable relaxation to the min operator found in the recursive steps used to solve the DTW problem. We instead propose a DTW layer based around bi-level optimisation and deep declarative networks, which we name DecDTW. By formulating DTW as a continuous, inequality constrained optimisation problem, we can compute gradients for the solution of the optimal alignment (with respect to the underlying time series) using implicit differentiation. An interesting byproduct of this formulation is that DecDTW outputs the optimal warping path between two time series as opposed to a soft approximation, recoverable from Soft-DTW. We show that this property is particularly useful for applications where downstream loss functions are defined on the optimal alignment path itself. This naturally occurs, for instance, when learning to improve the accuracy of predicted alignments against ground truth alignments. We evaluate DecDTW on two such applications, namely the audio-to-score alignment task in music information retrieval and the visual place recognition task in robotics, demonstrating state-of-the-art results in both.
Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning
Authors: Ting Chen,Ruixiang ZHANG,Geoffrey Hinton

We present Bit Diffusion: a simple and generic approach for generating discrete data with continuous state and continuous time diffusion models. The main idea behind our approach is to first represent the discrete data as binary bits, and then train a continuous diffusion model to model these bits as real numbers which we call analog bits. To generate samples, the model first generates the analog bits, which are then thresholded to obtain the bits that represent the discrete variables. We further propose two simple techniques, namely Self-Conditioning and Asymmetric Time Intervals, which lead to a significant improvement in sample quality. Despite its simplicity, the proposed approach can achieve strong performance in both discrete image generation and image captioning tasks. For discrete image generation, we significantly improve previous state-of-the-art on both CIFAR-10 (which has 3K discrete 8-bit tokens) and ImageNet-64x64 (which has 12K discrete 8-bit tokens), outperforming the best autoregressive model in both sample quality (measured by FID) and efficiency. For image captioning on MS-COCO dataset, our approach achieves competitive results compared to autoregressive models.
Understanding Edge-of-Stability Training Dynamics with a Minimalist Example
Authors: Xingyu Zhu,Zixuan Wang,Xiang Wang,Mo Zhou,Rong Ge

Recently, researchers observed that gradient descent for deep neural networks operates in an ``edge-of-stability'' (EoS) regime: the sharpness (maximum eigenvalue of the Hessian) is often larger than stability threshold $2/\eta$ (where $\eta$ is the step size). Despite this, the loss oscillates and converges in the long run, and the sharpness at the end is just slightly below $2/\eta$. While many other well-understood nonconvex objectives such as matrix factorization or two-layer networks can also converge despite large sharpness, there is often a larger gap between sharpness of the endpoint and $2/\eta$. In this paper, we study EoS phenomenon by constructing a simple function that has the same behavior. We give rigorous analysis for its training dynamics in a large local region and explain why the final converging point has sharpness close to $2/\eta$. Globally we observe that the training dynamics for our example has an interesting bifurcating behavior, which was also observed in the training of neural nets.
Learning Proximal Operators to Discover Multiple Optima
Authors: Lingxiao Li,Noam Aigerman,Vladimir Kim,Jiajin Li,Kristjan Greenewald,Mikhail Yurochkin,Justin Solomon

Finding multiple solutions of non-convex optimization problems is a ubiquitous yet challenging task. Most past algorithms either apply single-solution optimization methods from multiple random initial guesses or search in the vicinity of found solutions using ad hoc heuristics. We present an end-to-end method to learn the proximal operator of a family of training problems so that multiple local minima can be quickly obtained from initial guesses by iterating the learned operator, emulating the proximal-point algorithm that has fast convergence. The learned proximal operator can be further generalized to recover multiple optima for unseen problems at test time, enabling applications such as object detection. The key ingredient in our formulation is a proximal regularization term, which elevates the convexity of our training loss: by applying recent theoretical results, we show that for weakly-convex objectives with Lipschitz gradients, training of the proximal operator converges globally with a practical degree of over-parameterization. We further present an exhaustive benchmark for multi-solution optimization to demonstrate the effectiveness of our method.
Guiding continuous operator learning through Physics-based boundary constraints
Authors: Nadim Saad,Gaurav Gupta,Shima Alizadeh,Danielle C. Maddix

Boundary conditions (BCs) are important groups of physics-enforced constraints that are necessary for solutions of Partial Differential Equations (PDEs) to satisfy at specific spatial locations. These constraints carry important physical meaning, and guarantee the existence and the uniqueness of the PDE solution. Current neural-network based approaches that aim to solve PDEs rely only on training data to help the model learn BCs implicitly, however, there is no guarantee of BC satisfaction by these models during evaluation. In this work, we propose Boundary enforcing Operator Network (BOON) that enables the BC satisfaction of neural operators by making structural changes to the operator kernel. We provide our refinement procedure, and demonstrate the satisfaction of physics-based BCs such as Dirichlet, Neumann, and periodic by the solutions obtained by BOON. Numerical experiments based on multiple PDEs with a wide variety of applications indicate that the proposed approach ensures satisfaction of BCs, and leads to more accurate solutions over the whole domain. The proposed method exhibits a (2X-20X) improvement in accuracy (0.000084 relative $L^2$ error for Burgers' equation). Code available at: https://github.com/amazon-science/boon.
Neural Radiance Field Codebooks
Authors: Matthew Wallingford,Aditya Kusupati,Alex Fang,Vivek Ramanujan,Aniruddha Kembhavi,Roozbeh Mottaghi,Ali Farhadi

Compositional representations of the world are a promising step towards enabling high-level scene understanding and efficient transfer to downstream tasks. Learning such representations for complex scenes and tasks remains an open challenge. Towards this goal, we introduce Neural Radiance Field Codebooks (NRC), a scalable method for learning object-centric representations through novel view reconstruction. NRC learns to reconstruct scenes from novel views using a dictionary of object codes which are decoded through a volumetric renderer. This enables the discovery of reoccurring visual and geometric patterns across scenes which are transferable to downstream tasks. We show that NRC representations transfer well to object navigation in THOR, outperforming 2D and 3D representation learning methods by 3.1\% success rate. We demonstrate that our approach is able to perform unsupervised segmentation for more complex synthetic (THOR) and real scenes (NYU Depth) better than prior methods (.101 ARI). Finally, we show that NRC improves on the task of depth ordering by 5.5% accuracy in THOR.