DeepNLP/ICLR-2023-Accepted-Papers huggingface dataset:
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
Authors: Gabriele Corso,Hannes Stärk,Bowen Jing,Regina Barzilay,Tommi S. Jaakkola

Predicting the binding structure of a small molecule ligand to a protein---a task known as molecular docking---is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.
Constructive TT-representation of the tensors given as index interaction functions with applications
Authors: Gleb Ryzhakov,Ivan Oseledets

This paper presents a method to build explicit tensor-train (TT) representations. We show that a wide class of tensors can be explicitly represented with sparse TT-cores, obtaining, in many cases, optimal TT-ranks. Numerical experiments show that our method outperforms the existing ones in several practical applications, including game theory problems. Theoretical estimations of the number of operations show that in some problems, such as permanent calculation, our methods are close to the known optimal asymptotics, which are obtained by a completely different type of methods.
Sparse tree-based Initialization for Neural Networks
Authors: Patrick Lutz,Ludovic Arnould,Claire Boyer,Erwan Scornet

Dedicated neural network (NN) architectures have been designed to handle specific data types (such as CNN for images or RNN for text), which ranks them among state-of-the-art methods for dealing with these data. Unfortunately, no architecture has been found for dealing with tabular data yet, for which tree ensemble methods (tree boosting, random forests) usually show the best predictive performances. In this work, we propose a new sparse initialization technique for (potentially deep) multilayer perceptrons (MLP):  we first train a tree-based procedure to detect feature interactions and use the resulting information to initialize the network, which is subsequently trained via standard gradient descent (GD) strategies. Numerical experiments on several tabular data sets showthe benefits of this new, simple and easy-to-use method, both in terms of generalization capacity and computation time, compared to default MLP initialization and even to existing complex deep learning solutions. In fact, this wise MLP initialization raises the performances of the resulting NN methods to that of gradient boosting on tabular data. Besides, such initializations are able to preserve the sparsity of weights introduced in the first layers of the network throughout the training, which emphasizes that the first layers act as a sparse feature extractor (like convolutional layers in CNN).
VoGE: A Differentiable Volume Renderer using Gaussian Ellipsoids for Analysis-by-Synthesis
Authors: Angtian Wang,Peng Wang,Jian Sun,Adam Kortylewski,Alan Yuille

Differentiable rendering allows the application of computer graphics on vision tasks, e.g. object pose and shape fitting, via analysis-by-synthesis, where gradients at occluded regions are important when inverting the rendering process.To obtain those gradients, state-of-the-art (SoTA) differentiable renderers use rasterization to collect a set of nearest components for each pixel and aggregate them based on the viewing distance. In this paper, we propose VoGE, which uses ray tracing to capture nearest components with their volume density distributions on the rays and aggregates via integral of the volume densities based on Gaussian ellipsoids, which brings more efficient and stable gradients. To efficiently render via VoGE, we propose an approximate close-form solution for the volume density aggregation and a coarse-to-fine rendering strategy. Finally, we provide a CUDA implementation of VoGE, which gives a competitive rendering speed in comparison to PyTorch3D. Quantitative and qualitative experiment results show VoGE outperforms SoTA counterparts when applied to various vision tasks, e.g., object pose estimation, shape/texture fitting, and occlusion reasoning. The VoGE code is available at: https://github.com/Angtian/VoGE.
The Lazy Neuron Phenomenon: On Emergence of Activation Sparsity in Transformers
Authors: Zonglin Li,Chong You,Srinadh Bhojanapalli,Daliang Li,Ankit Singh Rawat,Sashank J. Reddi,Ke Ye,Felix Chern,Felix Yu,Ruiqi Guo,Sanjiv Kumar

This paper studies a curious phenomenon that machine learning model with Transformer architectures have sparse activation maps. By activation map we refer to the intermediate output of the multi-layer perceptrons (MLPs) after a ReLU activation function, and by "sparse" we mean that on average very few entries (e.g., 3.0% for T5-Base and 6.3% for ViT-B16) are nonzero for each input to MLP. Moreover, larger Transformers with more layers and wider MLP hidden dimensions are sparser as measured by the percentage of nonzero entries. Through extensive experiments we demonstrate that the emergence of sparsity is a prevalent phenomenon that occurs for both natural language processing and vision tasks, on both training and evaluation data, for Transformers of various configurations, at layers of all depth levels. We discuss how sparsity immediately implies a way to significantly reduce the FLOP count and improve efficiency for Transformers. Moreover, we demonstrate perhaps surprisingly that enforcing an even sparser activation via Top-k thresholding with a small k brings a collection of desired properties, namely less sensitivity to noisy training data, more robustness to input corruptions, and better calibration for their prediction confidence.
FoSR: First-order spectral rewiring for addressing oversquashing in GNNs
Authors: Kedar Karhadkar,Pradeep Kr. Banerjee,Guido Montufar

Graph neural networks (GNNs) are able to leverage the structure of graph data by passing messages along the edges of the graph. While this allows GNNs to learn features depending on the graph structure, for certain graph topologies it leads to inefficient information propagation and a problem known as oversquashing. This has recently been linked with the curvature and spectral gap of the graph. On the other hand, adding edges to the message-passing graph can lead to increasingly similar node representations and a problem known as oversmoothing. We propose a computationally efficient algorithm that prevents oversquashing by systematically adding edges to the graph based on spectral expansion. We combine this with a relational architecture, which lets the GNN preserve the original graph structure and provably prevents oversmoothing. We find experimentally that our algorithm outperforms existing graph rewiring methods in several graph classification tasks.
Generative Modeling Helps Weak Supervision (and Vice Versa)
Authors: Benedikt Boecking,Nicholas Roberts,Willie Neiswanger,Stefano Ermon,Frederic Sala,Artur Dubrawski

Many promising applications of supervised machine learning face hurdles in the acquisition of labeled data in sufficient quantity and quality, creating an expensive bottleneck. To overcome such limitations, techniques that do not depend on ground truth labels have been studied, including weak supervision and generative modeling. While these techniques would seem to be usable in concert, improving one another, how to build an interface between them is not well-understood. In this work, we propose a model fusing programmatic weak supervision and generative adversarial networks and provide theoretical justification motivating this fusion. The proposed approach captures discrete latent variables in the data alongside the weak supervision derived label estimate. Alignment of the two allows for better modeling of sample-dependent accuracies of the weak supervision sources, improving the estimate of unobserved labels. It is the first approach to enable data augmentation through weakly supervised synthetic images and pseudolabels. Additionally, its learned latent variables can be inspected qualitatively. The model outperforms baseline weak supervision label models on a number of multiclass image classification datasets, improves the quality of generated images, and further improves end-model performance through data augmentation with synthetic samples.
Provable Memorization Capacity of Transformers
Authors: Junghwan Kim,Michelle Kim,Barzan Mozafari

Quantifying memorization capacity is essential for understanding the expressiveness and generalizability of deep learning model architectures. However, the memorization capacity of the Transformer architecture has yet to be explored. In this work, we present the first study of the memorization capacity of the Transformer architecture. We prove that Transformers are capable of memorizing $N$ sequence-to-sequence mappings of length $n$ with $d$-dimensional input tokens using $\tilde{O}(d + n + \sqrt{nN})$ parameters. Our theory supports memorization both with and without permutation equivariance, utilizing positional encodings in the latter case. Building on our theory, we also analyze the memorization capacity of Transformers in the sequence classification and language modeling tasks. To verify these theoretical findings, we conduct experiments analyzing the memorization capacity of Transformers in the natural language domain.
Bridge the Inference Gaps of Neural Processes via Expectation Maximization
Authors: Qi Wang,Marco Federici,Herke van Hoof

The neural process (NP) is a family of computationally efficient models for learning distributions over functions. However, it suffers from under-fitting and shows suboptimal performance in practice. Researchers have primarily focused on incorporating diverse structural inductive biases, e.g. attention or convolution, in modeling. The topic of inference suboptimality and an analysis of the NP from the optimization objective perspective has hardly been studied in earlier work. To fix this issue, we propose a surrogate objective of the target log-likelihood of the meta dataset within the expectation maximization framework. The resulting model, referred to as the Self-normalized Importance weighted Neural Process (SI-NP), can learn a more accurate functional prior and has an improvement guarantee concerning the target log-likelihood. Experimental results show the competitive performance of SI-NP over other NPs objectives and illustrate that structural inductive biases, such as attention modules, can also augment our method to achieve SOTA performance.
Masked Vision and Language Modeling for Multi-modal Representation Learning
Authors: Gukyeong Kwon,Zhaowei Cai,Avinash Ravichandran,Erhan Bas,Rahul Bhotika,Stefano Soatto

In this paper, we study how to use masked signal modeling in vision and language (V+L) representation learning. Instead of developing masked language modeling (MLM) and masked image modeling (MIM) independently, we propose to build joint masked vision and language modeling, where the masked signal of one modality is reconstructed with the help from another modality. This is motivated by the nature of image-text paired data that both of the image and the text convey almost the same information but in different formats. The masked signal reconstruction of one modality conditioned on another modality can also implicitly learn cross-modal alignment between language tokens and image patches. Our experiments on various V+L tasks show that the proposed method, along with common V+L alignment losses, not only achieves state-of-the-art performance by using a large amount of data but also outperforms the other competitors by a significant margin in the regimes of limited training data.
Agent-based Graph Neural Networks
Authors: Karolis Martinkus,Pál András Papp,Benedikt Schesch,Roger Wattenhofer

We present a novel graph neural network we call AgentNet, which is designed specifically for graph-level tasks. AgentNet is inspired by sublinear algorithms, featuring a computational complexity that is independent of the graph size. The architecture of AgentNet differs fundamentally from the architectures of traditional graph neural networks. In AgentNet, some trained \textit{neural agents} intelligently walk the graph, and then collectively decide on the output. We provide an extensive theoretical analysis of AgentNet: We show that the agents can learn to systematically explore their neighborhood and that AgentNet can distinguish some structures that are even indistinguishable by 2-WL. Moreover, AgentNet is able to separate any two graphs which are sufficiently different in terms of subgraphs. We confirm these theoretical results with synthetic experiments on hard-to-distinguish graphs and real-world graph classification tasks. In both cases, we compare favorably not only to standard GNNs but also to computationally more expensive GNN extensions.
On the Performance of Temporal Difference Learning With Neural Networks
Authors: HAOXING TIAN,Ioannis Paschalidis,Alex Olshevsky

Neural Temporal Difference (TD) Learning is an approximate temporal difference method for policy evaluation that uses a neural network for function approximation. Analysis of Neural TD Learning has proven to be challenging. In this paper we provide a convergence analysis of Neural TD Learning with a projection onto $B(\theta_0, \omega)$, a ball of fixed radius $\omega$ around the initial point $\theta_0$. We show an approximation bound of $O(\epsilon + 1/\sqrt{m})$ where $\epsilon$ is the approximation quality of the best neural network in $B(\theta_0, \omega)$ and $m$ is the width of all hidden layers in the network.
Certified Defences Against Adversarial Patch Attacks on Semantic Segmentation
Authors: Maksym Yatsura,Kaspar Sakmann,N. Grace Hua,Matthias Hein,Jan Hendrik Metzen

Adversarial patch attacks are an emerging security threat for real world deep learning applications. We present Demasked Smoothing, the first approach (up to our knowledge) to certify the robustness of semantic segmentation models against this threat model. Previous work on certifiably defending against patch attacks has mostly focused on image classification task and often required changes in the model architecture and additional training which is undesirable and computationally expensive. In Demasked Smoothing, any segmentation model can be applied without particular training, fine-tuning, or restriction of the architecture. Using different masking strategies, Demasked Smoothing can be applied both for certified detection and certified recovery. In extensive experiments we show that Demasked Smoothing can on average certify 63% of the pixel predictions for a 1% patch in the detection task and 46% against a 0.5% patch for the recovery task on the ADE20K dataset.
Markup-to-Image Diffusion Models with Scheduled Sampling
Authors: Yuntian Deng,Noriyuki Kojima,Alexander M Rush

Building on recent advances in image generation, we present a fully data-driven approach to rendering markup into images. The approach is based on diffusion models, which parameterize the distribution of data using a sequence of denoising operations on top of a Gaussian noise distribution. We view the diffusion denoising process a sequential decision making process, and show that it exhibits compounding errors similar to exposure bias issues in imitation learning problems. To mitigate these issues, we adapt the scheduled sampling algorithm to diffusion training. We conduct experiments on four markup datasets: formulas (LaTeX), table layouts (HTML), sheet music (LilyPond), and molecular images (SMILES). These experiments each verify the effectiveness of diffusion and the use of scheduled sampling to fix generation issues. These results also show that the markup-to-image task presents a useful controlled compositional setting for diagnosing and analyzing generative image models.
How Much Space Has Been Explored? Measuring the Chemical Space Covered by Databases and Machine-Generated Molecules
Authors: Yutong Xie,Ziqiao Xu,Jiaqi Ma,Qiaozhu Mei

Forming a molecular candidate set that contains a wide range of potentially effective compounds is crucial to the success of drug discovery. While most databases and machine-learning-based generation models aim to optimize particular chemical properties, there is limited literature on how to properly measure the coverage of the chemical space by those candidates included or generated. This problem is challenging due to the lack of formal criteria to select good measures of the chemical space. In this paper, we propose a novel evaluation framework for measures of the chemical space based on two analyses: an axiomatic analysis with three intuitive axioms that a good measure should obey, and an empirical analysis on the correlation between a measure and a proxy gold standard. Using this framework, we are able to identify #Circles, a new measure of chemical space coverage, which is superior to existing measures both analytically and empirically. We further evaluate how well the existing databases and generation models cover the chemical space in terms of #Circles. The results suggest that many generation models fail to explore a larger space over existing databases, which leads to new opportunities for improving generation models by encouraging exploration.
Understanding new tasks through the lens of training data via exponential tilting
Authors: Subha Maity,Mikhail Yurochkin,Moulinath Banerjee,Yuekai Sun

Deploying machine learning models on new tasks is a major challenge due to differences in distributions of the train (source) data and the new (target) data. However, the training data likely captures some of the properties of the new task.  We consider the problem of reweighing the training samples to gain insights into the distribution of the target task. Specifically, we formulate a distribution shift model based on the exponential tilt assumption and learn train data importance weights minimizing the KL divergence between labeled train and unlabeled target datasets. The learned train data weights can then be used for downstream tasks such as target performance evaluation, fine-tuning, and model selection. We demonstrate the efficacy of our method on Waterbirds and Breeds benchmarks.
Calibrating Sequence likelihood Improves Conditional Language Generation
Authors: Yao Zhao,Mikhail Khalman,Rishabh Joshi,Shashi Narayan,Mohammad Saleh,Peter J Liu

Conditional language models are predominantly trained with maximum likelihood estimation (MLE), giving probability mass to sparsely observed target sequences. While MLE trained models assign high probability to plausible sequences given the context, the model probabilities often do not accurately rank-order generated sequences by quality.  This has been empirically observed in beam search decoding as output quality degrading with large beam sizes,  and decoding strategies benefiting from heuristics such as length normalization and repetition-blocking. In this work, we introduce sequence likelihood calibration (SLiC) where the likelihood of model generated sequences are calibrated to better align with reference sequences in the model’s latent space.  With SLiC, decoding heuristics become unnecessary and decoding candidates’ quality significantly improves regardless of the decoding method. Furthermore, SLiC shows no sign of diminishing returns with model scale, and presents alternative ways to improve quality with limited training and inference budgets. With SLiC, we exceed or match SOTA results on a wide range of generation tasks spanning abstractive summarization, question generation, abstractive question answering and data-to-text generation, even with modest-sized models.
Learning differentiable solvers for systems with hard constraints
Authors: Geoffrey Négiar,Michael W. Mahoney,Aditi Krishnapriyan

We introduce a practical method to enforce partial differential equation (PDE) constraints for functions defined by neural networks (NNs), with a high degree of accuracy and up to a desired tolerance. We develop a differentiable PDE-constrained layer that can be incorporated into any NN architecture. Our method leverages differentiable optimization and the implicit function theorem to effectively enforce physical constraints. Inspired by dictionary learning, our model learns a family of functions, each of which defines a mapping from PDE parameters to PDE solutions. At inference time, the model finds an optimal linear combination of the functions in the learned family by solving a PDE-constrained optimization problem. Our method provides continuous solutions over the domain of interest that accurately satisfy desired physical constraints. Our results show that incorporating hard constraints directly into the NN architecture achieves much lower test error when compared to training on an unconstrained objective.
FedDAR: Federated Domain-Aware Representation Learning
Authors: Aoxiao Zhong,Hao He,Zhaolin Ren,Na Li,Quanzheng Li

Cross-silo Federated learning (FL) has become a promising tool in machine learning applications for healthcare. It allows hospitals/institutions to train models with sufficient data while the data is kept private. To make sure the FL model is robust when facing heterogeneous data among FL clients, most efforts focus on personalizing models for clients. However, the latent relationships between clients' data are ignored. In this work, we focus on a special non-iid FL problem, called Domain-mixed FL, where each client's data distribution is assumed to be a mixture of several predefined domains.  Recognizing the diversity of domains and the similarity within domains, we propose a novel method, FedDAR, which learns a domain shared representation and domain-wise personalized prediction heads in a decoupled manner. For simplified linear regression settings, we have theoretically proved that FedDAR enjoys a linear convergence rate.  For general settings, we have performed intensive empirical studies on both synthetic and real-world medical datasets which demonstrate its superiority over prior FL methods. Our code is available at https://github.com/zlz0414/FedDAR.