ICML 2023 论文列表

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

Two different approaches exist to handle missing values for prediction: either imputation, prior to fitting any predictive algorithms, or dedicated methods able to natively incorporate missing values. While imputation is widely (and easily) use, it is unfortunately biased when low-capacity predictors (such as linear models) are applied afterward. However, in practice, naive imputation exhibits good predictive performance. In this paper, we study the impact of imputation in a high-dimensional linear model with MCAR missing data. We prove that zero imputation performs an implicit regularization closely related to the ridge method, often used in high-dimensional problems. Leveraging on this connection, we establish that the imputation bias is controlled by a ridge bias, which vanishes in high dimension. As a predictor, we argue in favor of the averaged SGD strategy, applied to zero-imputed data. We establish an upper bound on its generalization error, highlighting that imputation is benign in the $d \gg \sqrt{n}$ regime. Experiments illustrate our findings.

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.

Diffusion models have found widespread adoption in various areas. However, their sampling process is slow because it requires hundreds to thousands of network evaluations to emulate a continuous process defined by differential equations. In this work, we use neural operators, an efficient method to solve the probability flow differential equations, to accelerate the sampling process of diffusion models. Compared to other fast sampling methods that have a sequential nature, we are the first to propose a parallel decoding method that generates images with only one model forward pass. We propose *diffusion model sampling with neural operator* (DSNO) that maps the initial condition, i.e., Gaussian distribution, to the continuous-time solution trajectory of the reverse diffusion process. To model the temporal correlations along the trajectory, we introduce temporal convolution layers that are parameterized in the Fourier space into the given diffusion model backbone. We show our method achieves state-of-the-art FID of 3.78 for CIFAR-10 and 7.83 for ImageNet-64 in the one-model-evaluation setting.

Supervised learning models have been used in various domains such as lending, college admission, face recognition, natural language processing, etc. However, they may inherit pre-existing biases from training data and exhibit discrimination against protected social groups. Various fairness notions have been proposed to address unfairness issues. In this work, we focus on Equalized Loss (EL), a fairness notion that requires the expected loss to be (approximately) equalized across different groups. Imposing EL on the learning process leads to a non-convex optimization problem even if the loss function is convex, and the existing fair learning algorithms cannot properly be adopted to find the fair predictor under the EL constraint. This paper introduces an algorithm that can leverage off-the-shelf convex programming tools (e.g., CVXPY (Diamond and Boyd, 2016; Agrawal et al., 2018)) to efficiently find the global optimum of this non-convex optimization. In particular, we propose the ELminimizer algorithm, which finds the optimal fair predictor under EL by reducing the non-convex optimization to a sequence of convex optimization problems. We theoretically prove that our algorithm finds the global optimal solution under certain conditions. Then, we support our theoretical results through several empirical studies

A common training technique for language models is teacher forcing (TF). TF attempts to match human language exactly, even though identical meanings can be expressed in different ways. This motivates use of sequence-level objectives for dialogue response generation. In this paper, we study the efficacy of various offline reinforcement learning (RL) methods to maximize such objectives. We present a comprehensive evaluation across multiple datasets, models, and metrics. Offline RL shows a clear performance improvement over teacher forcing while not inducing training instability or sacrificing practical training budgets.

Multivariate probabilistic time series forecasts are commonly evaluated via proper scoring rules, i.e., functions that are minimal in expectation for the ground-truth distribution. However, this property is not sufficient to guarantee good discrimination in the non-asymptotic regime. In this paper, we provide the first systematic finite-sample study of proper scoring rules for time series forecasting evaluation. Through a power analysis, we identify the ``region of reliability'' of a scoring rule, i.e., the set of practical conditions where it can be relied on to identify forecasting errors. We carry out our analysis on a comprehensive synthetic benchmark, specifically designed to test several key discrepancies between ground-truth and forecast distributions, and we gauge the generalizability of our findings to real-world tasks with an application to an electricity production problem. Our results reveal critical shortcomings in the evaluation of multivariate probabilistic forecasts as commonly performed in the literature.

We study first-order methods with preconditioning for solving structured convex optimization problems. We propose a new family of preconditioners generated by the symmetric polynomials. They provide the first-order optimization methods with a provable improvement of the condition number, cutting the gaps between highest eigenvalues, without explicit knowledge of the actual spectrum. We give a stochastic interpretation of this preconditioning in terms of the coordinate volume sampling and compare it with other classical approaches, including the Chebyshev polynomials. We show how to incorporate a polynomial preconditioning into the Gradient and Fast Gradient Methods and establish their better global complexity bounds. Finally, we propose a simple adaptive search procedure that automatically ensures the best polynomial preconditioning for the Gradient Method, minimizing the objective along a low-dimensional Krylov subspace. Numerical experiments confirm the efficiency of our preconditioning strategies for solving various machine learning problems.

The wide application of pre-trained models is driving the trend of once-for-all training in one-shot neural architecture search (NAS). However, training within a huge sample space damages the performance of individual subnets and requires much computation to search for a optimal model. In this paper, we present PreNAS, a search-free NAS approach that accentuates target models in one-shot training. Specifically, the sample space is dramatically reduced in advance by a zero-cost selector, and weight-sharing one-shot training is performed on the preferred architectures to alleviate update conflicts. Extensive experiments have demonstrated that PreNAS consistently outperforms state-of-the-art one-shot NAS competitors for both Vision Transformer and convolutional architectures, and importantly, enables instant specialization with zero search cost. Our code is available at https://github.com/tinyvision/PreNAS.

Federated Semi-supervised Learning (FedSSL) has emerged as a new paradigm for allowing distributed clients to collaboratively train a machine learning model over scarce labeled data and abundant unlabeled data. However, existing works for FedSSL rely on a closed-world assumption that all local training data and global testing data are from seen classes observed in the labeled dataset. It is crucial to go one step further: adapting FL models to an open-world setting, where unseen classes exist in the unlabeled data. In this paper, we propose a novel **Fed**erated**o**pen-world **S**emi-**S**upervised **L**earning (**FedoSSL**) framework, which can solve the key challenge in distributed and open-world settings, i.e., the biased training process for heterogeneously distributed unseen classes. Specifically, since the advent of a certain unseen class depends on a client basis, the locally unseen classes (exist in multiple clients) are likely to receive differentiated superior aggregation effects than the globally unseen classes (exist only in one client). We adopt an uncertainty-aware suppressed loss to alleviate the biased training between locally unseen and globally unseen classes. Besides, we enable a calibration module supplementary to the global aggregation to avoid potential conflicting knowledge transfer caused by inconsistent data distribution among different clients. The proposed FedoSSL can be easily adapted to state-of-the-art FL methods, which is also validated via extensive experiments on benchmarks and real-world datasets (CIFAR-10, CIFAR-100 and CINIC-10).

This paper studies the fair range clustering problem in which the data points are from different demographic groups and the goal is to pick $k$ centers with the minimum clustering cost such that each group is at least minimally represented in the centers set and no group dominates the centers set. More precisely, given a set of $n$ points in a metric space $(P, d)$ where each point belongs to one of the $\ell$ different demographics (i.e., $P = P_1 \uplus P_2 \uplus \cdots \uplus P_\ell$) and a set of $\ell$ intervals $[\alpha_1, \beta_1], \cdots, [\alpha_\ell, \beta_\ell]$ on desired number of centers from each group, the goal is to pick a set of $k$ centers $C$ with minimum $\ell_p$-clustering cost (i.e., $(\sum_{v\in P} d(v,C)^p)^{1/p}$) such that for each group $i\in \ell$, $|C\cap P_i| \in [\alpha_i, \beta_i]$. In particular, the fair range $\ell_p$-clustering captures fair range $k$-center, $k$-median and $k$-means as its special cases. In this work, we provide an efficient constant factor approximation algorithm for the fair range $\ell_p$-clustering for all values of $p\in [1,\infty)$.

We introduce a new class of spatially stochastic physics and data informed deep latent models for parametric partial differential equations (PDEs) which operate through scalable variational neural processes. We achieve this by assigning probability measures to the spatial domain, which allows us to treat collocation grids probabilistically as random variables to be marginalised out. Adapting this spatial statistics view, we solve forward and inverse problems for parametric PDEs in a way that leads to the construction of Gaussian process models of solution fields. The implementation of these random grids poses a unique set of challenges for inverse physics informed deep learning frameworks and we propose a new architecture called Grid Invariant Convolutional Networks (GICNets) to overcome these challenges. We further show how to incorporate noisy data in a principled manner into our physics informed model to improve predictions for problems where data may be available but whose measurement location does not coincide with any fixed mesh or grid. The proposed method is tested on a nonlinear Poisson problem, Burgers equation, and Navier-Stokes equations, and we provide extensive numerical comparisons. We demonstrate significant computational advantages over current physics informed neural learning methods for parametric PDEs while improving the predictive capabilities and flexibility of these models.

We propose a new method, dubbed One Class Signed Distance Function (OCSDF), to perform One Class Classification (OCC) by provably learning the Signed Distance Function (SDF) to the boundary of the support of any distribution. The distance to the support can be interpreted as a normality score, and its approximation using 1-Lipschitz neural networks provides robustness bounds against $l2$ adversarial attacks, an under-explored weakness of deep learning-based OCC algorithms. As a result, OCSDF comes with a new metric, certified AUROC, that can be computed at the same cost as any classical AUROC. We show that OCSDF is competitive against concurrent methods on tabular and image data while being way more robust to adversarial attacks, illustrating its theoretical properties. Finally, as exploratory research perspectives, we theoretically and empirically show how OCSDF connects OCC with image generation and implicit neural surface parametrization.

In many computer vision applications, images are acquired with arbitrary or random rotations and translations, and in such setups, it is desirable to obtain semantic representations disentangled from the image orientation. Examples of such applications include semiconductor wafer defect inspection, plankton microscope images, and inference on single-particle cryo-electron microscopy (cryo-EM) micro-graphs. In this work, we propose Invariant Representation Learning with Implicit Neural Representation (IRL-INR), which uses an implicit neural representation (INR) with a hypernetwork to obtain semantic representations disentangled from the orientation of the image. We show that IRL-INR can effectively learn disentangled semantic representations on more complex images compared to those considered in prior works and show that these semantic representations synergize well with SCAN to produce state-of-the-art unsupervised clustering results.

We consider fairness in dimensionality reduction. Nonlinear dimensionality reduction yields low dimensional representations that let users visualize and explore high-dimensional data. However, traditional dimensionality reduction may yield biased visualizations overemphasizing relationships of societal phenomena to sensitive attributes or protected groups. We introduce a framework of fair neighbor embedding, the Fair Neighbor Retrieval Visualizer, which formulates fair nonlinear dimensionality reduction as an information retrieval task whose performance and fairness are quantified by information retrieval criteria. The method optimizes low-dimensional embeddings that preserve high-dimensional data neighborhoods without yielding biased association of such neighborhoods to protected groups. In experiments the method yields fair visualizations outperforming previous methods.

In the presence of noisy labels, designing robust loss functions is critical for securing the generalization performance of deep neural networks. Cross Entropy (CE) loss has been shown to be not robust to noisy labels due to its unboundedness. To alleviate this issue, existing works typically design specialized robust losses with the symmetric condition, which usually lead to the underfitting issue. In this paper, our key idea is to induce a loss bound at the logit level, thus universally enhancing the noise robustness of existing losses. Specifically, we propose logit clipping (LogitClip), which clamps the norm of the logit vector to ensure that it is upper bounded by a constant. In this manner, CE loss equipped with our LogitClip method is effectively bounded, mitigating the overfitting to examples with noisy labels. Moreover, we present theoretical analyses to certify the noise-tolerant ability of LogitClip. Extensive experiments show that LogitClip not only significantly improves the noise robustness of CE loss, but also broadly enhances the generalization performance of popular robust losses.

Self-supervised learning (SSL) learns high-quality representations from large pools of unlabeled training data. As datasets grow larger, it becomes crucial to identify the examples that contribute the most to learning such representations. This enables efficient SSL by reducing the volume of data required. Nevertheless, quantifying the value of examples for SSL has remained an open question. In this work, we address this problem for the first time, by proving that examples that contribute the most to contrastive SSL are those that have the most similar augmentations to other examples, in expectation. We provide rigorous guarantees for the generalization performance of contrastive learning on such subsets. Through extensive experiments, we show that we can safely exclude 20% of examples from CIFAR100 and 40% from STL10 and TinyImageNet, without affecting downstream task performance. In general, subsets selected by our method outperform random subsets by over 3% across these datasets. Interestingly, we also discover the subsets that contribute the most to contrastive learning are those that contribute the least to supervised learning.

Recent end-to-end multi-object detectors simplify the inference pipeline by removing hand-crafted processes such as non-maximum suppression (NMS). However, during training, they still heavily rely on heuristics and hand-crafted processes which deteriorate the reliability of the predicted confidence score. In this paper, we propose a novel framework to train an end-to-end multi-object detector consisting of only two terms: negative log-likelihood (NLL) and a regularization term. In doing so, the multi-object detection problem is treated as density estimation of the ground truth bounding boxes utilizing a regularized mixture density model. The proposed end-to-end multi-object Detection with a Regularized Mixture Model (D-RMM) is trained by minimizing the NLL with the proposed regularization term, maximum component maximization (MCM) loss, preventing duplicate predictions. Our method reduces the heuristics of the training process and improves the reliability of the predicted confidence score. Moreover, our D-RMM outperforms the previous end-to-end detectors on MS COCO dataset. Code is available at https://github.com/lhj815/D-RMM.

With recent advances in natural language processing, rationalization becomes an essential self-explaining diagram to disentangle the black box by selecting a subset of input texts to account for the major variation in prediction. Yet, existing association-based approaches on rationalization cannot identify true rationales when two or more snippets are highly inter-correlated and thus provide a similar contribution to prediction accuracy, so-called spuriousness. To address this limitation, we novelly leverage two causal desiderata, non-spuriousness and efficiency, into rationalization from the causal inference perspective. We formally define a series of probabilities of causation based on a newly proposed structural causal model of rationalization, with its theoretical identification established as the main component of learning necessary and sufficient rationales. The superior performance of the proposed causal rationalization is demonstrated on real-world review and medical datasets with extensive experiments compared to state-of-the-art methods.