NeurIPS 2023 论文列表

Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.

Nanophotonic structures have versatile applications including solar cells, anti-reflective coatings, electromagnetic interference shielding, optical filters, and light emitting diodes. To design and understand these nanophotonic structures, electrodynamic simulations are essential. These simulations enable us to model electromagnetic fields over time and calculate optical properties. In this work, we introduce frameworks and benchmarks to evaluate nanophotonic structures in the context of parametric structure design problems. The benchmarks are instrumental in assessing the performance of optimization algorithms and identifying an optimal structure based on target optical properties. Moreover, we explore the impact of varying grid sizes in electrodynamic simulations, shedding light on how evaluation fidelity can be strategically leveraged in enhancing structure designs.

Dataset distillation (DD) aims to synthesize a small dataset whose test performance is comparable to a full dataset using the same model. State-of-the-art (SoTA) methods optimize synthetic datasets primarily by matching heuristic indicators extracted from two networks: one from real data and one from synthetic data (see Fig.1, Left), such as gradients and training trajectories. DD is essentially a compression problem that emphasizes on maximizing the preservation of information contained in the data. We argue that well-defined metrics which measure the amount of shared information between variables in information theory are necessary for success measurement, but are never considered by previous works. Thus, we introduce mutual information (MI) as the metric to quantify the shared information between the synthetic and the real datasets, and devise MIM4DD numerically maximizing the MI via a newly designed optimizable objective within a contrastive learning framework to update the synthetic dataset. Specifically, we designate the samples in different datasets who share the same labels as positive pairs, and vice versa negative pairs. Then we respectively pull and push those samples in positive and negative pairs into contrastive space via minimizing NCE loss. As a result, the targeted MI can be transformed into a lower bound represented by feature maps of samples, which is numerically feasible. Experiment results show that MIM4DD can be implemented as an add-on module to existing SoTA DD methods.

The accurate predictions and principled uncertainty measures provided by GP regression incur $O(n^3)$ cost which is prohibitive for modern-day large-scale applications. This has motivated extensive work on computationally efficient approximations. We introduce a new perspective by exploring robustness properties and limiting behaviour of GP nearest-neighbour (GPnn) prediction. We demonstrate through theory and simulation that as the data-size $n$ increases, accuracy of estimated parameters and GP model assumptions become increasingly irrelevant to GPnn predictive accuracy. Consequently, it is sufficient to spend small amounts of work on parameter estimation in order to achieve high MSE accuracy, even in the presence of gross misspecification. In contrast, as $n \rightarrow \infty$, uncertainty calibration and NLL are shown to remain sensitive to just one parameter, the additive noise-variance; but we show that this source of inaccuracy can be corrected for, thereby achieving both well-calibrated uncertainty measures and accurate predictions at remarkably low computational cost. We exhibit a very simple GPnn regression algorithm with stand-out performance compared to other state-of-the-art GP approximations as measured on large UCI datasets. It operates at a small fraction of those other methods' training costs, for example on a basic laptop taking about 30 seconds to train on a dataset of size $n = 1.6 \times 10^6$.

The development of foundation vision models has pushed the general visual recognition to a high level, but cannot well address the fine-grained recognition in specialized domain such as invasive species classification. Identifying and managing invasive species has strong social and ecological value. Currently, most invasive species datasets are limited in scale and cover a narrow range of species, which restricts the development of deep-learning based invasion biometrics systems. To fill the gap of this area, we introduced Species196, a large-scale semi-supervised dataset of 196-category invasive species. It collects over 19K images with expert-level accurate annotations (Species196-L), and 1.2M unlabeled images of invasive species (Species196-U). The dataset provides four experimental settings for benchmarking the existing models and algorithms, namely, supervised learning, semi-supervised learning and self-supervised pretraining. To facilitate future research on these four learning paradigms, we conduct an empirical study of the representative methods on the introduced dataset. The dataset will be made publicly available at https://species-dataset.github.io/.

Humans outperform object recognizers despite the fact that models perform well on current datasets, including those explicitly designed to challenge machines with debiased images or distribution shift. This problem persists, in part, because we have no guidance on the absolute difficulty of an image or dataset making it hard to objectively assess progress toward human-level performance, to cover the range of human abilities, and to increase the challenge posed by a dataset. We develop a dataset difficulty metric MVT, Minimum Viewing Time, that addresses these three problems. Subjects view an image that flashes on screen and then classify the object in the image. Images that require brief flashes to recognize are easy, those which require seconds of viewing are hard. We compute the ImageNet and ObjectNet image difficulty distribution, which we find significantly undersamples hard images. Nearly 90% of current benchmark performance is derived from images that are easy for humans. Rather than hoping that we will make harder datasets, we can for the first time objectively guide dataset difficulty during development. We can also subset recognition performance as a function of difficulty: model performance drops precipitously while human performance remains stable. Difficulty provides a new lens through which to view model performance, one which uncovers new scaling laws: vision-language models stand out as being the most robust and human-like while all other techniques scale poorly. We release tools to automatically compute MVT, along with image sets which are tagged by difficulty. Objective image difficulty has practical applications – one can measure how hard a test set is before deploying a real-world system – and scientific applications such as discovering the neural correlates of image difficulty and enabling new object recognition techniques that eliminate the benchmark-vs- real-world performance gap.

Noisy marginals are a common form of confidentiality-protecting data release and are useful for many downstream tasks such as contingency table analysis, construction of Bayesian networks, and even synthetic data generation. Privacy mechanisms that provide unbiased noisy answers to linear queries (such as marginals) are known as matrix mechanisms. We propose ResidualPlanner, a matrix mechanism for marginals with Gaussian noise that is both optimal and scalable. ResidualPlanner can optimize for many loss functions that can be written as a convex function of marginal variances (prior work was restricted to just one predefined objective function). ResidualPlanner can optimize the accuracy of marginals in large scale settings in seconds, even when the previous state of the art (HDMM) runs out of memory. It even runs on datasets with 100 attributes in a couple of minutes. Furthermore ResidualPlanner can efficiently compute variance/covariance values for each marginal (prior methods quickly run out of memory, even for relatively small datasets).

Spectral clustering is a popular and effective algorithm designed to find $k$ clusters in a graph $G$. In the classical spectral clustering algorithm, the vertices of $G$ are embedded into $\mathbb{R}^k$ using $k$ eigenvectors of the graph Laplacian matrix. However, computing this embedding is computationally expensive and dominates the running time of the algorithm. In this paper, we present a simple spectral clustering algorithm based on a vertex embedding with $O(\log(k))$ vectors computed by the power method. The vertex embedding is computed in nearly-linear time with respect to the size of the graph, and the algorithm provably recovers the ground truth clusters under natural assumptions on the input graph. We evaluate the new algorithm on several synthetic and real-world datasets, finding that it is significantly faster than alternative clustering algorithms, while producing results with approximately the same clustering accuracy.

The prosperity of deep neural networks (DNNs) is largely benefited from open-source datasets, based on which users can evaluate and improve their methods. In this paper, we revisit backdoor-based dataset ownership verification (DOV), which is currently the only feasible approach to protect the copyright of open-source datasets. We reveal that these methods are fundamentally harmful given that they could introduce malicious misclassification behaviors to watermarked DNNs by the adversaries. In this paper, we design DOV from another perspective by making watermarked models (trained on the protected dataset) correctly classify some `hard' samples that will be misclassified by the benign model. Our method is inspired by the generalization property of DNNs, where we find a \emph{hardly-generalized domain} for the original dataset (as its \emph{domain watermark}). It can be easily learned with the protected dataset containing modified samples. Specifically, we formulate the domain generation as a bi-level optimization and propose to optimize a set of visually-indistinguishable clean-label modified data with similar effects to domain-watermarked samples from the hardly-generalized domain to ensure watermark stealthiness. We also design a hypothesis-test-guided ownership verification via our domain watermark and provide the theoretical analyses of our method. Extensive experiments on three benchmark datasets are conducted, which verify the effectiveness of our method and its resistance to potential adaptive methods.

Different distribution shifts require different algorithmic and operational interventions. Methodological research must be grounded by the specific shifts they address. Although nascent benchmarks provide a promising empirical foundation, they \emph{implicitly} focus on covariate shifts, and the validity of empirical findings depends on the type of shift, e.g., previous observations on algorithmic performance can fail to be valid when the $Y|X$ distribution changes. We conduct a thorough investigation of natural shifts in 5 tabular datasets over 86,000 model configurations, and find that $Y|X$-shifts are most prevalent. To encourage researchers to develop a refined language for distribution shifts, we build ``WhyShift``, an empirical testbed of curated real-world shifts where we characterize the type of shift we benchmark performance over. Since $Y|X$-shifts are prevalent in tabular settings, we \emph{identify covariate regions} that suffer the biggest $Y|X$-shifts and discuss implications for algorithmic and data-based interventions. Our testbed highlights the importance of future research that builds an understanding of why distributions differ.

HTTP/3 is a new application layer protocol supported by most browsers. It uses QUIC as an underlying transport protocol. QUIC provides multiple benefits, like faster connection establishment, reduced latency, and improved connection migration. Hence, most popular browsers like Chrome/Chromium, Microsoft Edge, Apple Safari, and Mozilla Firefox have started supporting it. In this paper, we present an HTTP/3-supported browser dataset collection tool named H3B. It collects the application and network-level logs during YouTube streaming. We consider YouTube, as it the most popular video streaming application supporting QUIC. Using this tool, we collected a dataset of over 5936 YouTube sessions covering 5464 hours of streaming over 5 different geographical locations and 5 different bandwidth patterns. We believe our tool and as well as the dataset could be used in multiple applications such as a better configuration of application/transport protocols based on the network conditions, intelligent integration of network and application, predicting YouTube's QoE etc. We analyze the dataset and observe that during an HTTP/3 streaming not all requests are served by HTTP/3. Instead whenever the network condition is not favorable the browser chooses to fallback, and the application requests are transmitted using HTTP/2 over the old-standing transport protocol TCP. We observe that such switching of protocols impacts the performance of video streaming applications.

Accurately depicting the complex traffic scene is a vital component for autonomous vehicles to execute correct judgments. However, existing benchmarks tend to oversimplify the scene by solely focusing on lane perception tasks. Observing that human drivers rely on both lanes and traffic signals to operate their vehicles safely, we present OpenLane-V2, the first dataset on topology reasoning for traffic scene structure. The objective of the presented dataset is to advance research in understanding the structure of road scenes by examining the relationship between perceived entities, such as traffic elements and lanes. Leveraging existing datasets, OpenLane-V2 consists of 2,000 annotated road scenes that describe traffic elements and their correlation to the lanes. It comprises three primary sub-tasks, including the 3D lane detection inherited from OpenLane, accompanied by corresponding metrics to evaluate the model’s performance. We evaluate various state-of-the-art methods, and present their quantitative and qualitative results on OpenLane-V2 to indicate future avenues for investigating topology reasoning in traffic scenes.

This paper presents FreD, a novel parameterization method for dataset distillation, which utilizes the frequency domain to distill a small-sized synthetic dataset from a large-sized original dataset. Unlike conventional approaches that focus on the spatial domain, FreD employs frequency-based transforms to optimize the frequency representations of each data instance. By leveraging the concentration of spatial domain information on specific frequency components, FreD intelligently selects a subset of frequency dimensions for optimization, leading to a significant reduction in the required budget for synthesizing an instance. Through the selection of frequency dimensions based on the explained variance, FreD demonstrates both theoretical and empirical evidence of its ability to operate efficiently within a limited budget, while better preserving the information of the original dataset compared to conventional parameterization methods. Furthermore, Based on the orthogonal compatibility of FreD with existing methods, we confirm that FreD consistently improves the performances of existing distillation methods over the evaluation scenarios with different benchmark datasets. We release the code at https://github.com/sdh0818/FreD.

The strategy of ensemble has become popular in adversarial defense, which trains multiple base classifiers to defend against adversarial attacks in a cooperative manner. Despite the empirical success, theoretical explanations on why an ensemble of adversarially trained classifiers is more robust than single ones remain unclear. To fill in this gap, we develop a new error theory dedicated to understanding ensemble adversarial defense, demonstrating a provable 0-1 loss reduction on challenging sample sets in adversarial defense scenarios. Guided by this theory, we propose an effective approach to improve ensemble adversarial defense, named interactive global adversarial training (iGAT). The proposal includes (1) a probabilistic distributing rule that selectively allocates to different base classifiers adversarial examples that are globally challenging to the ensemble, and (2) a regularization term to rescue the severest weaknesses of the base classifiers. Being tested over various existing ensemble adversarial defense techniques, iGAT is capable of boosting their performance by up to 17\% evaluated using CIFAR10 and CIFAR100 datasets under both white-box and black-box attacks.

Knowledge tracing (KT) is a task that predicts students' future performance based on their historical learning interactions. With the rapid development of deep learning techniques, existing KT approaches follow a data-driven paradigm that uses massive problem-solving records to model students' learning processes. However, although the educational contexts contain various factors that may have an influence on student learning outcomes, existing public KT datasets mainly consist of anonymized ID-like features, which may hinder the research advances towards this field. Therefore, in this work, we present, \emph{XES3G5M}, a large-scale dataset with rich auxiliary information about questions and their associated knowledge components (KCs)\footnote{\label{ft:kc}A KC is a generalization of everyday terms like concept, principle, fact, or skill.}. The XES3G5M dataset is collected from a real-world online math learning platform, which contains 7,652 questions, and 865 KCs with 5,549,635 interactions from 18,066 students. To the best of our knowledge, the XES3G5M dataset not only has the largest number of KCs in math domain but contains the richest contextual information including tree structured KC relations, question types, textual contents and analysis and student response timestamps. Furthermore, we build a comprehensive benchmark on 19 state-of-the-art deep learning based knowledge tracing (DLKT) models. Extensive experiments demonstrate the effectiveness of leveraging the auxiliary information in our XES3G5M with DLKT models. We hope the proposed dataset can effectively facilitate the KT research work.

Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits. We delve deeply into the dataset generation search space by crafting 35 datasets that encompass static and dynamic brain connectivity, running in excess of 15 baseline methods for benchmarking. Additionally, we provide generic frameworks for learning on both static and dynamic graphs. Our extensive experiments lead to several key observations. Notably, using correlation vectors as node features, incorporating larger number of regions of interest, and employing sparser graphs lead to improved performance. To foster further advancements in graph-based data driven neuroimaging analysis, we offer a comprehensive open-source Python package that includes the benchmark datasets, baseline implementations, model training, and standard evaluation.

Fairness and robustness are two important goals in the design of modern distributed learning systems. Despite a few prior works attempting to achieve both fairness and robustness, some key aspects of this direction remain underexplored. In this paper, we try to answer three largely unnoticed and unaddressed questions that are of paramount significance to this topic: (i) What makes jointly satisfying fairness and robustness difficult? (ii) Is it possible to establish theoretical guarantee for the dual property of fairness and robustness? (iii) How much does fairness have to sacrifice at the expense of robustness being incorporated into the system? To address these questions, we first identify data heterogeneity as the key difficulty of combining fairness and robustness. Accordingly, we propose a fair and robust framework called H-nobs which can offer certified fairness and robustness through the adoption of two key components, a fairness-promoting objective function and a simple robust aggregation scheme called norm-based screening (NBS). We explain in detail why NBS is the suitable scheme in our algorithm in contrast to other robust aggregation measures. In addition, we derive three convergence theorems for H-nobs in cases of the learning model being nonconvex, convex, and strongly convex respectively, which provide theoretical guarantees for both fairness and robustness. Further, we empirically investigate the influence of the robust mechanism (NBS) on the fairness performance of H-nobs, the very first attempt of such exploration.

Machine learning research has long focused on models rather than datasets, and prominent datasets are used for common ML tasks without regard to the breadth, difficulty, and faithfulness of the underlying problems. Neglecting the fundamental importance of data has given rise to inaccuracy, bias, and fragility in real-world applications, and research is hindered by saturation across existing dataset benchmarks. In response, we present DataPerf, a community-led benchmark suite for evaluating ML datasets and data-centric algorithms. We aim to foster innovation in data-centric AI through competition, comparability, and reproducibility. We enable the ML community to iterate on datasets, instead of just architectures, and we provide an open, online platform with multiple rounds of challenges to support this iterative development. The first iteration of DataPerf contains five benchmarks covering a wide spectrum of data-centric techniques, tasks, and modalities in vision, speech, acquisition, debugging, and diffusion prompting, and we support hosting new contributed benchmarks from the community. The benchmarks, online evaluation platform, and baseline implementations are open source, and the MLCommons Association will maintain DataPerf to ensure long-term benefits to academia and industry.

Understanding different human attributes and how they affect model behavior may become a standard need for all model creation and usage, from traditional computer vision tasks to the newest multimodal generative AI systems. In computer vision specifically, we have relied on datasets augmented with perceived attribute signals (eg, gender presentation, skin tone, and age) and benchmarks enabled by these datasets. Typically labels for these tasks come from human annotators. However, annotating attribute signals, especially skin tone, is a difficult and subjective task. Perceived skin tone is affected by technical factors, like lighting conditions, and social factors that shape an annotator's lived experience. This paper examines the subjectivity of skin tone annotation through a series of annotation experiments using the Monk Skin Tone (MST) scale, a small pool of professional photographers, and a much larger pool of trained crowdsourced annotators. Along with this study we release the Monk Skin Tone Examples (MST-E) dataset, containing 1515 images and 31 videos spread across the full MST scale. MST-E is designed to help train human annotators to annotate MST effectively.Our study shows that annotators can reliably annotate skin tone in a way that aligns with an expert in the MST scale, even under challenging environmental conditions. We also find evidence that annotators from different geographic regions rely on different mental models of MST categories resulting in annotations that systematically vary across regions. Given this, we advise practitioners to use a diverse set of annotators and a higher replication count for each image when annotating skin tone for fairness research.