NeurIPS 2024 论文列表

The expensive fine-grained annotation and data scarcity have become the primary obstacles for the widespread adoption of deep learning-based Whole Slide Images (WSI) classification algorithms in clinical practice. Unlike few-shot learning methods in natural images that can leverage the labels of each image, existing few-shot WSI classification methods only utilize a small number of fine-grained labels or weakly supervised slide labels for training in order to avoid expensive fine-grained annotation. They lack sufficient mining of available WSIs, severely limiting WSI classification performance. To address the above issues, we propose a novel and efficient dual-tier few-shot learning paradigm for WSI classification, named FAST. FAST consists of a dual-level annotation strategy and a dual-branch classification framework. Firstly, to avoid expensive fine-grained annotation, we collect a very small number of WSIs at the slide level, and annotate an extremely small number of patches. Then, to fully mining the available WSIs, we use all the patches and available patch labels to build a cache branch, which utilizes the labeled patches to learn the labels of unlabeled patches and through knowledge retrieval for patch classification. In addition to the cache branch, we also construct a prior branch that includes learnable prompt vectors, using the text encoder of visual-language models for patch classification. Finally, we integrate the results from both branches to achieve WSI classification. Extensive experiments on binary and multi-class datasets demonstrate that our proposed method significantly surpasses existing few-shot classification methods and approaches the accuracy of fully supervised methods with only 0.22% annotation costs. All codes and models will be publicly available on https://github.com/fukexue/FAST.

Denoising Diffusion Probabilistic Models (DDPM) have recently gained significant attention. DDPMs compose a Markovian process that begins in the data domain and gradually adds noise until reaching pure white noise. DDPMs generate high-quality samples from complex data distributions by defining an inverse process and training a deep neural network to learn this mapping. However, these models are inefficient because they require many diffusion steps to produce aesthetically pleasing samples. Additionally, unlike generative adversarial networks (GANs), the latent space of diffusion models is less interpretable. In this work, we propose to generalize the denoising diffusion process into an Upsampling Diffusion Probabilistic Model (UDPM). In the forward process, we reduce the latent variable dimension through downsampling, followed by the traditional noise perturbation. As a result, the reverse process gradually denoises and upsamples the latent variable to produce a sample from the data distribution. We formalize the Markovian diffusion processes of UDPM and demonstrate its generation capabilities on the popular FFHQ, AFHQv2, and CIFAR10 datasets. UDPM generates images with as few as three network evaluations, whose overall computational cost is less than a single DDPM or EDM step while achieving an FID score of 6.86. This surpasses current state-of-the-art efficient diffusion models that use a single denoising step for sampling. Additionally, UDPM offers an interpretable and interpolable latent space, which gives it an advantage over traditional DDPMs. Our code is available online: \url{https://github.com/shadyabh/UDPM/}

Counterfactual explanations provide ways of achieving a favorable model outcome with minimum input perturbation. However, counterfactual explanations can also be leveraged to reconstruct the model by strategically training a surrogate model to give similar predictions as the original (target) model. In this work, we analyze how model reconstruction using counterfactuals can be improved by further leveraging the fact that the counterfactuals also lie quite close to the decision boundary. Our main contribution is to derive novel theoretical relationships between the error in model reconstruction and the number of counterfactual queries required using polytope theory. Our theoretical analysis leads us to propose a strategy for model reconstruction that we call Counterfactual Clamping Attack (CCA) which trains a surrogate model using a unique loss function that treats counterfactuals differently than ordinary instances. Our approach also alleviates the related problem of decision boundary shift that arises in existing model reconstruction approaches when counterfactuals are treated as ordinary instances. Experimental results demonstrate that our strategy improves fidelity between the target and surrogate model predictions on several datasets.

While image-to-text models have demonstrated significant advancements in various vision-language tasks, they remain susceptible to adversarial attacks. Existing white-box attacks on image-to-text models require access to the architecture, gradients, and parameters of the target model, resulting in low practicality. Although the recently proposed gray-box attacks have improved practicality, they suffer from semantic loss during the training process, which limits their targeted attack performance. To advance adversarial attacks of image-to-text models, this paper focuses on a challenging scenario: decision-based black-box targeted attacks where the attackers only have access to the final output text and aim to perform targeted attacks. Specifically, we formulate the decision-based black-box targeted attack as a large-scale optimization problem. To efficiently solve the optimization problem, a three-stage process \textit{Ask, Attend, Attack}, called \textit{AAA}, is proposed to coordinate with the solver. \textit{Ask} guides attackers to create target texts that satisfy the specific semantics. \textit{Attend} identifies the crucial regions of the image for attacking, thus reducing the search space for the subsequent \textit{Attack}. \textit{Attack} uses an evolutionary algorithm to attack the crucial regions, where the attacks are semantically related to the target texts of \textit{Ask}, thus achieving targeted attacks without semantic loss. Experimental results on transformer-based and CNN+RNN-based image-to-text models confirmed the effectiveness of our proposed \textit{AAA}.

In online learning, a decision maker repeatedly selects one of a set of actions, with the goal of minimizing the overall loss incurred. Following the recent line of research on algorithms endowed with additional predictive features, we revisit this problem by allowing the decision maker to acquire additional information on the actions to be selected. In particular, we study the power of \emph{best-action queries}, which reveal beforehand the identity of the best action at a given time step. In practice, predictive features may be expensive, so we allow the decision maker to issue at most $k$ such queries. We establish tight bounds on the performance any algorithm can achieve when given access to $k$ best-action queries for different types of feedback models. In particular, we prove that in the full feedback model, $k$ queries are enough to achieve an optimal regret of $\Theta(\min\{\sqrt T, \frac{T}{k}\})$. This finding highlights the significant multiplicative advantage in the regret rate achievable with even a modest (sublinear) number $k \in \Omega(\sqrt{T})$ of queries. Additionally, we study the challenging setting in which the only available feedback is obtained during the time steps corresponding to the $k$ best-action queries. There, we provide a tight regret rate of $\Theta(\min\{\frac{T}{\sqrt k},\frac{T^2}{k^2}\})$, which improves over the standard $\Theta(\frac{T}{\sqrt k})$ regret rate for label efficient prediction for $k \in \Omega(T^{2/3})$.

Multimodal foundation models that can holistically process text alongside images, video, audio, and other sensory modalities are increasingly used in a variety of real-world applications. However, it is challenging to characterize and study progress in multimodal foundation models, given the range of possible modeling decisions, tasks, and domains. In this paper, we introduce Holistic Evaluation of Multimodal Models (HEMM) to systematically evaluate the capabilities of multimodal foundation models across a set of 3 dimensions: basic skills, information flow, and real-world use cases. Basic multimodal skills are internal abilities required to solve problems, such as learning interactions across modalities, fine-grained alignment, multi-step reasoning, and the ability to handle external knowledge. Information flow studies how multimodal content changes during a task through querying, translation, editing, and fusion. Use cases span domain-specific challenges introduced in real-world multimedia, affective computing, natural sciences, healthcare, and human-computer interaction applications. Through comprehensive experiments across the 30 tasks in HEMM, we (1) identify key dataset dimensions (e.g., basic skills, information flows, and use cases) that pose challenges to today’s models, and (2) distill performance trends regarding how different modeling dimensions (e.g., scale, pre-training data, multimodal alignment, pre-training, and instruction tuning objectives) influence performance. Our conclusions regarding challenging multimodal interactions, use cases, and tasks requiring reasoning and external knowledge, the benefits of data and model scale, and the impacts of instruction-tuning yield actionable insights for future work in multimodal foundation models.

Latent dynamical systems have been widely used to characterize the dynamics of neural population activity in the brain. However, these models typically ignore the fact that the brain contains multiple cell types. This limits their ability to capture the functional roles of distinct cell classes, and to predict the effects of cell-specific perturbations on neural activity or behavior. To overcome these limitations, we introduce the `"cell-type dynamical systems" (CTDS) model. This model extends latent linear dynamical systems to contain distinct latent variables for each cell class, with biologically inspired constraints on both dynamics and emissions. To illustrate our approach, we consider neural recordings with distinct excitatory (E) and inhibitory (I) populations. The CTDS model defines separate latents for both cell types, and constrains the dynamics so that E (I) latents have a strictly positive (negative) effects on other latents. We applied CTDS to recordings from rat frontal orienting fields (FOF) and anterior dorsal striatum (ADS) during an auditory decision-making task. The model achieved higher accuracy than a standard linear dynamical system (LDS), and revealed that the animal's choice can be decoded from both E and I latents and thus is not restricted to a single cell-class. We also performed in-silico optogenetic perturbation experiments in the FOF and ADS, and found that CTDS was able to replicate the experimentally observed effects of different perturbations on behavior, whereas a standard LDS model---which does not differentiate between cell types---did not. Crucially, our model allowed us to understand the effects of these perturbations by revealing the dynamics of different cell-specific latents. Finally, CTDS can also be used to identify cell types for neurons whose class labels are unknown in electrophysiological recordings. These results illustrate the power of the CTDS model to provide more accurate and more biologically interpretable descriptions of neural population dynamics and their relationship to behavior.

Training on model-generated synthetic data is a promising approach for finetuning LLMs, but it remains unclear when it helps or hurts. In this paper, we investigate this question for math reasoning via an empirical study, followed by building a conceptual understanding of our observations. First, we find that while the typical approach of finetuning a model on synthetic correct or positive problem-solution pairs generated by capable models offers modest performance gains, sampling more correct solutions from the finetuned learner itself followed by subsequent fine-tuning on this self-generated data doubles the efficiency of the same synthetic problems. At the same time, training on model-generated positives can amplify various spurious correlations, resulting in flat or even inverse scaling trends as the amount of data increases. Surprisingly, we find that several of these issues can be addressed if we also utilize negative responses, i.e., model-generated responses that are deemed incorrect by a final answer verifier. Crucially, these negatives must be constructed such that the training can appropriately recover the utility or advantage of each intermediate step in the negative response. With this per-step scheme, we are able to attain consistent gains over only positive data, attaining performance similar to amplifying the amount of synthetic data by $\mathbf{8 \times}$. We show that training on per-step negatives can help to unlearn spurious correlations in the positive data, and is equivalent to advantage-weighted reinforcement learning (RL), implying that it inherits robustness benefits of RL over imitating positive data alone.

We introduce a new representation for 3D molecules based on their continuous atomic density fields. Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous space using neural fields. Our model, FuncMol, encodes molecular fields into latent codes using a conditional neural field, samples noisy codes from a Gaussian-smoothed distribution with Langevin MCMC (walk), denoises these samples in a single step (jump), and finally decodes them into molecular fields. FuncMol performs all-atom generation of 3D molecules without assumptions on the molecular structure and scales well with the size of molecules, unlike most approaches. Our method achieves competitive results on drug-like molecules and easily scales to macro-cyclic peptides, with at least one order of magnitude faster sampling. The code is available at https://github.com/prescient-design/funcmol.

Matrix factorization models have been extensively studied as a valuable test-bed for understanding the implicit biases of overparameterized models. Although both low nuclear norm and low rank regularization have been studied for these models, a unified understanding of when, how, and why they achieve different implicit regularization effects remains elusive. In this work, we systematically investigate the implicit regularization of matrix factorization for solving matrix completion problems. We empirically discover that the connectivity of observed data plays a key role in the implicit bias, with a transition from low nuclear norm to low rank as data shifts from disconnected to connected with increased observations. We identify a hierarchy of intrinsic invariant manifolds in the loss landscape that guide the training trajectory to evolve from low-rank to higher-rank solutions. Based on this finding, we theoretically characterize the training trajectory as following the hierarchical invariant manifold traversal process, generalizing the characterization of Li et al.(2020) to include the disconnected case. Furthermore, we establish conditions that guarantee minimum nuclear norm, closely aligning with our experimental findings, and we provide a dynamics characterization condition for ensuring minimum rank. Our work reveals the intricate interplay between data connectivity, training dynamics, and implicit regularization in matrix factorization models.

Exploring unknown environments efficiently is a fundamental challenge in unsupervised goal-conditioned reinforcement learning. While selecting exploratory goals at the frontier of previously explored states is an effective strategy, the policy during training may still have limited capability of reaching rare goals on the frontier, resulting in reduced exploratory behavior. We propose "Cluster Edge Exploration" (CE$^2$), a new goal-directed exploration algorithm that when choosing goals in sparsely explored areas of the state space gives priority to goal states that remain accessible to the agent. The key idea is clustering to group states that are easily reachable from one another by the current policy under training in a latent space, and traversing to states holding significant exploration potential on the boundary of these clusters before doing exploratory behavior. In challenging robotics environments including navigating a maze with a multi-legged ant robot, manipulating objects with a robot arm on a cluttered tabletop, and rotating objects in the palm of an anthropomorphic robotic hand, CE$^2$ demonstrates superior efficiency in exploration compared to baseline methods and ablations.

Irregularly Sampled Medical Time Series (ISMTS) are commonly found in the healthcare domain, where different variables exhibit unique temporal patterns while interrelated. However, many existing methods fail to efficiently consider the differences and correlations among medical variables together, leading to inadequate capture of fine-grained features at the variable level in ISMTS. We propose Knowledge-Empowered Dynamic Graph Network (KEDGN), a graph neural network empowered by variables' textual medical knowledge, aiming to model variable-specific temporal dependencies and inter-variable dependencies in ISMTS. Specifically, we leverage a pre-trained language model to extract semantic representations for each variable from their textual descriptions of medical properties, forming an overall semantic view among variables from a medical perspective. Based on this, we allocate variable-specific parameter spaces to capture variable-specific temporal patterns and generate a complete variable graph to measure medical correlations among variables. Additionally, we employ a density-aware mechanism to dynamically adjust the variable graph at different timestamps, adapting to the time-varying correlations among variables in ISMTS. The variable-specific parameter spaces and dynamic graphs are injected into the graph convolutional recurrent network to capture intra-variable and inter-variable dependencies in ISMTS together. Experiment results on four healthcare datasets demonstrate that KEDGN significantly outperforms existing methods.

Data point selection (DPS) is becoming a critical topic in deep learning due to the ease of acquiring uncurated training data compared to the difficulty of obtaining curated or processed data. Existing approaches to DPS are predominantly based on a bi-level optimisation (BLO) formulation, which is demanding in terms of memory and computation, and exhibits some theoretical defects regarding minibatches. Thus, we propose a novel Bayesian approach to DPS. We view the DPS problem as posterior inference in a novel Bayesian model where the posterior distributions of the instance-wise weights and the main neural network parameters are inferred under a reasonable prior and likelihood model. We employ stochastic gradient Langevin MCMC sampling to learn the main network and instance-wise weights jointly, ensuring convergence even with minibatches. Our update equation is comparable to the widely used SGD and much more efficient than existing BLO-based methods. Through controlled experiments in both the vision and language domains, we present the proof-of-concept. Additionally, we demonstrate that our method scales effectively to large language models and facilitates automated per-task optimization for instruction fine-tuning datasets.

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of subgraphs. While previous approaches attempted to generate smaller subsets of subgraphs through random or learnable sampling, these methods often yielded suboptimal selections or were limited to small subset sizes, ultimately compromising their effectiveness. This paper introduces a new Subgraph GNN framework to address these issues. Our approach diverges from most previous methods by associating subgraphs with node clusters rather than with individual nodes. We show that the resulting collection of subgraphs can be viewed as the product of coarsened and original graphs, unveiling a new connectivity structure on which we perform generalized message passing. Crucially, controlling the coarsening function enables meaningful selection of any number of subgraphs. In addition, we reveal novel permutation symmetries in the resulting node feature tensor, characterize associated linear equivariant layers, and integrate them into our Subgraph GNN. We also introduce novel node marking strategies and provide a theoretical analysis of their expressive power and other key aspects of our approach. Extensive experiments on multiple graph learning benchmarks demonstrate that our method is significantly more flexible than previous approaches, as it can seamlessly handle any number of subgraphs, while consistently outperforming baseline approaches. Our code is available at https://github.com/BarSGuy/Efficient-Subgraph-GNNs.

Solving constrained nonlinear programs (NLPs) is of great importance in various domains such as power systems, robotics, and wireless communication networks. One widely used approach for addressing NLPs is the interior point method (IPM). The most computationally expensive procedure in IPMs is to solve systems of linear equations via matrix factorization. Recently, machine learning techniques have been adopted to expedite classic optimization algorithms. In this work, we propose using Long Short-Term Memory (LSTM) neural networks to approximate the solution of linear systems and integrate this approximating step into an IPM. The resulting approximate NLP solution is then utilized to warm-start an interior point solver. Experiments on various types of NLPs, including Quadratic Programs and Quadratically Constrained Quadratic Programs, show that our approach can significantly accelerate NLP solving, reducing iterations by up to 60% and solution time by up to 70% compared to the default solver.

Vision-based Semantic Scene Completion (SSC) has gained much attention due to its widespread applications in various 3D perception tasks. Existing sparse-to-dense approaches typically employ shared context-independent queries across various input images, which fails to capture distinctions among them as the focal regions of different inputs vary and may result in undirected feature aggregation of cross-attention. Additionally, the absence of depth information may lead to points projected onto the image plane sharing the same 2D position or similar sampling points in the feature map, resulting in depth ambiguity. In this paper, we present a novel context and geometry aware voxel transformer. It utilizes a context aware query generator to initialize context-dependent queries tailored to individual input images, effectively capturing their unique characteristics and aggregating information within the region of interest. Furthermore, it extend deformable cross-attention from 2D to 3D pixel space, enabling the differentiation of points with similar image coordinates based on their depth coordinates. Building upon this module, we introduce a neural network named CGFormer to achieve semantic scene completion. Simultaneously, CGFormer leverages multiple 3D representations (i.e., voxel and TPV) to boost the semantic and geometric representation abilities of the transformed 3D volume from both local and global perspectives. Experimental results demonstrate that CGFormer achieves state-of-the-art performance on the SemanticKITTI and SSCBench-KITTI-360 benchmarks, attaining a mIoU of 16.87 and 20.05, as well as an IoU of 45.99 and 48.07, respectively. Remarkably, CGFormer even outperforms approaches employing temporal images as inputs or much larger image backbone networks.

Zero-shot coordination (ZSC) is a new cooperative multi-agent reinforcement learning (MARL) challenge that aims to train an ego agent to work with diverse, unseen partners during deployment. The significant difference between the deployment-time partners' distribution and the training partners' distribution determined by the training algorithm makes ZSC a unique out-of-distribution (OOD) generalization challenge. The potential distribution gap between evaluation and deployment-time partners leads to inadequate evaluation, which is exacerbated by the lack of appropriate evaluation metrics. In this paper, we present **ZSC-Eval**, the first evaluation toolkit and benchmark for ZSC algorithms. ZSC-Eval consists of: 1) Generation of evaluation partner candidates through behavior-preferring rewards to approximate deployment-time partners' distribution; 2) Selection of evaluation partners by Best-Response Diversity (BR-Div); 3) Measurement of generalization performance with various evaluation partners via the Best-Response Proximity (BR-Prox) metric. We use ZSC-Eval to benchmark ZSC algorithms in Overcooked and Google Research Football environments and get novel empirical findings. We also conduct a human experiment of current ZSC algorithms to verify the ZSC-Eval's consistency with human evaluation. ZSC-Eval is now available at https://github.com/sjtu-marl/ZSC-Eval.

This paper presents UltraEdit, a large-scale (~ 4M editing samples), automatically generated dataset for instruction-based image editing. Our key idea is to address the drawbacks in existing image editing datasets like InstructPix2Pix and MagicBrush, and provide a *systematic* approach to producing massive and high-quality image editing samples: 1) UltraEdit includes more diverse editing instructions by combining LLM creativity and in-context editing examples by human raters; 2) UltraEdit is anchored on real images (photographs or artworks), which offers more diversity and less biases than those purely synthesized by text-to-image models; 3) UltraEdit supports region-based editing with high-quality, automatically produced region annotations. Our experiments show that canonical diffusion-based editing baselines trained on UltraEdit set new records on challenging MagicBrush and Emu-Edit benchmarks, respectively. Our analysis further confirms the crucial role of real image anchors and region-based editing data. The dataset, code, and models will be made public.

Rigorous software testing is crucial for developing and maintaining high-quality code, making automated test generation a promising avenue for both improving software quality and boosting the effectiveness of code generation methods. However, while code generation with Large Language Models (LLMs) is an extraordinarily active research area, test generation remains relatively unexplored. We address this gap and investigate the capability of LLM-based Code Agents to formalize user issues into test cases. To this end, we propose a novel benchmark based on popular GitHub repositories, containing real-world issues, ground-truth bug-fixes, and golden tests. We find that LLMs generally perform surprisingly well at generating relevant test cases, with Code Agents designed for code repair exceeding the performance of systems designed specifically for test generation. Further, as test generation is a similar but more structured task than code generation, it allows for a more fine-grained analysis using issue reproduction rate and coverage changes, providing a dual metric for analyzing systems designed for code repair. Finally, we find that generated tests are an effective filter for proposed code fixes, doubling the precision of SWE-Agent. We release all data and code at https://github.com/logic-star-ai/SWT-Bench.