NeurIPS 2023 论文列表

The design of \emph{de novo} functional proteins that bind with specific ligand molecules is crucial in various domains like therapeutics and bio-engineering. One vital yet challenging step is to design the protein pocket, the cavity region of protein where the ligand binds with. Existing methods suffer from inefficient generation, insufficient context modeling (ligand molecule), and incapability of generating sidechain atoms. To overcome the limitations, we propose a \textbf{F}ull-\textbf{A}tom \textbf{I}terative \textbf{R}efinement framework (\textbf{FAIR}) for protein pocket sequence (i.e., residue types) and 3D structure co-design. Generally, FAIR consists of two steps that follow a coarse-to-fine pipeline (backbone atoms to full atoms including sidechain) for full-atom generation. For efficiency, all residue types and structures are updated together in each round (i.e., full-shot refinement). In the first step, the residue types and backbone coordinates are updated with a hierarchical context encoder and two structure refinement modules capturing inter-residue and pocket-ligand interactions. The second step further models the sidechain atoms of pockets and updates residue types to achieve sequence-structure consistency. The structure of the binding ligand is also updated along with the above refinement iterations accounting for its flexibility. Finally, extensive evaluations show that FAIR outperforms baselines in efficiently designing high-quality pocket sequences and structures. Specifically, the average improvements on AAR and RMSD are over 10$\%$.

Deep regression models typically learn in an end-to-end fashion without explicitly emphasizing a regression-aware representation. Consequently, the learned representations exhibit fragmentation and fail to capture the continuous nature of sample orders, inducing suboptimal results across a wide range of regression tasks. To fill the gap, we propose Rank-N-Contrast (RNC), a framework that learns continuous representations for regression by contrasting samples against each other based on their rankings in the target space. We demonstrate, theoretically and empirically, that RNC guarantees the desired order of learned representations in accordance with the target orders, enjoying not only better performance but also significantly improved robustness, efficiency, and generalization. Extensive experiments using five real-world regression datasets that span computer vision, human-computer interaction, and healthcare verify that RNC achieves state-of-the-art performance, highlighting its intriguing properties including better data efficiency, robustness to spurious targets and data corruptions, and generalization to distribution shifts.

Selective classification allows a machine learning model to reject some hard inputs and thus improve the reliability of its predictions. In this area, the ensemble method is powerful in practice, but there has been no solid analysis on why the ensemble method works. Inspired by an interesting empirical result that the improvement of the ensemble largely comes from top-ambiguity samples where its member models diverge, we prove that, based on some assumptions, the ensemble has a lower selective risk than the member model for any coverage within a range. The proof is nontrivial since the selective risk is a non-convex function of the model prediction. The assumptions and the theoretical results are supported by systematic experiments on both computer vision and natural language processing tasks.

The use of non-Cartesian grids is a niche but important topic in sub-fields of the numerical sciences such as simulation and scientific visualization. However, non-Cartesian approaches are virtually unexplored in machine learning. This is likely due to the difficulties in the representation of data on non-Cartesian domains and the lack of support for standard machine learning operations on non-Cartesian data. This paper proposes a new data structure called the lattice tensor which generalizes traditional tensor spatio-temporal operations to lattice tensors, enabling the use of standard machine learning algorithms on non-Cartesian data. However, data need not reside on a non-Cartesian structure, we use non-Dyadic downsampling schemes to bring Cartesian data into a non-Cartesian space for further processing. We introduce a software library that implements the lattice tensor container (with some common machine learning operations), and demonstrate its effectiveness. Our method provides a general framework for machine learning on non-Cartesian domains, addressing the challenges mentioned above and filling a gap in the current literature.

Engineering design problems frequently require solving systems of partial differential equations with boundary conditions specified on object geometries in the form of a triangular mesh. These boundary geometries are provided by a designer and are problem dependent. The efficiency of the design process greatly benefits from fast turnaround times when repeatedly solving PDEs on various geometries. However, most current work that uses machine learning to speed up the solution process relies heavily on a fixed parameterization of the geometry, which cannot be changed after training. This severely limits the possibility of reusing a trained model across a variety of design problems. In this work, we propose a novel neural operator architecture which accepts boundary geometry, in the form of triangular meshes, as input and produces an approximate solution to a given PDE as output. Once trained, the model can be used to rapidly estimate the PDE solution over a new geometry, without the need for retraining or representation of the geometry to a pre-specified parameterization.

Generative data augmentation, which scales datasets by obtaining fake labeled examples from a trained conditional generative model, boosts classification performance in various learning tasks including (semi-)supervised learning, few-shot learning, and adversarially robust learning. However, little work has theoretically investigated the effect of generative data augmentation. To fill this gap, we establish a general stability bound in this not independently and identically distributed (non-i.i.d.) setting, where the learned distribution is dependent on the original train set and generally not the same as the true distribution. Our theoretical result includes the divergence between the learned distribution and the true distribution. It shows that generative data augmentation can enjoy a faster learning rate when the order of divergence term is $o(\max\left( \log(m)\beta_m, 1 / \sqrt{m})\right)$, where $m$ is the train set size and $\beta_m$ is the corresponding stability constant. We further specify the learning setup to the Gaussian mixture model and generative adversarial nets. We prove that in both cases, though generative data augmentation does not enjoy a faster learning rate, it can improve the learning guarantees at a constant level when the train set is small, which is significant when the awful overfitting occurs. Simulation results on the Gaussian mixture model and empirical results on generative adversarial nets support our theoretical conclusions.

This paper presents \textit{PolyDiffuse}, a novel structured reconstruction algorithm that transforms visual sensor data into polygonal shapes with Diffusion Models (DM), an emerging machinery amid exploding generative AI, while formulating reconstruction as a generation process conditioned on sensor data. The task of structured reconstruction poses two fundamental challenges to DM: 1) A structured geometry is a ''set'' (e.g., a set of polygons for a floorplan geometry), where a sample of $N$ elements has $N!$ different but equivalent representations, making the denoising highly ambiguous; and 2) A ''reconstruction'' task has a single solution, where an initial noise needs to be chosen carefully, while any initial noise works for a generation task. Our technical contribution is the introduction of a Guided Set Diffusion Model where 1) the forward diffusion process learns \textit{guidance networks} to control noise injection so that one representation of a sample remains distinct from its other permutation variants, thus resolving denoising ambiguity; and 2) the reverse denoising process reconstructs polygonal shapes, initialized and directed by the guidance networks, as a conditional generation process subject to the sensor data. We have evaluated our approach for reconstructing two types of polygonal shapes: floorplan as a set of polygons and HD map for autonomous cars as a set of polylines. Through extensive experiments on standard benchmarks, we demonstrate that PolyDiffuse significantly advances the current state of the art and enables broader practical applications. The code and data are available on our project page: https://poly-diffuse.github.io.

It is essential for users to understand what their AI systems can and can't do in order to use them safely. However, the problem of enabling users to assess AI systems with sequential decision-making (SDM) capabilities is relatively understudied. This paper presents a new approach for modeling the capabilities of black-box AI systems that can plan and act, along with the possible effects and requirements for executing those capabilities in stochastic settings. We present an active-learning approach that can effectively interact with a black-box SDM system and learn an interpretable probabilistic model describing its capabilities. Theoretical analysis of the approach identifies the conditions under which the learning process is guaranteed to converge to the correct model of the agent; empirical evaluations on different agents and simulated scenarios show that this approach is few-shot generalizable and can effectively describe the capabilities of arbitrary black-box SDM agents in a sample-efficient manner.

Real-time perception requires planned resource utilization. Computational planning in real-time perception is governed by two considerations -- accuracy and latency. There exist run-time decisions (e.g. choice of input resolution) that induce tradeoffs affecting performance on a given hardware, arising from intrinsic (content, e.g. scene clutter) and extrinsic (system, e.g. resource contention) characteristics. Earlier runtime execution frameworks employed rule-based decision algorithms and operated with a fixed algorithm latency budget to balance these concerns, which is sub-optimal and inflexible. We propose Chanakya, a learned approximate execution framework that naturally derives from the streaming perception paradigm, to automatically learn decisions induced by these tradeoffs instead. Chanakya is trained via novel rewards balancing accuracy and latency implicitly, without approximating either objectives. Chanakya simultaneously considers intrinsic and extrinsic context, and predicts decisions in a flexible manner. Chanakya, designed with low overhead in mind, outperforms state-of-the-art static and dynamic execution policies on public datasets on both server GPUs and edge devices.

Fine-tuning language models (LMs) has yielded success on diverse downstream tasks, but as LMs grow in size, backpropagation requires a prohibitively large amount of memory. Zeroth-order (ZO) methods can in principle estimate gradients using only two forward passes but are theorized to be catastrophically slow for optimizing large models. In this work, we propose a memory-efficient zerothorder optimizer (MeZO), adapting the classical ZO-SGD method to operate in-place, thereby fine-tuning LMs with the same memory footprint as inference. For example, with a single A100 80GB GPU, MeZO can train a 30-billion parameter model, whereas fine-tuning with backpropagation can train only a 2.7B LM with the same budget. We conduct comprehensive experiments across model types (masked and autoregressive LMs), model scales (up to 66B), and downstream tasks (classification, multiple-choice, and generation). Our results demonstrate that (1) MeZO significantly outperforms in-context learning and linear probing; (2) MeZO achieves comparable performance to fine-tuning with backpropagation across multiple tasks, with up to 12× memory reduction and up to 2× GPU-hour reduction in our implementation; (3) MeZO is compatible with both full-parameter and parameter-efficient tuning techniques such as LoRA and prefix tuning; (4) MeZO can effectively optimize non-differentiable objectives (e.g., maximizing accuracy or F1). We support our empirical findings with theoretical insights, highlighting how adequate pre-training and task prompts enable MeZO to fine-tune huge models, despite classical ZO analyses suggesting otherwise.

Diffusion models have been shown to be capable of generating high-quality images, suggesting that they could contain meaningful internal representations. Unfortunately, the feature maps that encode a diffusion model's internal information are spread not only over layers of the network, but also over diffusion timesteps, making it challenging to extract useful descriptors. We propose Diffusion Hyperfeatures, a framework for consolidating multi-scale and multi-timestep feature maps into per-pixel feature descriptors that can be used for downstream tasks. These descriptors can be extracted for both synthetic and real images using the generation and inversion processes. We evaluate the utility of our Diffusion Hyperfeatures on the task of semantic keypoint correspondence: our method achieves superior performance on the SPair-71k real image benchmark. We also demonstrate that our method is flexible and transferable: our feature aggregation network trained on the inversion features of real image pairs can be used on the generation features of synthetic image pairs with unseen objects and compositions. Our code is available at https://diffusion-hyperfeatures.github.io.

Reinforcement learning algorithms typically consider discrete-time dynamics, even though the underlying systems are often continuous in time. In this paper, we introduce a model-based reinforcement learning algorithm that represents continuous-time dynamics using nonlinear ordinary differential equations (ODEs). We capture epistemic uncertainty using well-calibrated probabilistic models, and use the optimistic principle for exploration. Our regret bounds surface the importance of the measurement selection strategy (MSS), since in continuous time we not only must decide how to explore, but also when to observe the underlying system. Our analysis demonstrates that the regret is sublinear when modeling ODEs with Gaussian Processes (GP) for common choices of MSS, such as equidistant sampling. Additionally, we propose an adaptive, data-dependent, practical MSS that, when combined with GP dynamics, also achieves sublinear regret with significantly fewer samples. We showcase the benefits of continuous-time modeling over its discrete-time counterpart, as well as our proposed adaptive MSS over standard baselines, on several applications.

We extend metric learning by studying the Riemannian manifold structure of the underlying data space induced by similarity measures between data points. The key quantity of interest here is the Riemannian metric, which characterizes the Riemannian geometry and defines straight lines and derivatives on the manifold. Being able to estimate the Riemannian metric allows us to gain insights into the underlying manifold and compute geometric features such as the geodesic curves. We model the observed similarity measures as noisy responses generated from a function of the intrinsic geodesic distance between data points. A new local regression approach is proposed to learn the Riemannian metric tensor and its derivatives based on a Taylor expansion for the squared geodesic distances, accommodating different types of data such as continuous, binary, or comparative responses. We develop theoretical foundation for our method by deriving the rates of convergence for the asymptotic bias and variance of the estimated metric tensor. The proposed method is shown to be versatile in simulation studies and real data applications involving taxi trip time in New York City and MNIST digits.

This paper studies the problem of learning the large-scale Gaussian graphical models that are multivariate totally positive of order two ($\text{MTP}_2$). By introducing the concept of bridge, which commonly exists in large-scale sparse graphs, we show that the entire problem can be equivalently optimized through (1) several smaller-scaled sub-problems induced by a \emph{bridge-block decomposition} on the thresholded sample covariance graph and (2) a set of explicit solutions on entries corresponding to \emph{bridges}. From practical aspect, this simple and provable discipline can be applied to break down a large problem into small tractable ones, leading to enormous reduction on the computational complexity and substantial improvements for all existing algorithms. The synthetic and real-world experiments demonstrate that our proposed method presents a significant speed-up compared to the state-of-the-art benchmarks.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

The strength of modern generative models lies in their ability to be controlled through prompts. Hard prompts comprise interpretable words and tokens, and are typically hand-crafted by humans. Soft prompts, on the other hand, consist of continuous feature vectors. These can be discovered using powerful optimization methods, but they cannot be easily edited, re-used across models, or plugged into a text-based interface. We describe an easy-to-use approach to automatically optimize hard text prompts through efficient gradient-based optimization. Our approach can be readily applied to text-to-image and text-only applications alike. This method allows API users to easily generate, discover, and mix and match image concepts without prior knowledge of how to prompt the model. Furthermore, using our method, we can bypass token-level content filters imposed by Midjourney by optimizing through the open-sourced text encoder.

When machine learning is outsourced to a rational agent, conflicts of interest might arise and severely impact predictive performance. In this work, we propose a theoretical framework for incentive-aware delegation of machine learning tasks. We model delegation as a principal-agent game, in which accurate learning can be incentivized by the principal using performance-based contracts. Adapting the economic theory of contract design to this setting, we define budget-optimal contracts and prove they take a simple threshold form under reasonable assumptions. In the binary-action case, the optimality of such contracts is shown to be equivalent to the classic Neyman-Pearson lemma, establishing a formal connection between contract design and statistical hypothesis testing. Empirically, we demonstrate that budget-optimal contracts can be constructed using small-scale data, leveraging recent advances in the study of learning curves and scaling laws. Performance and economic outcomes are evaluated using synthetic and real-world classification tasks.

Recent studies have demonstrated the susceptibility of deep neural networks to backdoor attacks. Given a backdoored model, its prediction of a poisoned sample with trigger will be dominated by the trigger information, though trigger information and benign information coexist. Inspired by the mechanism of the optical polarizer that a polarizer could pass light waves with particular polarizations while filtering light waves with other polarizations, we propose a novel backdoor defense method by inserting a learnable neural polarizer into the backdoored model as an intermediate layer, in order to purify the poisoned sample via filtering trigger information while maintaining benign information. The neural polarizer is instantiated as one lightweight linear transformation layer, which is learned through solving a well designed bi-level optimization problem, based on a limited clean dataset. Compared to other fine-tuning-based defense methods which often adjust all parameters of the backdoored model, the proposed method only needs to learn one additional layer, such that it is more efficient and requires less clean data. Extensive experiments demonstrate the effectiveness and efficiency of our method in removing backdoors across various neural network architectures and datasets, especially in the case of very limited clean data. Codes are available at \href{https://github.com/SCLBD/BackdoorBench}{https://github.com/SCLBD/BackdoorBench} (PyTorch) and \href{https://github.com/JulieCarlon/NPD-MindSpore}{https://github.com/JulieCarlon/NPD-MindSpore} (MindSpore).

A potent class of generative models known as Diffusion Probabilistic Models (DPMs) has become prominent. A forward diffusion process adds gradually noise to data, while a model learns to gradually denoise. Sampling from pre-trained DPMs is obtained by solving differential equations (DE) defined by the learnt model, a process which has shown to be prohibitively slow. Numerous efforts on speeding-up this process have consisted on crafting powerful ODE solvers. Despite being quick, such solvers do not usually reach the optimal quality achieved by available slow SDE solvers. Our goal is to propose SDE solvers that reach optimal quality without requiring several hundreds or thousands of NFEs to achieve that goal. We propose Stochastic Explicit Exponential Derivative-free Solvers (SEEDS), improving and generalizing Exponential Integrator approaches to the stochastic case on several frameworks. After carefully analyzing the formulation of exact solutions of diffusion SDEs, we craft SEEDS to analytically compute the linear part of such solutions. Inspired by the Exponential Time-Differencing method, SEEDS use a novel treatment of the stochastic components of solutions, enabling the analytical computation of their variance, and contains high-order terms allowing to reach optimal quality sampling $\sim3$-$5\times$ faster than previous SDE methods. We validate our approach on several image generation benchmarks, showing that SEEDS outperform or are competitive with previous SDE solvers. Contrary to the latter, SEEDS are derivative and training free, and we fully prove strong convergence guarantees for them.