NeurIPS 2023 Papers

The structure of protein-protein complexes is critical for understanding binding dynamics, biological mechanisms, and intervention strategies. Rigid protein docking, a fundamental problem in this field, aims to predict the 3D structure of complexes from their unbound states without conformational changes. In this scenario, we have access to two types of valuable information: sequence-modal information, such as coevolutionary data obtained from multiple sequence alignments, and structure-modal information, including the 3D conformations of rigid structures. However, existing docking methods typically utilize single-modal information, resulting in suboptimal predictions. In this paper, we propose xTrimoBiDock (or BiDock for short), a novel rigid docking model that effectively integrates sequence- and structure-modal information through bi-level optimization. Specifically, a cross-modal transformer combines multimodal information to predict an inter-protein distance map. To achieve rigid docking, the roto-translation transformation is optimized to align the docked pose with the predicted distance map. In order to tackle this bi-level optimization problem, we unroll the gradient descent of the inner loop and further derive a better initialization for roto-translation transformation based on spectral estimation. Compared to baselines, BiDock achieves a promising result of a maximum 234% relative improvement in challenging antibody-antigen docking problem.

Text-guided image editing is widely needed in daily life, ranging from personal use to professional applications such as Photoshop. However, existing methods are either zero-shot or trained on an automatically synthesized dataset, which contains a high volume of noise. Thus, they still require lots of manual tuning to produce desirable outcomes in practice. To address this issue, we introduce MagicBrush, the first large-scale, manually annotated dataset for instruction-guided real image editing that covers diverse scenarios: single-turn, multi-turn, mask-provided, and mask-free editing. MagicBrush comprises over 10K manually annotated triplets (source image, instruction, target image), which supports trainining large-scale text-guided image editing models. We fine-tune InstructPix2Pix on MagicBrush and show that the new model can produce much better images according to human evaluation. We further conduct extensive experiments to evaluate current image editing baselines from multiple dimensions including quantitative, qualitative, and human evaluations. The results reveal the challenging nature of our dataset and the gap between current baselines and real-world editing needs.

Foundation models are trained on increasingly immense and opaque datasets. Even while these models are now key in AI system building, it can be difficult to answer the straightforward question: has the model already encountered a given example during training? We therefore propose a widespread adoption of Data Portraits: artifacts that record training data and allow for downstream inspection. First we outline the properties of such an artifact and discuss how existing solutions can be used to increase transparency. We then propose and implement a solution based on data sketching, stressing fast and space efficient querying. Using our tools, we document a popular language modeling corpus (The Pile) and a recently released code modeling dataset (The Stack). We show that our solution enables answering questions about test set leakage and model plagiarism. Our tool is lightweight and fast, costing only 3% of the dataset size in overhead. We release a live interface of our tools at https://dataportraits.org/ and call on dataset and model creators to release Data Portraits as a complement to current documentation practices.

Graphs are widely used to model interconnected entities and improve downstream predictions in various real-world applications. However, real-world graphs nowadays are often associated with complex attributes on multiple types of nodes and even links that are hard to model uniformly, while the widely used graph neural networks (GNNs) often require sufficient training toward specific downstream predictions to achieve strong performance. In this work, we take a fundamentally different approach than GNNs, to simultaneously achieve deep joint modeling of complex attributes and flexible structures of real-world graphs and obtain unsupervised generic graph representations that are not limited to specific downstream predictions. Our framework, built on a natural integration of language models (LMs) and random walks (RWs), is straightforward, powerful and data-efficient. Specifically, we first perform attributed RWs on the graph and design an automated program to compose roughly meaningful textual sequences directly from the attributed RWs; then we fine-tune an LM using the RW-based textual sequences and extract embedding vectors from the LM, which encapsulates both attribute semantics and graph structures. In our experiments, we evaluate the learned node embeddings towards different downstream prediction tasks on multiple real-world attributed graph datasets and observe significant improvements over a comprehensive set of state-of-the-art unsupervised node embedding methods. We believe this work opens a door for more sophisticated technical designs and empirical evaluations toward the leverage of LMs for the modeling of real-world graphs.

Over the last decade, deep neural networks have transformed our society, and they are already widely applied in various machine learning applications. State-of-the-art deep neural networks are becoming larger in size every year to deliver increasing model accuracy, and as a result, model training consumes substantial computing resources and will only consume more in the future. Using current training methods, in each iteration, to process a data point $x \in \mathbb{R}^d$ in a layer, we need to spend $\Theta(md)$ time to evaluate all the $m$ neurons in the layer. This means processing the entire layer takes $\Theta(nmd)$ time for $n$ data points. Recent work [Song, Yang and Zhang, NeurIPS 2021] reduces this time per iteration to $o(nmd)$, but requires exponential time to preprocess either the data or the neural network weights, making it unlikely to have practical usage. In this work, we present a new preprocessing method that simply stores the weight-data correlation in a tree data structure in order to quickly and dynamically detect which neurons fire at each iteration. Our method requires only $O(nmd)$ time in preprocessing and still achieves $o(nmd)$ time per iteration. We complement our new algorithm with a lower bound, proving that assuming a popular conjecture from complexity theory, one could not substantially speed up our algorithm for dynamic detection of firing neurons.

In this paper, we introduce an SE(3) diffusion model-based point cloud registration framework for 6D object pose estimation in real-world scenarios. Our approach formulates the 3D registration task as a denoising diffusion process, which progressively refines the pose of the source point cloud to obtain a precise alignment with the model point cloud. Training our framework involves two operations: An SE(3) diffusion process and an SE(3) reverse process. The SE(3) diffusion process gradually perturbs the optimal rigid transformation of a pair of point clouds by continuously injecting noise (perturbation transformation). By contrast, the SE(3) reverse process focuses on learning a denoising network that refines the noisy transformation step-by-step, bringing it closer to the optimal transformation for accurate pose estimation. Unlike standard diffusion models used in linear Euclidean spaces, our diffusion model operates on the SE(3) manifold. This requires exploiting the linear Lie algebra $\mathfrak{se}(3)$ associated with SE(3) to constrain the transformation transitions during the diffusion and reverse processes. Additionally, to effectively train our denoising network, we derive a registration-specific variational lower bound as the optimization objective for model learning. Furthermore, we show that our denoising network can be constructed with a surrogate registration model, making our approach applicable to different deep registration networks. Extensive experiments demonstrate that our diffusion registration framework presents outstanding pose estimation performance on the real-world TUD-L, LINEMOD, and Occluded-LINEMOD datasets.

Irregularly sampled time series are increasingly prevalent, particularly in medical domains. While various specialized methods have been developed to handle these irregularities, effectively modeling their complex dynamics and pronounced sparsity remains a challenge. This paper introduces a novel perspective by converting irregularly sampled time series into line graph images, then utilizing powerful pre-trained vision transformers for time series classification in the same way as image classification. This method not only largely simplifies specialized algorithm designs but also presents the potential to serve as a universal framework for time series modeling. Remarkably, despite its simplicity, our approach outperforms state-of-the-art specialized algorithms on several popular healthcare and human activity datasets. Especially in the rigorous leave-sensors-out setting where a portion of variables is omitted during testing, our method exhibits strong robustness against varying degrees of missing observations, achieving an impressive improvement of 42.8% in absolute F1 score points over leading specialized baselines even with half the variables masked. Code and data are available at https://github.com/Leezekun/ViTST.

We study the connection between gradient-based meta-learning and convex optimisation. We observe that gradient descent with momentum is a special case of meta-gradients, and building on recent results in optimisation, we prove convergence rates for meta learning in the single task setting. While a meta-learned update rule can yield faster convergence up to constant factor, it is not sufficient for acceleration. Instead, some form of optimism is required. We show that optimism in meta-learning can be captured through the recently proposed Bootstrapped Meta-Gradient (Flennerhag et. al., 2022) method, providing deeper insight into its underlying mechanics.

Segmenting untrimmed videos into chapters enables users to quickly navigate to the information of their interest. This important topic has been understudied due to the lack of publicly released datasets. To address this issue, we present VidChapters-7M, a dataset of 817K user-chaptered videos including 7M chapters in total. VidChapters-7M is automatically created from videos online in a scalable manner by scraping user-annotated chapters and hence without any additional manual annotation. We introduce the following three tasks based on this data. First, the video chapter generation task consists of temporally segmenting the video and generating a chapter title for each segment. To further dissect the problem, we also define two variants of this task: video chapter generation given ground-truth boundaries, which requires generating a chapter title given an annotated video segment, and video chapter grounding, which requires temporally localizing a chapter given its annotated title. We benchmark both simple baselines as well as state-of-the-art video-language models on these three tasks. We also show that pretraining on VidChapters-7M transfers well to dense video captioning tasks, largely improving the state of the art on the YouCook2 and ViTT benchmarks. Finally, our experiments reveal that downstream performance scales well with the size of the pretraining dataset.

Bayesian neural networks (BNNs) provide a formalism to quantify and calibrate uncertainty in deep learning. Current inference approaches for BNNs often resort to few-sample estimation for scalability, which can harm predictive performance, while its alternatives tend to be computationally prohibitively expensive. We tackle this challenge by revealing a previously unseen connection between inference on BNNs and volume computation problems. With this observation, we introduce a novel collapsed inference scheme that performs Bayesian model averaging using collapsed samples. It improves over a Monte-Carlo sample by limiting sampling to a subset of the network weights while pairing it with some closed-form conditional distribution over the rest. A collapsed sample represents uncountably many models drawn from the approximate posterior and thus yields higher sample efficiency. Further, we show that the marginalization of a collapsed sample can be solved analytically and efficiently despite the non-linearity of neural networks by leveraging existing volume computation solvers. Our proposed use of collapsed samples achieves a balance between scalability and accuracy. On various regression and classification tasks, our collapsed Bayesian deep learning approach demonstrates significant improvements over existing methods and sets a new state of the art in terms of uncertainty estimation as well as predictive performance.

Diffusion Probabilistic Models (DPMs) have recently shown remarkable performance in image generation tasks, which are capable of generating highly realistic images. When adopting DPMs for image restoration tasks, the crucial aspect lies in how to integrate the conditional information to guide the DPMs to generate accurate and natural output, which has been largely overlooked in existing works. In this paper, we present a unified conditional framework based on diffusion models for image restoration. We leverage a lightweight UNet to predict initial guidance and the diffusion model to learn the residual of the guidance. By carefully designing the basic module and integration module for the diffusion model block, we integrate the guidance and other auxiliary conditional information into every block of the diffusion model to achieve spatially-adaptive generation conditioning. To handle high-resolution images, we propose a simple yet effective inter-step patch-splitting strategy to produce arbitrary-resolution images without grid artifacts. We evaluate our conditional framework on three challenging tasks: extreme low-light denoising, deblurring, and JPEG restoration, demonstrating its significant improvements in perceptual quality and the generalization to restoration tasks. The code will be released at https://zhangyi-3.github.io/project/UCDIR/.

We study the training dynamics of shallow neural networks, in a two-timescale regime in which the stepsizes for the inner layer are much smaller than those for the outer layer. In this regime, we prove convergence of the gradient flow to a global optimum of the non-convex optimization problem in a simple univariate setting. The number of neurons need not be asymptotically large for our result to hold, distinguishing our result from popular recent approaches such as the neural tangent kernel or mean-field regimes. Experimental illustration is provided, showing that the stochastic gradient descent behaves according to our description of the gradient flow and thus converges to a global optimum in the two-timescale regime, but can fail outside of this regime.

Large Language Models (LLMs) are progressively being utilized as machine learning services and interface tools for various applications. However, the security implications of LLMs, particularly in relation to adversarial and Trojan attacks, remain insufficiently examined. In this paper, we propose TrojLLM, an automatic and black-box framework to effectively generate universal and stealthy triggers. When these triggers are incorporated into the input data, the LLMs' outputs can be maliciously manipulated. Moreover, the framework also supports embedding Trojans within discrete prompts, enhancing the overall effectiveness and precision of the triggers' attacks. Specifically, we propose a trigger discovery algorithm for generating universal triggers for various inputs by querying victim LLM-based APIs using few-shot data samples. Furthermore, we introduce a novel progressive Trojan poisoning algorithm designed to generate poisoned prompts that retain efficacy and transferability across a diverse range of models. Our experiments and results demonstrate TrojLLM's capacity to effectively insert Trojans into text prompts in real-world black-box LLM APIs including GPT-3.5 and GPT-4, while maintaining exceptional performance on clean test sets. Our work sheds light on the potential security risks in current models and offers a potential defensive approach. The source code of TrojLLM is available at https://github.com/UCF-ML-Research/TrojLLM.

We study the convergence to local Nash equilibria of gradient methods for two-player zero-sum differentiable games. It is well-known that, in the continuous-time setting, such dynamics converge locally when $S \succ 0$ and may diverge when $S=0$, where $S\succeq 0$ is the symmetric part of the Jacobian at equilibrium that accounts for the "potential" component of the game. We show that these dynamics also converge as soon as $S$ is nonzero (*partial curvature*) and the eigenvectors of the antisymmetric part $A$ are in general position with respect to the kernel of $S$. We then study the convergence rate when $S \ll A$ and prove that it typically depends on the *average* of the eigenvalues of $S$, instead of the minimum as an analogy with minimization problems would suggest. To illustrate our results, we consider the problem of computing mixed Nash equilibria of continuous games. We show that, thanks to partial curvature, conic particle methods -- which optimize over both weights and supports of the mixed strategies -- generically converge faster than fixed-support methods. For min-max games, it is thus beneficial to add degrees of freedom "with curvature": this can be interpreted as yet another benefit of over-parameterization.

Combining test statistics from independent trials or experiments is a popular method of meta-analysis. However, there is very limited theoretical understanding of the power of the combined test, especially in high-dimensional models considering composite hypotheses tests. We derive a mathematical framework to study standard {meta-analysis} testing approaches in the context of the many normal means model, which serves as the platform to investigate more complex models. We introduce a natural and mild restriction on the meta-level combination functions of the local trials. This allows us to mathematically quantify the cost of compressing $m$ trials into real-valued test statistics and combining these. We then derive minimax lower and matching upper bounds for the separation rates of standard combination methods for e.g. p-values and e-values, quantifying the loss relative to using the full, pooled data. We observe an elbow effect, revealing that in certain cases combining the locally optimal tests in each trial results in a sub-optimal {meta-analysis} method and develop approaches to achieve the global optima. We also explore the possible gains of allowing limited coordination between the trial designs. Our results connect meta-analysis with bandwidth constraint distributed inference and build on recent information theoretic developments in the latter field.

Inspired by the insights in cognitive science with respect to human memory and reasoning mechanism, a novel evolvable LLM-based (Large Language Model) agent framework is proposed as Rememberer. By equipping the LLM with a long-term experience memory, Rememberer is capable of exploiting the experiences from the past episodes even for different task goals, which excels an LLM-based agent with fixed exemplars or equipped with a transient working memory. We further introduce **R**einforcement **L**earning with **E**xperience **M**emory (**RLEM**) to update the memory. Thus, the whole system can learn from the experiences of both success and failure, and evolve its capability without fine-tuning the parameters of the LLM. In this way, the proposed Rememberer constitutes a semi-parametric RL agent. Extensive experiments are conducted on two RL task sets to evaluate the proposed framework. The average results with different initialization and training sets exceed the prior SOTA by 4% and 2% for the success rate on two task sets and demonstrate the superiority and robustness of Rememberer.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMED, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMED serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMED-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMED, we conduct experiments and establish baselines on new datasets.

In this paper, we present continuous parametric optical flow, a parametric representation of dense and continuous motion over arbitrary time interval. In contrast to existing discrete-time representations (i.e., flow in between consecutive frames), this new representation transforms the frame-to-frame pixel correspondences to dense continuous flow. In particular, we present a temporal-parametric model that employs B-splines to fit point trajectories using a limited number of frames. To further improve the stability and robustness of the trajectories, we also add an encoder with a neural ordinary differential equation (NODE) to represent features associated with specific times. We also contribute a synthetic dataset and introduce two evaluation perspectives to measure the accuracy and robustness of continuous flow estimation. Benefiting from the combination of explicit parametric modeling and implicit feature optimization, our model focuses on motion continuity and outperforms the flow-based and point-tracking approaches for fitting long-term and variable sequences.

Recent neural architecture search (NAS) frameworks have been successful in finding optimal architectures for given conditions (e.g., performance or latency). However, they search for optimal architectures in terms of their performance on clean images only, while robustness against various types of perturbations or corruptions is crucial in practice. Although there exist several robust NAS frameworks that tackle this issue by integrating adversarial training into one-shot NAS, however, they are limited in that they only consider robustness against adversarial attacks and require significant computational resources to discover optimal architectures for a single task, which makes them impractical in real-world scenarios. To address these challenges, we propose a novel lightweight robust zero-cost proxy that considers the consistency across features, parameters, and gradients of both clean and perturbed images at the initialization state. Our approach facilitates an efficient and rapid search for neural architectures capable of learning generalizable features that exhibit robustness across diverse perturbations. The experimental results demonstrate that our proxy can rapidly and efficiently search for neural architectures that are consistently robust against various perturbations on multiple benchmark datasets and diverse search spaces, largely outperforming existing clean zero-shot NAS and robust NAS with reduced search cost.