NeurIPS 2024 Papers

Flow Matching (FM) (also referred to as stochastic interpolants or rectified flows) stands out as a class of generative models that aims to bridge in finite time the target distribution $\nu^\star$ with an auxiliary distribution $\mu$ leveraging a fixed coupling $\pi$ and a bridge which can either be deterministic or stochastic. These two ingredients define a path measure which can then be approximated by learning the drift of its Markovian projection. The main contribution of this paper is to provide relatively mild assumption on $\nu^\star$, $\mu$ and $\pi$ to obtain non-asymptotics guarantees for Diffusion Flow Matching (DFM) models using as bridge the conditional distribution associated with the Brownian motion. More precisely, it establishes bounds on the Kullback-Leibler divergence between the target distribution and the one generated by such DFM models under moment conditions on the score of $\nu^\star$, $\mu$ and $\pi$, and a standard $\mathrm{L}^2$-drift-approximation error assumption.

Toxicity classification in textual content remains a significant problem. Data with labels from a single annotator fall short of capturing the diversity of human perspectives. Therefore, there is a growing need to incorporate crowdsourced annotations for training an effective toxicity classifier. Additionally, the standard approach to training a classifier using empirical risk minimization (ERM) may fail to address the potential shifts between the training set and testing set due to exploiting spurious correlations. This work introduces a novel bi-level optimization framework that integrates crowdsourced annotations with the soft-labeling technique and optimizes the soft-label weights by Group Distributionally Robust Optimization (GroupDRO) to enhance the robustness against out-of-distribution (OOD) risk. We theoretically prove the convergence of our bi-level optimization algorithm. Experimental results demonstrate that our approach outperforms existing baseline methods in terms of both average and worst-group accuracy, confirming its effectiveness in leveraging crowdsourced annotations to achieve more effective and robust toxicity classification.

Spiking neural networks (SNNs), inspired by biological processes, use spike signals for inter-layer communication, presenting an energy-efficient alternative to traditional neural networks. To realize the theoretical advantages of SNNs in energy efficiency, it is essential to deploy them onto neuromorphic chips. On clock-driven synchronous chips, employing shorter time steps can enhance energy efficiency but reduce SNN performance. Compared to the clock-driven synchronous chip, the event-driven asynchronous chip achieves much lower energy consumption but only supports some specific network operations. Recently, a series of SNN projects have achieved tremendous success, significantly improving the SNN's performance. However, event-driven asynchronous chips do not support some of the proposed structures, making it impossible to integrate these SNNs into asynchronous hardware. In response to these problems, we propose the Spiking Token Mixer (STMixer) architecture, which consists exclusively of operations supported by asynchronous scenarios, including convolutional, fully connected layers and residual paths. Our series of experiments also demonstrates that STMixer achieves performance on par with spiking transformers in synchronous scenarios with very low timesteps. This indicates its ability to achieve the same level of performance with lower power consumption in synchronous scenarios. The codes are available at \url{https://github.com/brain-intelligence-lab/STMixer_demo}.

We introduce the **A**utoregressive **P**DE **E**mulator Benchmark (APEBench), a comprehensive benchmark suite to evaluate autoregressive neural emulators for solving partial differential equations. APEBench is based on JAX and provides a seamlessly integrated differentiable simulation framework employing efficient pseudo-spectral methods, enabling 46 distinct PDEs across 1D, 2D, and 3D. Facilitating systematic analysis and comparison of learned emulators, we propose a novel taxonomy for unrolled training and introduce a unique identifier for PDE dynamics that directly relates to the stability criteria of classical numerical methods. APEBench enables the evaluation of diverse neural architectures, and unlike existing benchmarks, its tight integration of the solver enables support for differentiable physics training and neural-hybrid emulators. Moreover, APEBench emphasizes rollout metrics to understand temporal generalization, providing insights into the long-term behavior of emulating PDE dynamics. In several experiments, we highlight the similarities between neural emulators and numerical simulators. The code is available at [github.com/tum-pbs/apebench](https://github.com/tum-pbs/apebench) and APEBench can be installed via `pip install apebench`.

Multiple Instance Learning (MIL) is widely used in medical imaging classification to reduce the labeling effort. While only bag labels are available for training, one typically seeks predictions at both bag and instance levels (classification and localization tasks, respectively). Early MIL methods treated the instances in a bag independently. Recent methods account for global and local dependencies among instances. Although they have yielded excellent results in classification, their performance in terms of localization is comparatively limited. We argue that these models have been designed to target the classification task, while implications at the instance level have not been deeply investigated. Motivated by a simple observation -- that neighboring instances are likely to have the same label -- we propose a novel, principled, and flexible mechanism to model local dependencies. It can be used alone or combined with any mechanism to model global dependencies (e.g., transformers). A thorough empirical validation shows that our module leads to state-of-the-art performance in localization while being competitive or superior in classification. Our code is at https://github.com/Franblueee/SmMIL.

In contextual dynamic pricing, a seller sequentially prices goods based on contextual information. Buyers will purchase products only if the prices are below their valuations. The goal of the seller is to design a pricing strategy that collects as much revenue as possible. We focus on two different valuation models. The first assumes that valuations linearly depend on the context and are further distorted by noise. Under minor regularity assumptions, our algorithm achieves an optimal regret bound of $\tilde{\mathcal{O}}(T^{2/3})$, improving the existing results. The second model removes the linearity assumption, requiring only that the expected buyer valuation is $\beta$-H\"older in the context. For this model, our algorithm obtains a regret $\tilde{\mathcal{O}}(T^{d+2\beta/d+3\beta})$, where $d$ is the dimension of the context space.

Cyber threat intelligence (CTI) is crucial in today's cybersecurity landscape, providing essential insights to understand and mitigate the ever-evolving cyber threats. The recent rise of Large Language Models (LLMs) have shown potential in this domain, but concerns about their reliability, accuracy, and hallucinations persist. While existing benchmarks provide general evaluations of LLMs, there are no benchmarks that address the practical and applied aspects of CTI-specific tasks. To bridge this gap, we introduce CTIBench, a benchmark designed to assess LLMs' performance in CTI applications. CTIBench includes multiple datasets focused on evaluating knowledge acquired by LLMs in the cyber-threat landscape. Our evaluation of several state-of-the-art models on these tasks provides insights into their strengths and weaknesses in CTI contexts, contributing to a better understanding of LLM capabilities in CTI.

Post-Translational Modifications (PTMs) are changes that occur in proteins after synthesis, influencing their structure, function, and cellular behavior. PTMs are essential in cell biology; they regulate protein function and stability, are involved in various cellular processes, and are linked to numerous diseases. A particularly interesting class of PTMs are chemical modifications such as phosphorylation introduced on amino acid side chains because they can drastically alter the physicochemical properties of the peptides once they are present. One or more PTMs can be attached to each amino acid of the peptide sequence. The most commonly applied technique to detect PTMs on proteins is bottom-up Mass Spectrometry-based proteomics (MS), where proteins are digested into peptides and subsequently analyzed using Tandem Mass Spectrometry (MS/MS). While an increasing number of machine learning models are published focusing on MS/MS-related property prediction of unmodified peptides, high-quality reference data for modified peptides is missing, impeding model development for this important class of peptides. To enable researchers to train machine learning models that can accurately predict the properties of modified peptides, we introduce four high-quality labeled datasets for applying machine and deep learning to tasks in MS-based proteomics. The four datasets comprise several subgroups of peptides with 1.2 million unique modified peptide sequences and 30 unique pairs of (amino-acid, PTM), covering both experimentally introduced and naturally occurring modifications on various amino acids. We evaluate the utility and importance of the dataset by providing benchmarking results on models trained with and without modifications and highlighting the impact of including modified sequences on downstream tasks. We demonstrate that predicting the properties of modified peptides is more challenging but has a broad impact since they are often the core of protein functionality and its regulation, and they have a potential role as biomarkers in clinical applications. Our datasets contribute to applied machine learning in proteomics by enabling the research community to experiment with methods to encode PTMs as model inputs and to benchmark against reference data for model comparison. With a proper data split for three common tasks in proteomics, we provide a robust way to evaluate model performance and assess generalization on unseen modified sequences.

Planning in real-world settings often entails addressing partial observability while aligning with users' requirements. We present a novel framework for expressing users' constraints and preferences about agent behavior in a partially observable setting using parameterized belief-state query (BSQ) policies in the setting of goal-oriented partially observable Markov decision processes (gPOMDPs). We present the first formal analysis of such constraints and prove that while the expected cost function of a parameterized BSQ policy w.r.t its parameters is not convex, it is piecewise constant and yields an implicit discrete parameter search space that is finite for finite horizons. This theoretical result leads to novel algorithms that optimize gPOMDP agent behavior with guaranteed user alignment. Analysis proves that our algorithms converge to the optimal user-aligned behavior in the limit. Empirical results show that parameterized BSQ policies provide a computationally feasible approach for user-aligned planning in partially observable settings.

Gradient-based algorithms have shown great promise in solving large (two-player) zero-sum games. However, their success has been mostly confined to the low-precision regime since the number of iterations grows polynomially in $1/\epsilon$, where $\epsilon > 0$ is the duality gap. While it has been well-documented that linear convergence---an iteration complexity scaling as $\text{log}(1/\epsilon)$---can be attained even with gradient-based algorithms, that comes at the cost of introducing a dependency on certain condition number-like quantities which can be exponentially large in the description of the game. To address this shortcoming, we examine the iteration complexity of several gradient-based algorithms in the celebrated framework of smoothed analysis, and we show that they have polynomial smoothed complexity, in that their number of iterations grows as a polynomial in the dimensions of the game, $\text{log}(1/\epsilon)$, and $1/\sigma$, where $\sigma$ measures the magnitude of the smoothing perturbation. Our result applies to optimistic gradient and extra-gradient descent/ascent, as well as a certain iterative variant of Nesterov's smoothing technique. From a technical standpoint, the proof proceeds by characterizing and performing a smoothed analysis of a certain error bound, the key ingredient driving linear convergence in zero-sum games. En route, our characterization also makes a natural connection between the convergence rate of such algorithms and perturbation-stability properties of the equilibrium, which is of interest beyond the model of smoothed complexity.

Kernel methods are widely utilized in machine learning field to learn, from training data, a latent function in a reproducing kernel Hilbert space. It is well known that the approximator thus obtained usually achieves a linear representation, which brings various computational benefits, while maintaining great representation power (i.e., universal approximation). However, when non-negativity constraints are imposed on the function's outputs, the literature usually takes the kernel method-based approximators as offering linear representations at the expense of limited model flexibility or good representation power by allowing for their nonlinear forms. The main contribution of this paper is to derive a sufficient condition for a positive definite kernel so that it may construct flexible and linear approximators of non-negative functions. We call a kernel function that offers these attributes an *inverse M-kernel*; it is reminiscent of the inverse M-matrix. Furthermore, we show that for a one-dimensional input space, universal exponential/Abel kernels are inverse M-kernels and construct linear universal approximators of non-negative functions. To the best of our knowledge, it is the first time that the existence of linear universal approximators of non-negative functions has been elucidated. We confirm the effectiveness of our results by experiments on the problems of non-negativity-constrained regression, density estimation, and intensity estimation. Finally, we discuss issues and perspectives on multi-dimensional input settings.

Signed Distance Function (SDF)-based volume rendering has demonstrated significant capabilities in surface reconstruction. Although promising, SDF-based methods often fail to capture detailed geometric structures, resulting in visible defects. By comparing SDF-based volume rendering to density-based volume rendering, we identify two main factors within the SDF-based approach that degrade surface quality: SDF-to-density representation and geometric regularization. These factors introduce challenges that hinder the optimization of the SDF field. To address these issues, we introduce NeuRodin, a novel two-stage neural surface reconstruction framework that not only achieves high-fidelity surface reconstruction but also retains the flexible optimization characteristics of density-based methods. NeuRodin incorporates innovative strategies that facilitate transformation of arbitrary topologies and reduce artifacts associated with density bias. Extensive evaluations on the Tanks and Temples and ScanNet++ datasets demonstrate the superiority of NeuRodin, showing strong reconstruction capabilities for both indoor and outdoor environments using solely posed RGB captures. Project website: https://open3dvlab.github.io/NeuRodin/

Structured state space models (SSMs), the core engine behind prominent neural networks such as S4 and Mamba, are linear dynamical systems adhering to a specified structure, most notably diagonal. In contrast to typical neural network modules, whose parameterizations are real, SSMs often use complex parameterizations. Theoretically explaining the benefits of complex parameterizations for SSMs is an open problem. The current paper takes a step towards its resolution, by establishing formal gaps between real and complex diagonal SSMs. Firstly, we prove that while a moderate dimension suffices in order for a complex SSM to express all mappings of a real SSM, a much higher dimension is needed for a real SSM to express mappings of a complex SSM. Secondly, we prove that even if the dimension of a real SSM is high enough to express a given mapping, typically, doing so requires the parameters of the real SSM to hold exponentially large values, which cannot be learned in practice. In contrast, a complex SSM can express any given mapping with moderate parameter values. Experiments corroborate our theory, and suggest a potential extension of the theory that accounts for selectivity, a new architectural feature yielding state of the art performance.

The *magnitude* of a metric space is a novel invariant that provides a measure of the 'effective size' of a space across multiple scales, while also capturing numerous geometrical properties, such as curvature, density, or entropy. We develop a family of magnitude-based measures of the intrinsic diversity of latent representations, formalising a novel notion of dissimilarity between magnitude functions of finite metric spaces. Our measures are provably stable under perturbations of the data, can be efficiently calculated, and enable a rigorous multi-scale characterisation and comparison of latent representations. We show their utility and superior performance across different domains and tasks, including the automated estimation of diversity, the detection of mode collapse, and the evaluation of generative models for text, image, and graph data.

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently, there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present Slice-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). Our dataset can be found here. Slice-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different models on the same task under standardized conditions. However, there was no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we established the SENSORIUM 2023 Benchmark Competition with dynamic input, featuring a new large-scale dataset from the primary visual cortex of ten mice. This dataset includes responses from 78,853 neurons to 2 hours of dynamic stimuli per neuron, together with behavioral measurements such as running speed, pupil dilation, and eye movements. The competition ranked models in two tracks based on predictive performance for neuronal responses on a held-out test set: one focusing on predicting in-domain natural stimuli and another on out-of-distribution (OOD) stimuli to assess model generalization. As part of the NeurIPS 2023 Competition Track, we received more than 160 model submissions from 22 teams. Several new architectures for predictive models were proposed, and the winning teams improved the previous state-of-the-art model by 50\%. Access to the dataset as well as the benchmarking infrastructure will remain online at www.sensorium-competition.net.

When matching parts of a surface to its whole, a fundamental question arises: Which points should be included in the matching process? The issue is intensified when using isometry to measure similarity, as it requires the validation of whether distances measured between pairs of surface points should influence the matching process. The approach we propose treats surfaces as manifolds equipped with geodesic distances, and addresses the partial shape matching challenge by introducing a novel criterion to meticulously search for consistent distances between pairs of points. The new criterion explores the relation between intrinsic geodesic distances between the points, geodesic distances between the points and surface boundaries, and extrinsic distances between boundary points measured in the embedding space. It is shown to be less restrictive compared to previous measures and achieves state-of-the-art results when used as a loss function in training networks for partial shape matching.

This paper studies decentralized bilevel optimization, in which multiple agents collaborate to solve problems involving nested optimization structures with neighborhood communications. Most existing literature primarily utilizes gradient tracking to mitigate the influence of data heterogeneity, without exploring other well-known heterogeneity-correction techniques such as EXTRA or Exact Diffusion. Additionally, these studies often employ identical decentralized strategies for both upper- and lower-level problems, neglecting to leverage distinct mechanisms across different levels. To address these limitations, this paper proposes SPARKLE, a unified single-loop primal-dual algorithm framework for decentralized bilevel optimization. SPARKLE offers the flexibility to incorporate various heterogeneity-correction strategies into the algorithm. Moreover, SPARKLE allows for different strategies to solve upper- and lower-level problems. We present a unified convergence analysis for SPARKLE, applicable to all its variants, with state-of-the-art convergence rates compared to existing decentralized bilevel algorithms. Our results further reveal that EXTRA and Exact Diffusion are more suitable for decentralized bilevel optimization, and using mixed strategies in bilevel algorithms brings more benefits than relying solely on gradient tracking.

Existing super-resolution (SR) methods optimize all model weights equally using $\mathcal{L}_1$ or $\mathcal{L}_2$ losses by uniformly sampling image patches without considering dataset imbalances or parameter redundancy, which limits their performance. To address this, we formulate the image SR task as an imbalanced distribution transfer learning problem from a statistical probability perspective, proposing a plug-and-play Weight-Balancing framework (WBSR) to achieve balanced model learning without changing the original model structure and training data. Specifically, we develop a Hierarchical Equalization Sampling (HES) strategy to address data distribution imbalances, enabling better feature representation from texture-rich samples. To tackle model optimization imbalances, we propose a Balanced Diversity Loss (BDLoss) function, focusing on learning texture regions while disregarding redundant computations in smooth regions. After joint training of HES and BDLoss to rectify these imbalances, we present a gradient projection dynamic inference strategy to facilitate accurate and efficient inference. Extensive experiments across various models, datasets, and scale factors demonstrate that our method achieves comparable or superior performance to existing approaches with about 34\% reduction in computational cost.