NeurIPS 2024 Papers

Conference on Neural Information Processing Systems

Decision breakdown

4,562papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Oral
    721.6%
  • Spotlight
    3828.4%
  • Poster
    4,06489.1%
  • Other / unlabeled
    441.0%

Browse all papers

Topic: General ML · supervised learning · 375 papers · Reset filters

Generalized Protein Pocket Generation with Prior-Informed Flow Matching

ZAIXI ZHANG, Marinka Zitnik, Qi Liu

Expand abstract

Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand. Current approaches to pocket generation often suffer from time-intensive physical computations or template-based methods, as well as compromised generation quality due to the overlooking of domain knowledge. To tackle these challenges, we propose PocketFlow, a generative model that incorporates protein-ligand interaction priors based on flow matching. During training, PocketFlow learns to model key types of protein-ligand interactions, such as hydrogen bonds. In the sampling, PocketFlow leverages multi-granularity guidance (overall binding affinity and interaction geometry constraints) to facilitate generating high-affinity and valid pockets. Extensive experiments show that PocketFlow outperforms baselines on multiple benchmarks, e.g., achieving an average improvement of 1.29 in Vina Score and 0.05 in scRMSD. Moreover, modeling interactions make PocketFlow a generalized generative model across multiple ligand modalities, including small molecules, peptides, and RNA.

Spotlight
Gliding over the Pareto Front with Uniform Designs

Xiaoyuan Zhang, Genghui Li, Xi Lin, Yichi Zhang, Yifan Chen, Qingfu Zhang

Expand abstract

Multiobjective optimization (MOO) plays a critical role in various real-world domains. A major challenge therein is generating $K$ uniform Pareto-optimal solutions to represent the entire Pareto front. To address this issue, this paper firstly introduces \emph{fill distance} to evaluate the $K$ design points, which provides a quantitative metric for the representativeness of the design. However, directly specifying the optimal design that minimizes the fill distance is nearly intractable due to the nested $\min-\max-\min$ optimization problem. To address this, we propose a surrogate ``max-packing'' design for the fill distance design, which is easier to optimize and leads to a rate-optimal design with a fill distance at most $4\times$ the minimum value. Extensive experiments on synthetic and real-world benchmarks demonstrate that our proposed paradigm efficiently produces high-quality, representative solutions and outperforms baseline methods.

Poster
Spiking Transformer with Experts Mixture

Zhaokun Zhou, Yijie Lu, Yanhao Jia, Kaiwei Che, Jun Niu, Liwei Huang, Xinyu Shi, Yuesheng Zhu, Guoqi Li, Zhaofei Yu, Li Yuan

Expand abstract

Spiking Neural Networks (SNNs) provide a sparse spike-driven mechanism which is believed to be critical for energy-efficient deep learning. Mixture-of-Experts (MoE), on the other side, aligns with the brain mechanism of distributed and sparse processing, resulting in an efficient way of enhancing model capacity and conditional computation. In this work, we consider how to incorporate SNNs’ spike-driven and MoE’s conditional computation into a unified framework. However, MoE uses softmax to get the dense conditional weights for each expert and TopK to hard-sparsify the network, which does not fit the properties of SNNs. To address this issue, we reformulate MoE in SNNs and introduce the Spiking Experts Mixture Mechanism (SEMM) from the perspective of sparse spiking activation. Both the experts and the router output spiking sequences, and their element-wise operation makes SEMM computation spike-driven and dynamic sparse-conditional. By developing SEMM into Spiking Transformer, the Experts Mixture Spiking Attention (EMSA) and the Experts Mixture Spiking Perceptron (EMSP) are proposed, which performs routing allocation for head-wise and channel-wise spiking experts, respectively. Experiments show that SEMM realizes sparse conditional computation and obtains a stable improvement on neuromorphic and static datasets with approximate computational overhead based on the Spiking Transformer baselines.

Poster
WindsorML: High-Fidelity Computational Fluid Dynamics Dataset For Automotive Aerodynamics

Neil Ashton, Jordan B. Angel, Aditya Ghate, Gaetan Kenway, Man Long Wong, Cetin C. Kiris, Astrid Walle, Danielle C. Maddix, Gary Page

Expand abstract

This paper presents a new open-source high-fidelity dataset for Machine Learning (ML) containing 355 geometric variants of the Windsor body, to help the development and testing of ML surrogate models for external automotive aerodynamics. Each Computational Fluid Dynamics (CFD) simulation was run with a GPU-native high-fidelity Wall-Modeled Large-Eddy Simulations (WMLES) using a Cartesian immersed-boundary method using more than 280M cells to ensure the greatest possible accuracy. The dataset contains geometry variants that exhibits a wide range of flow characteristics that are representative of those observed on road-cars. The dataset itself contains the 3D time-averaged volume \& boundary data as well as the geometry and force \& moment coefficients. This paper discusses the validation of the underlying CFD methods as well as contents and structure of the dataset. To the authors knowledge, this represents the first, large-scale high-fidelity CFD dataset for the Windsor body with a permissive open-source license (CC-BY-SA).

Poster
LLaMo: Large Language Model-based Molecular Graph Assistant

Jinyoung Park, Minseong Bae, Dohwan Ko, Hyunwoo J. Kim

Expand abstract

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to- end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

Poster
Exploiting Representation Curvature for Boundary Detection in Time Series

Yooju Shin, Jaehyun Park, Susik Yoon, Hwanjun Song, Byung Suk Lee, Jae-Gil Lee

Expand abstract

*Boundaries* are the timestamps at which a class in a time series changes. Recently, representation-based boundary detection has gained popularity, but its emphasis on consecutive distance difference backfires, especially when the changes are gradual. In this paper, we propose a boundary detection method, **RECURVE**, based on a novel change metric, the ***curvature*** of a representation trajectory, to accommodate both gradual and abrupt changes. Here, a sequence of representations in the representation space is interpreted as a trajectory, and a curvature at each timestamp can be computed. Using the theory of random walk, we formally show that the mean curvature is lower near boundaries than at other points. Extensive experiments using diverse real-world time-series datasets confirm the superiority of RECURVE over state-of-the-art methods.

Poster
Provable and Efficient Dataset Distillation for Kernel Ridge Regression

Yilan Chen, Wei Huang, Tsui-Wei Weng

Expand abstract

Deep learning models are now trained on increasingly larger datasets, making it crucial to reduce computational costs and improve data quality. Dataset distillation aims to distill a large dataset into a small synthesized dataset such that models trained on it can achieve similar performance to those trained on the original dataset. While there have been many empirical efforts to improve dataset distillation algorithms, a thorough theoretical analysis and provable, efficient algorithms are still lacking. In this paper, by focusing on dataset distillation for kernel ridge regression (KRR), we show that one data point per class is already necessary and sufficient to recover the original model's performance in many settings. For linear ridge regression and KRR with surjective feature mappings, we provide necessary and sufficient conditions for the distilled dataset to recover the original model's parameters. For KRR with injective feature mappings of deep neural networks, we show that while one data point per class is not sufficient in general, $k+1$ data points can be sufficient for deep linear neural networks, where $k$ is the number of classes. Our theoretical results enable directly constructing analytical solutions for distilled datasets, resulting in a provable and efficient dataset distillation algorithm for KRR. We verify our theory experimentally and show that our algorithm outperforms previous work such as KIP while being significantly more efficient, e.g. 15840$\times$ faster on CIFAR-100. Our code is available at \href{https://github.com/Trustworthy-ML-Lab/provable-efficient-dataset-distill-KRR}{GitHub}.

Poster
Large Scale Transfer Learning for Tabular Data via Language Modeling

Joshua P Gardner, Juan Carlos Perdomo, Ludwig Schmidt

Expand abstract

Tabular data – structured, heterogeneous, spreadsheet-style data with rows and columns – is widely used in practice across many domains. However, while recent foundation models have reduced the need for developing task-specific datasets and predictors in domains such as language modeling and computer vision, this transfer learning paradigm has not had similar impact in the tabular domain. In this work, we seek to narrow this gap and present TABULA-8B, a language model for tabular prediction. We define a process for extracting a large, high-quality training dataset from the TabLib corpus, proposing methods for tabular data filtering and quality control. Using the resulting dataset, which comprises over 2.1B rows from 4.2M unique tables, we fine-tune a Llama 3-8B large language model (LLM) for tabular data prediction (classification and binned regression) using a novel packing and attention scheme for tabular prediction. Through evaluation across a test suite of 329 datasets, we find that TABULA-8B has zero-shot accuracy on unseen tables that is over 15 percentage points (pp) higher than random guessing, a feat that is not possible with existing state-of-the-art tabular prediction models (e.g. XGBoost, TabPFN). In the few-shot setting (1-32 shots), without any fine-tuning on the target datasets, TABULA-8B is 5-15 pp more accurate than XGBoost and TabPFN models that are explicitly trained on equal, or even up to 16× more data. We release our model, code, and data along with the publication of this paper.

Poster
Fine-Tuning Personalization in Federated Learning to Mitigate Adversarial Clients

Youssef Allouah, Abdellah El Mrini, Rachid Guerraoui, Nirupam Gupta, Rafael Pinot

Expand abstract

Federated learning (FL) is an appealing paradigm that allows a group of machines (a.k.a. clients) to learn collectively while keeping their data local. However, due to the heterogeneity between the clients’ data distributions, the model obtained through the use of FL algorithms may perform poorly on some client’s data. Personalization addresses this issue by enabling each client to have a different model tailored to their own data while simultaneously benefiting from the other clients’ data. We consider an FL setting where some clients can be adversarial, and we derive conditions under which full collaboration fails. Specifically, we analyze the generalization performance of an interpolated personalized FL framework in the presence of adversarial clients, and we precisely characterize situations when full collaboration performs strictly worse than fine-tuned personalization. Our analysis determines how much we should scale down the level of collaboration, according to data heterogeneity and the tolerable fraction of adversarial clients. We support our findings with empirical results on mean estimation and binary classification problems, considering synthetic and benchmark image classification datasets

Poster
Derivative-enhanced Deep Operator Network

Yuan Qiu, Nolan Bridges, Peng Chen

Expand abstract

The deep operator networks (DeepONet), a class of neural operators that learn mappings between function spaces, have recently been developed as surrogate models for parametric partial differential equations (PDEs). In this work we propose a derivative-enhanced deep operator network (DE-DeepONet), which leverages derivative information to enhance the solution prediction accuracy and provides a more accurate approximation of solution-to-parameter derivatives, especially when training data are limited. DE-DeepONet explicitly incorporates linear dimension reduction of high dimensional parameter input into DeepONet to reduce training cost and adds derivative loss in the loss function to reduce the number of required parameter-solution pairs. We further demonstrate that the use of derivative loss can be extended to enhance other neural operators, such as the Fourier neural operator (FNO). Numerical experiments validate the effectiveness of our approach.

Poster
Towards General Loop Invariant Generation: A Benchmark of Programs with Memory Manipulation

Chang Liu, Xiwei Wu, Yuan Feng, Qinxiang Cao, Junchi Yan

Expand abstract

Program verification is vital for ensuring software reliability, especially in the context of increasingly complex systems. Loop invariants, remaining true before and after each iteration of loops, are crucial for this verification process. Traditional provers and machine learning based methods for generating loop invariants often require expert intervention or extensive labeled data, and typically only handle numerical property verification. These methods struggle with programs involving complex data structures and memory manipulations, limiting their applicability and automation capabilities. This paper introduces a new benchmark named LIG-MM, specifically for programs with complex data structures and memory manipulations. We collect 312 programs from various sources, including daily programs from college homework, the international competition (SV-COMP), benchmarks from previous papers (SLING), and programs from real-world software systems (Linux Kernel, GlibC, LiteOS, and Zephyr). Based on LIG-MM, our findings indicate that previous methods, including GPT-4, fail to automate verification for these programs. Consequently, we propose a novel LLM-SE framework that coordinates LLM with symbolic execution, fine-tuned using self-supervised learning, to generate loop invariants. Experimental results on LIG-MM demonstrate that our LLM-SE outperforms state-of-the-art methods, offering a new direction toward automated program verification in real-world scenarios.

Poster
MILP-StuDio: MILP Instance Generation via Block Structure Decomposition

Haoyang Liu, Jie Wang, Wanbo Zhang, Zijie Geng, Yufei Kuang, Xijun Li, Bin Li, Yongdong Zhang, Feng Wu

Expand abstract

Mixed-integer linear programming (MILP) is one of the most popular mathematical formulations with numerous applications. In practice, improving the performance of MILP solvers often requires a large amount of high-quality data, which can be challenging to collect. Researchers thus turn to generation techniques to generate additional MILP instances. However, existing approaches do not take into account specific block structures—which are closely related to the problem formulations—in the constraint coefficient matrices (CCMs) of MILPs. Consequently, they are prone to generate computationally trivial or infeasible instances due to the disruptions of block structures and thus problem formulations. To address this challenge, we propose a novel MILP generation framework, called Block Structure Decomposition (MILP-StuDio), to generate high-quality instances by preserving the block structures. Specifically, MILP-StuDio begins by identifying the blocks in CCMs and decomposing the instances into block units, which serve as the building blocks of MILP instances. We then design three operators to construct new instances by removing, substituting, and appending block units in the original instances, enabling us to generate instances with flexible sizes. An appealing feature of MILP-StuDio is its strong ability to preserve the feasibility and computational hardness of the generated instances. Experiments on the commonly-used benchmarks demonstrate that using instances generated by MILP-StuDio is able to significantly reduce over 10% of the solving time for learning-based solvers.

Poster
Satformer: Accurate and Robust Traffic Data Estimation for Satellite Networks

Liang Qin, Xiyuan Liu, Wenting Wei, Liang Chengbin, Huaxi Gu

Expand abstract

The operations and maintenance of satellite networks heavily depend on traffic measurements. Due to the large-scale and highly dynamic nature of satellite networks, global measurement encounters significant challenges in terms of complexity and overhead. Estimating global network traffic data from partial traffic measurements is a promising solution. However, the majority of current estimation methods concentrate on low-rank linear decomposition, which is unable to accurately estimate. The reason lies in its inability to capture the intricate nonlinear spatio-temporal relationship found in large-scale, highly dynamic traffic data. This paper proposes Satformer, an accurate and robust method for estimating traffic data in satellite networks. In Satformer, we innovatively incorporate an adaptive sparse spatio-temporal attention mechanism. In the mechanism, more attention is paid to specific local regions of the input tensor to improve the model's sensitivity on details and patterns. This method enhances its capability to capture nonlinear spatio-temporal relationships. Experiments on small, medium, and large-scale satellite networks datasets demonstrate that Satformer outperforms mathematical and neural baseline methods notably. It provides substantial improvements in reducing errors and maintaining robustness, especially for larger networks. The approach shows promise for deployment in actual systems.

Poster
Data Acquisition via Experimental Design for Data Markets

Charles Lu, Baihe Huang, Sai Praneeth Karimireddy, Praneeth Vepakomma, Michael Jordan, Ramesh Raskar

Expand abstract

The acquisition of training data is crucial for machine learning applications. Data markets can increase the supply of data, particularly in data-scarce domains such as healthcare, by incentivizing potential data providers to join the market. A major challenge for a data buyer in such a market is choosing the most valuable data points from a data seller. Unlike prior work in data valuation, which assumes centralized data access, we propose a federated approach to the data acquisition problem that is inspired by linear experimental design. Our proposed data acquisition method achieves lower prediction error without requiring labeled validation data and can be optimized in a fast and federated procedure. The key insight of our work is that a method that directly estimates the benefit of acquiring data for test set prediction is particularly compatible with a decentralized market setting.

Poster
Learning Better Representations From Less Data For Propositional Satisfiability

Mohamed Ghanem, Frederik Schmitt, Julian Siber, Bernd Finkbeiner

Expand abstract

Training neural networks on NP-complete problems typically demands very large amounts of training data and often needs to be coupled with computationally expensive symbolic verifiers to ensure output correctness. In this paper, we present NeuRes, a neuro-symbolic approach to address both challenges for propositional satisfiability, being the quintessential NP-complete problem. By combining certificate-driven training and expert iteration, our model learns better representations than models trained for classification only, with a much higher data efficiency -- requiring orders of magnitude less training data. NeuRes employs propositional resolution as a proof system to generate proofs of unsatisfiability and to accelerate the process of finding satisfying truth assignments, exploring both possibilities in parallel. To realize this, we propose an attention-based architecture that autoregressively selects pairs of clauses from a dynamic formula embedding to derive new clauses. Furthermore, we employ expert iteration whereby model-generated proofs progressively replace longer teacher proofs as the new ground truth. This enables our model to reduce a dataset of proofs generated by an advanced solver by $\sim$$32$% after training on it with no extra guidance. This shows that NeuRes is not limited by the optimality of the teacher algorithm owing to its self-improving workflow. We show that our model achieves far better performance than NeuroSAT in terms of both correctly classified and proven instances.

Spotlight
Learning Where to Edit Vision Transformers

Yunqiao Yang, Long-Kai Huang, Shengzhuang Chen, Kede Ma, Ying Wei

Expand abstract

Model editing aims to data-efficiently correct predictive errors of large pre-trained models while ensuring generalization to neighboring failures and locality to minimize unintended effects on unrelated examples. While significant progress has been made in editing Transformer-based large language models, effective strategies for editing vision Transformers (ViTs) in computer vision remain largely untapped. In this paper, we take initial steps towards correcting predictive errors of ViTs, particularly those arising from subpopulation shifts. Taking a locate-then-edit approach, we first address the ``where-to-edit`` challenge by meta-learning a hypernetwork on CutMix-augmented data generated for editing reliability. This trained hypernetwork produces generalizable binary masks that identify a sparse subset of structured model parameters, responsive to real-world failure samples. Afterward, we solve the ``how-to-edit`` problem by simply fine-tuning the identified parameters using a variant of gradient descent to achieve successful edits. To validate our method, we construct an editing benchmark that introduces subpopulation shifts towards natural underrepresented images and AI-generated images, thereby revealing the limitations of pre-trained ViTs for object recognition. Our approach not only achieves superior performance on the proposed benchmark but also allows for adjustable trade-offs between generalization and locality. Our code is available at https://github.com/hustyyq/Where-to-Edit.

Poster
CodeRosetta: Pushing the Boundaries of Unsupervised Code Translation for Parallel Programming

Ali TehraniJamsaz, Arijit Bhattacharjee, Le Chen, Nesreen K. Ahmed, Amir Yazdanbakhsh, Ali Jannesari

Expand abstract

Automatic translation of programming languages has garnered renewed interest, driven by recent advancements in large language models (LLMs). Encoder-decoder transformer models, in particular, have shown promise in translating between different programming languages. However, translating between a language and its high-performance computing (HPC) extension remains underexplored due to inherent challenges like complex parallel semantics understanding. In this paper, we introduce CodeRosetta, an encoder-decoder transformer model explicitly designed for translating between programming languages and also their HPC extensions. CodeRosetta is evaluated on C++ to CUDA and Fortran to C++ translation. It employs a customized learning-based framework with tailored pretraining and training objectives that enable it to effectively capture code semantics and parallel structural nuances, allowing for bidirectional code translation. Our results show that CodeRosetta outperforms state-of-the-art baselines in C++ to CUDA translation by 2.9 BLEU and 1.72 CodeBLUE points while improving compilation accuracy by 6.05%. Compared to general closed-source LLMs, our proposed bidirectional learning-based method improves C++ to CUDA translation by 22.08 BLEU and 14.39 CodeBLUE with 2.75% higher compilation accuracy. Finally, CodeRosetta exhibits proficiency in Fortran to parallel C++ translation, marking it, to our knowledge, as the first encoder-decoder model for such a complex translation task, improving CodeBLEU at least by 4.63 points compared to closed-source LLMs and Open Code LLM.

Poster
DECRL: A Deep Evolutionary Clustering Jointed Temporal Knowledge Graph Representation Learning Approach

Qian Chen, Ling Chen

Expand abstract

Temporal Knowledge Graph (TKG) representation learning aims to map temporal evolving entities and relations to embedded representations in a continuous low-dimensional vector space. However, existing approaches cannot capture the temporal evolution of high-order correlations in TKGs. To this end, we propose a **D**eep **E**volutionary **C**lustering jointed temporal knowledge graph **R**epresentation **L**earning approach (**DECRL**). Specifically, a deep evolutionary clustering module is proposed to capture the temporal evolution of high-order correlations among entities. Furthermore, a cluster-aware unsupervised alignment mechanism is introduced to ensure the precise one-to-one alignment of soft overlapping clusters across timestamps, thereby maintaining the temporal smoothness of clusters. In addition, an implicit correlation encoder is introduced to capture latent correlations between any pair of clusters under the guidance of a global graph. Extensive experiments on seven real-world datasets demonstrate that DECRL achieves the state-of-the-art performances, outperforming the best baseline by an average of 9.53\%, 12.98\%, 10.42\%, and 14.68\% in MRR, Hits@1, Hits@3, and Hits@10, respectively.

Poster
Dissecting the Interplay of Attention Paths in a Statistical Mechanics Theory of Transformers

Lorenzo Tiberi, Francesca Mignacco, Kazuki Irie, Haim Sompolinsky

Expand abstract

Despite the remarkable empirical performance of Transformers, their theoretical understanding remains elusive. Here, we consider a deep multi-head self-attention network, that is closely related to Transformers yet analytically tractable. We develop a statistical mechanics theory of Bayesian learning in this model, deriving exact equations for the network's predictor statistics under the finite-width thermodynamic limit, i.e., $N,P\rightarrow\infty$, $P/N=\mathcal{O}(1)$, where $N$ is the network width and $P$ is the number of training examples. Our theory shows that the predictor statistics are expressed as a sum of independent kernels, each one pairing different "attention paths", defined as information pathways through different attention heads across layers. The kernels are weighted according to a "task-relevant kernel combination" mechanism that aligns the total kernel with the task labels. As a consequence, this interplay between attention paths enhances generalization performance. Experiments confirm our findings on both synthetic and real-world sequence classification tasks. Finally, our theory explicitly relates the kernel combination mechanism to properties of the learned weights, allowing for a qualitative transfer of its insights to models trained via gradient descent. As an illustration, we demonstrate an efficient size reduction of the network, by pruning those attention heads that are deemed less relevant by our theory.

Poster
Interventionally Consistent Surrogates for Complex Simulation Models

Joel Dyer, Nicholas George Bishop, Yorgos Felekis, Fabio Massimo Zennaro, Ani Calinescu, Theodoros Damoulas, Michael J. Wooldridge

Expand abstract

Large-scale simulation models of complex socio-technical systems provide decision-makers with high-fidelity testbeds in which policy interventions can be evaluated and _what-if_ scenarios explored. Unfortunately, the high computational cost of such models inhibits their widespread use in policy-making settings. Surrogate models can address these computational limitations, but to do so they must behave consistently with the simulator under interventions of interest. In this paper, we build upon recent developments in causal abstractions to develop a framework for learning interventionally consistent surrogate models for large-scale, complex simulation models. We provide theoretical results showing that our proposed approach induces surrogates to behave consistently with high probability with respect to the simulator across interventions of interest, facilitating rapid experimentation with policy interventions in complex systems. We further demonstrate with empirical studies that conventionally trained surrogates can misjudge the effect of interventions and misguide decision-makers towards suboptimal interventions, while surrogates trained for _interventional_ consistency with our method closely mimic the behaviour of the original simulator under interventions of interest.

Poster