NeurIPS 2024 Papers

Road network representation learning aims to learn compressed and effective vectorized representations for road segments that are applicable to numerous tasks. In this paper, we identify the limitations of existing methods, particularly their overemphasis on the distance effect as outlined in the First Law of Geography. In response, we propose to endow road network representation with the principles of the recent Third Law of Geography. To this end, we propose a novel graph contrastive learning framework that employs geographic configuration-aware graph augmentation and spectral negative sampling, ensuring that road segments with similar geographic configurations yield similar representations, and vice versa, aligning with the principles stated in the Third Law. The framework further fuses the Third Law with the First Law through a dual contrastive learning objective to effectively balance the implications of both laws. We evaluate our framework on two real-world datasets across three downstream tasks. The results show that the integration of the Third Law significantly improves the performance of road segment representations in downstream tasks.

Different camera sensors have different noise patterns, and thus an image denoising model trained on one sensor often does not generalize well to a different sensor. One plausible solution is to collect a large dataset for each sensor for training or fine-tuning, which is inevitably time-consuming. To address this cross-domain challenge, we present a novel adaptive domain learning (ADL) scheme for cross-domain RAW image denoising by utilizing existing data from different sensors (source domain) plus a small amount of data from the new sensor (target domain). The ADL training scheme automatically removes the data in the source domain that are harmful to fine-tuning a model for the target domain (some data are harmful as adding them during training lowers the performance due to domain gaps). Also, we introduce a modulation module to adopt sensor-specific information (sensor type and ISO) to understand input data for image denoising. We conduct extensive experiments on public datasets with various smartphone and DSLR cameras, which show our proposed model outperforms prior work on cross-domain image denoising, given a small amount of image data from the target domain sensor.

Editing biological sequences has extensive applications in synthetic biology and medicine, such as designing regulatory elements for nucleic-acid therapeutics and treating genetic disorders. The primary objective in biological-sequence editing is to determine the optimal modifications to a sequence which augment certain biological properties while adhering to a minimal number of alterations to ensure predictability and potentially support safety. In this paper, we propose GFNSeqEditor, a novel biological-sequence editing algorithm which builds on the recently proposed area of generative flow networks (GFlowNets). Our proposed GFNSeqEditor identifies elements within a starting seed sequence that may compromise a desired biological property. Then, using a learned stochastic policy, the algorithm makes edits at these identified locations, offering diverse modifications for each sequence to enhance the desired property. The number of edits can be regulated through specific hyperparameters. We conducted extensive experiments on a range of real-world datasets and biological applications, and our results underscore the superior performance of our proposed algorithm compared to existing state-of-the-art sequence editing methods.

Current test-time adaptation (TTA) approaches aim to adapt a machine learning model to environments that change continuously. Yet, it is unclear whether TTA methods can maintain their adaptability over prolonged periods. To answer this question, we introduce a diagnostic setting - **recurring TTA** where environments not only change but also recur over time, creating an extensive data stream. This setting allows us to examine the error accumulation of TTA models, in the most basic scenario, when they are regularly exposed to previous testing environments. Furthermore, we simulate a TTA process on a simple yet representative $\epsilon$-**perturbed Gaussian Mixture Model Classifier**, deriving theoretical insights into the dataset- and algorithm-dependent factors contributing to gradual performance degradation. Our investigation leads us to propose **persistent TTA (PeTTA)**, which senses when the model is diverging towards collapse and adjusts the adaptation strategy, striking a balance between the dual objectives of adaptation and model collapse prevention. The supreme stability of PeTTA over existing approaches, in the face of lifelong TTA scenarios, has been demonstrated over comprehensive experiments on various benchmarks. Our project page is available at [https://hthieu166.github.io/petta](https://hthieu166.github.io/petta).

In long-term time series forecasting (LTSF) tasks, an increasing number of works have acknowledged that discrete time series originate from continuous dynamic systems and have attempted to model their underlying dynamics. Recognizing the chaotic nature of real-world data, our model, Attraos, incorporates chaos theory into LTSF, perceiving real-world time series as low-dimensional observations from unknown high-dimensional chaotic dynamical systems. Under the concept of attractor invariance, Attraos utilizes non-parametric Phase Space Reconstruction embedding along with a novel multi-resolution dynamic memory unit to memorize historical dynamical structures, and evolves by a frequency-enhanced local evolution strategy. Detailed theoretical analysis and abundant empirical evidence consistently show that Attraos outperforms various LTSF methods on mainstream LTSF datasets and chaotic datasets with only one-twelfth of the parameters compared to PatchTST.

Real-world machine learning systems often encounter model performance degradation due to distributional shifts in the underlying data generating process (DGP). Existing approaches to addressing shifts, such as concept drift adaptation, are limited by their *reason-agnostic* nature. By choosing from a pre-defined set of actions, such methods implicitly assume that the causes of model degradation are irrelevant to what actions should be taken, limiting their ability to select appropriate adaptations. In this paper, we propose an alternative paradigm to overcome these limitations, called *self-healing machine learning* (SHML). Contrary to previous approaches, SHML autonomously diagnoses the reason for degradation and proposes diagnosis-based corrective actions. We formalize SHML as an optimization problem over a space of adaptation actions to minimize the expected risk under the shifted DGP. We introduce a theoretical framework for self-healing systems and build an agentic self-healing solution *$\mathcal{H}$-LLM* which uses large language models to perform self-diagnosis by reasoning about the structure underlying the DGP, and self-adaptation by proposing and evaluating corrective actions. Empirically, we analyze different components of *$\mathcal{H}$-LLM* to understand *why* and *when* it works, demonstrating the potential of self-healing ML.

Bayesian Optimization (BO) is widely used for optimising black-box functions but requires us to specify the length scale hyperparameter, which defines the smoothness of the functions the optimizer will consider. Most current BO algorithms choose this hyperparameter by maximizing the marginal likelihood of the observed data, albeit risking misspecification if the objective function is less smooth in regions we have not yet explored. The only prior solution addressing this problem with theoretical guarantees was A-GP-UCB, proposed by Berkenkamp et al. (2019). This algorithm progressively decreases the length scale, expanding the class of functions considered by the optimizer. However, A-GP-UCB lacks a stopping mechanism, leading to over-exploration and slow convergence. To overcome this, we introduce Length scale Balancing (LB) - a novel approach, aggregating multiple base surrogate models with varying length scales. LB intermittently adds smaller length scale candidate values while retaining longer scales, balancing exploration and exploitation. We formally derive a cumulative regret bound of LB and compare it with the regret of an oracle BO algorithm using the optimal length scale. Denoting the factor by which the regret bound of A-GP-UCB was away from oracle as $g(T)$, we show that LB is only $\log g(T)$ away from oracle regret. We also empirically evaluate our algorithm on synthetic and real-world benchmarks and show it outperforms A-GP-UCB and maximum likelihood estimation.

Agda is a dependently-typed programming language and a proof assistant, pivotal in proof formalization and programming language theory. This paper extends the Agda ecosystem into machine learning territory, and, vice versa, makes Agda-related resources available to machine learning practitioners. We introduce and release a novel dataset of Agda program-proofs that is elaborate and extensive enough to support various machine learning applications -- the first of its kind. Leveraging the dataset's ultra-high resolution, which details proof states at the sub-type level, we propose a novel neural architecture targeted at faithfully representing dependently-typed programs on the basis of structural rather than nominal principles. We instantiate and evaluate our architecture in a premise selection setup, where it achieves promising initial results, surpassing strong baselines.

Across scientific domains, generating new models or optimizing existing ones while meeting specific criteria is crucial. Traditional machine learning frameworks for guided design use a generative model and a surrogate model (discriminator), requiring large datasets. However, real-world scientific applications often have limited data and complex landscapes, making data-hungry models inefficient or impractical. We propose a new framework, PropEn, inspired by ``matching'', which enables implicit guidance without training a discriminator. By matching each sample with a similar one that has a better property value, we create a larger training dataset that inherently indicates the direction of improvement. Matching, combined with an encoder-decoder architecture, forms a domain-agnostic generative framework for property enhancement. We show that training with a matched dataset approximates the gradient of the property of interest while remaining within the data distribution, allowing efficient design optimization. Extensive evaluations in toy problems and scientific applications, such as therapeutic protein design and airfoil optimization, demonstrate PropEn's advantages over common baselines. Notably, the protein design results are validated with wet lab experiments, confirming the competitiveness and effectiveness of our approach. Our code is available at https://github.com/prescient-design/propen.

The joint prediction of continuous fields and statistical estimation of the underlying discrete parameters is a common problem for many physical systems, governed by PDEs. Hitherto, it has been separately addressed by employing operator learning surrogates for field prediction while using simulation-based inference (and its variants) for statistical parameter determination. Here, we argue that solving both problems within the same framework can lead to consistent gains in accuracy and robustness. To this end, we propose a novel and flexible formulation of the operator learning problem that jointly predicts continuous quantities and infers distributions of discrete parameters, thereby amortizing the cost of both the inverse and the surrogate models to a joint pre-training step. We present the capabilities of the proposed methodology for predicting continuous and discrete biomarkers in full-body haemodynamics simulations under different levels of missing information. We also consider a test case for atmospheric large-eddy simulation of a two-dimensional dry cold bubble, where we infer both continuous time-series and information about the system's conditions. We present comparisons against different baselines to showcase significantly increased accuracy in both the inverse and the surrogate tasks.

Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric deep learning (GDL), have demonstrated significant efficiency and accuracy advantages over traditional sampling methods. Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and challenges in predicting physically valid structures exist. To accommodate various docking settings and achieve accurate, efficient, and physically reliable docking, we propose a novel two-stage docking framework, DeltaDock, consisting of pocket prediction and site-specific docking. We innovatively reframe the pocket prediction task as a pocket-ligand alignment problem rather than direct prediction in the first stage. Then we follow a bi-level coarse-to-fine iterative refinement process to perform site-specific docking. Comprehensive experiments demonstrate the superior performance of DeltaDock. Notably, in the blind docking setting, DeltaDock achieves a 31\% relative improvement over the docking success rate compared with the previous state-of-the-art GDL model DiffDock. With the consideration of physical validity, this improvement increases to about 300\%.

We consider the problem of active learning for global sensitivity analysis of expensive black-box functions. Our aim is to efficiently learn the importance of different input variables, e.g., in vehicle safety experimentation, we study the impact of the thickness of various components on safety objectives. Since function evaluations are expensive, we use active learning to prioritize experimental resources where they yield the most value. We propose novel active learning acquisition functions that directly target key quantities of derivative-based global sensitivity measures (DGSMs) under Gaussian process surrogate models. We showcase the first application of active learning directly to DGSMs, and develop tractable uncertainty reduction and information gain acquisition functions for these measures. Through comprehensive evaluation on synthetic and real-world problems, our study demonstrates how these active learning acquisition strategies substantially enhance the sample efficiency of DGSM estimation, particularly with limited evaluation budgets. Our work paves the way for more efficient and accurate sensitivity analysis in various scientific and engineering applications.

We consider the problem of $K$-armed dueling bandits in the stochastic setting, under the sole assumption of the existence of a Condorcet winner. We study the objective of weak regret minimization, where the learner doesn't incur any loss if one of the selected arms is a Condorcet winner—unlike strong regret minimization, where the learner has to select the Condorcet winner twice to incur no loss. This study is particularly motivated by practical scenarios such as content recommendation and online advertising, where frequently only one optimal choice out of the two presented options is necessary to achieve user satisfaction or engagement. This necessitates the development of strategies with more exploration. While existing literature introduces strategies for weak regret with constant bounds (that do not depend on the time horizon), the optimality of these strategies remains an unresolved question. This problem turns out to be really challenging as the optimal regret should heavily depend on the full structure of the dueling problem at hand, and in particular on whether the Condorcet winner has a large minimal optimality gap with the other arms. Our contribution is threefold: first, when said optimality gap is not negligible compared to other properties of the gap matrix, we characterize the optimal budget as a function of $K$ and the optimality gap. Second, we propose a new strategy called \wrtinf that achieves this optimal regret and improves over the state-of-the-art both in $K$ and the optimality gap. When the optimality gap is negligible, we propose another algorithm that outperforms our first algorithm, highlighting the subtlety of this dueling bandit problem. Finally, we provide numerical simulations to assess our theoretical findings.

Mobility impairment caused by limb loss, aging, stroke, and other movement deficiencies is a significant challenge faced by millions of individuals worldwide. Advanced assistive technologies, such as prostheses and orthoses, have the potential to greatly improve the quality of life for such individuals. A critical component in the design of these technologies is the accurate forecasting of reference joint motion for impaired limbs, which is hindered by the scarcity of joint locomotion data available for these patients. To address this, we propose ReMAP, a novel model repurposing strategy that leverages deep learning's reprogramming property, incorporating network inversion principles and retrieval-augmented mapping. Our approach adapts models originally designed for able-bodied individuals to forecast joint motion in limb-impaired patients without altering model parameters. We demonstrate the efficacy of ReMAP through extensive empirical studies on data from below-knee amputated patients, showcasing significant improvements over traditional transfer learning and fine-tuning methods. These findings have significant implications for advancing assistive technology and mobility for patients with amputations, stroke, or aging.

We introduce a machine learning approach to model checking temporal logic, with application to formal hardware verification. Model checking answers the question of whether every execution of a given system satisfies a desired temporal logic specification. Unlike testing, model checking provides formal guarantees. Its application is expected standard in silicon design and the EDA industry has invested decades into the development of performant symbolic model checking algorithms. Our new approach combines machine learning and symbolic reasoning by using neural networks as formal proof certificates for linear temporal logic. We train our neural certificates from randomly generated executions of the system and we then symbolically check their validity using satisfiability solving which, upon the affirmative answer, establishes that the system provably satisfies the specification. We leverage the expressive power of neural networks to represent proof certificates as well as the fact that checking a certificate is much simpler than finding one. As a result, our machine learning procedure for model checking is entirely unsupervised, formally sound, and practically effective. We experimentally demonstrate that our method outperforms the state-of-the-art academic and commercial model checkers on a set of standard hardware designs written in SystemVerilog.

Large language models (LLMs) have demonstrated notable potential in conducting complex tasks and are increasingly utilized in various financial applications. However, high-quality sequential financial investment decision-making remains challenging. These tasks require multiple interactions with a volatile environment for every decision, demanding sufficient intelligence to maximize returns and manage risks. Although LLMs have been used to develop agent systems that surpass human teams and yield impressive investment returns, opportunities to enhance multi-source information synthesis and optimize decision-making outcomes through timely experience refinement remain unexplored. Here, we introduce FinCon, an LLM-based multi-agent framework tailored for diverse financial tasks. Inspired by effective real-world investment firm organizational structures, FinCon utilizes a manager-analyst communication hierarchy. This structure allows for synchronized cross-functional agent collaboration towards unified goals through natural language interactions and equips each agent with greater memory capacity than humans. Additionally, a risk-control component in FinCon enhances decision quality by episodically initiating a self-critiquing mechanism to update systematic investment beliefs. The conceptualized beliefs serve as verbal reinforcement for the future agent’s behavior and can be selectively propagated to the appropriate node that requires knowledge updates. This feature significantly improves performance while reducing unnecessary peer-to-peer communication costs. Moreover, FinCon demonstrates strong generalization capabilities in various financial tasks, including stock trading and portfolio management.

Single-stage neural combinatorial optimization solvers have achieved near-optimal results on various small-scale combinatorial optimization (CO) problems without requiring expert knowledge. However, these solvers exhibit significant performance degradation when applied to large-scale CO problems. Recently, two-stage neural methods motivated by divide-and-conquer strategies have shown efficiency in addressing large-scale CO problems. Nevertheless, the performance of these methods highly relies on problem-specific heuristics in either the dividing or the conquering procedure, which limits their applicability to general CO problems. Moreover, these methods employ separate training schemes and ignore the interdependencies between the dividing and conquering strategies, often leading to sub-optimal solutions. To tackle these drawbacks, this article develops a unified neural divide-and-conquer framework (i.e., UDC) for solving general large-scale CO problems. UDC offers a Divide-Conquer-Reunion (DCR) training method to eliminate the negative impact of a sub-optimal dividing policy. Employing a high-efficiency Graph Neural Network (GNN) for global instance dividing and a fixed-length sub-path solver for conquering divided sub-problems, the proposed UDC framework demonstrates extensive applicability, achieving superior performance in 10 representative large-scale CO problems. The code is available at https://github.com/CIAM-Group/NCO_code/tree/main/single_objective/UDC-Large-scale-CO-master

The large communication and computation overhead of federated learning (FL) is one of the main challenges facing its practical deployment over resource-constrained clients and systems. In this work, SpaFL: a communication-efficient FL framework is proposed to optimize sparse model structures with low computational overhead. In SpaFL, a trainable threshold is defined for each filter/neuron to prune its all connected parameters, thereby leading to structured sparsity. To optimize the pruning process itself, only thresholds are communicated between a server and clients instead of parameters, thereby learning how to prune. Further, global thresholds are used to update model parameters by extracting aggregated parameter importance. The generalization bound of SpaFL is also derived, thereby proving key insights on the relation between sparsity and performance. Experimental results show that SpaFL improves accuracy while requiring much less communication and computing resources compared to sparse baselines. The code is available at https://github.com/news-vt/SpaFL_NeruIPS_2024

State-of-the-art (SOTA) semi-supervised learning techniques, such as FixMatch and it's variants, have demonstrated impressive performance in classification tasks. However, these methods are not directly applicable to regression tasks. In this paper, we present RankUp, a simple yet effective approach that adapts existing semi-supervised classification techniques to enhance the performance of regression tasks. RankUp achieves this by converting the original regression task into a ranking problem and training it concurrently with the original regression objective. This auxiliary ranking classifier outputs a classification result, thus enabling integration with existing semi-supervised classification methods. Moreover, we introduce regression distribution alignment (RDA), a complementary technique that further enhances RankUp's performance by refining pseudo-labels through distribution alignment. Despite its simplicity, RankUp, with or without RDA, achieves SOTA results in across a range of regression benchmarks, including computer vision, audio, and natural language processing tasks. Our code and log data are open-sourced at [https://github.com/pm25/semi-supervised-regression](https://github.com/pm25/semi-supervised-regression).