ICML 2025 Papers

Data assimilation for nonlinear state space models (SSMs) is inherently challenging due to non-Gaussian posteriors. We propose Deep Bayesian Filtering (DBF), a novel approach to data assimilation in nonlinear SSMs. DBF introduces latent variables $h_t$ in addition to physical variables $z_t$, ensuring Gaussian posteriors by (i) constraining state transitions in the latent space to be linear and (ii) learning a Gaussian inverse observation operator $r(h_t|o_t)$. This structured posterior design enables analytical recursive computation, avoiding the accumulation of Monte Carlo sampling errors over time steps. DBF optimizes these operators and other latent SSM parameters by maximizing the evidence lower bound. Experiments demonstrate that DBF outperforms existing methods in scenarios with highly non-Gaussian posteriors.

Real-world time series are often governed by complex nonlinear dynamics. Understanding these underlying dynamics is crucial for precise future prediction. While deep learning has achieved major success in time series forecasting, many existing approaches do not explicitly model the dynamics. To bridge this gap, we introduce DeepEDM, a framework that integrates nonlinear dynamical systems modeling with deep neural networks. Inspired by empirical dynamic modeling (EDM) and rooted in Takens' theorem, DeepEDM presents a novel deep model that learns a latent space from time-delayed embeddings, and employs kernel regression to approximate the underlying dynamics, while leveraging efficient implementation of softmax attention and allowing for accurate prediction of future time steps. To evaluate our method, we conduct comprehensive experiments on synthetic data of nonlinear dynamical systems as well as real-world time series across domains. Our results show that DeepEDM is robust to input noise, and outperforms state-of-the-art methods in forecasting accuracy. Our code is available at: https://abrarmajeedi.github.io/deep_edm.

Optimal stopping is a fundamental problem in optimization with applications in risk management, finance, robotics, and machine learning. We extend the standard framework to a multi-agent setting, named multi-agent optimal stopping (MAOS), where agents cooperate to make optimal stopping decisions in a finite-space, discrete-time environment. Since solving MAOS becomes computationally prohibitive as the number of agents is very large, we study the mean-field optimal stopping (MFOS) problem, obtained as the number of agents tends to infinity. We establish that MFOS provides a good approximation to MAOS and prove a dynamic programming principle (DPP) based on mean-field control theory. We then propose two deep learning approaches: one that learns optimal stopping decisions by simulating full trajectories and another that leverages the DPP to compute the value function and to learn the optimal stopping rule using backward induction. Both methods train neural networks to approximate optimal stopping policies. We demonstrate the effectiveness and the scalability of our work through numerical experiments on 6 different problems in spatial dimension up to 300. To the best of our knowledge, this is the first work to formalize and computationally solve MFOS in discrete time and finite space, opening new directions for scalable MAOS methods.

We revisit the problem of selecting $k$-out-of-$n$ elements with the goal of optimizing an objective function, and ask whether it can be solved approximately with sublinear query complexity. For objective functions that are monotone submodular, [Li, Feldman, Kazemi, Karbasi, NeurIPS'22; Kuhnle, AISTATS'21] gave an $\Omega(n/k)$ query lower bound for approximating to within any constant factor. We strengthen their lower bound to a nearly tight $\tilde{\Omega}(n)$. This lower bound holds even for estimating the value of the optimal subset. When the objective function is additive, we prove that finding an approximately optimal subset still requires near-linear query complexity, but we can estimate the value of the optimal subset in $\tilde{O}(n/k)$ queries, and that this is tight up to polylog factors.

Text classification is a fundamental task in Natural Language Processing (NLP). Short text classification has recently captured much attention due to its increased amount from various sources with limited labels and its inherent challenges for its sparsity in words and semantics. Recent studies have adopted self-supervised contrastive learning across different representations to improve performance. However, most of the current models face several challenges. Firstly, the augmentation step might not be able to generate positive and negative samples that are semantically similar and dissimilar to the anchor respectively. Secondly, the text data could be enhanced with external auxiliary information that might introduce noise to the sparse text data. In addition, they are limited in capturing higher-order information such as group-wise interactions. In this work, we propose a novel document simplicial complex construction based on text data for a higher-order message-passing mechanism. We enhance the short text classification performance by contrasting the structural representation with the sequential representation generated by the transformer mechanism for improved outcomes and mitigated issues. The proposed framework, Contrastive Learning with Simplicial Convolutional Networks (C-SCN), leverages the expressive power of graph neural networks, models higher-order information beyond pair-wise relations and enriches features through contrastive learning. Experimental results on four benchmark datasets demonstrate the capability of C-SCN to outperform existing models in analysing sequential and complex short-text data.

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (**P**eptide **M**ass **D**eviation) and RMD (**R**esidual**M**ass **D**eviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models—those whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

Neural ordinary differential equations (NODEs) have demonstrated strong capabilities in modeling time series. However, existing NODE- based methods often focus solely on the surface-level dynamics derived from observed states, which limits their ability to capture more complex underlying behaviors. To overcome this challenge, we propose KoNODE, a Koopman-driven NODE framework that explicitly models the evolution of ODE parameters over time to encode deep-level information. KoNODE captures the essential yet simple intrinsic linear dynamics that govern the surface dynamics by employing Koopman operators. Our framework operates at three hierarchical levels: the observed state dynamics, the parameter dynamics, and the Koopman linear dynamics, representing the fundamental driving rules of the state dynamics. The proposed approach offers significant improvements in two critical time series tasks: long-term prediction (enabled by the simple linear dynamics) and generalization to new data (driven by the evolving ODE parameters). We validate KoNODE through experiments on synthetic data from complex dynamic systems and real-world datasets, demonstrating its effectiveness in practical scenarios.

Ensemble learning is a powerful approach for improving generalization under distribution shifts, but its effectiveness heavily depends on how individual models are combined. Existing methods often optimize ensemble weights based on validation data, which may not represent unseen test distributions, leading to suboptimal performance in out-of-distribution (OoD) settings. Inspired by Distributionally Robust Optimization (DRO), we propose Structure-informed Risk Minimization (SRM), a principled framework that learns robust ensemble weights without access to test data. Unlike standard DRO, which defines uncertainty sets based on divergence metrics alone, SRM incorporates structural information of training distributions, ensuring that the uncertainty set aligns with plausible real-world shifts. This approach mitigates the over-pessimism of traditional worst-case optimization while maintaining robustness. We introduce a computationally efficient optimization algorithm with theoretical guarantees and demonstrate that SRM achieves superior OoD generalization compared to existing ensemble combination strategies across diverse benchmarks. Code is available at: https://github.com/deep-real/SRM.

Scaling up inference-time compute has proven to be a valuable strategy in improving the performance of Large Language Models (LLMs) without fine-tuning. An important task that can benefit from additional inference-time compute is self-repair; given an initial flawed response or guess, the LLM corrects its own mistake and produces an improved response or fix. We leverage the in-context learning ability of LLMs to perform self-repair in the coding domain. The key contribution of our paper is an approach that synthesises and selects an ordered set of golden example pairs, or AuPairs, of these initial guesses and subsequent fixes for the corresponding problems. Each such AuPair is provided as a single in-context example at inference time to generate a repaired solution. For an inference-time compute budget of $N$ LLM calls per problem, $N$ AuPairs are used to generate $N$ repaired solutions, out of which the highest-scoring solution is the final answer. The underlying intuition is that if the LLM is given a different example of fixing an incorrect guess each time, it can subsequently generate a diverse set of repaired solutions. Our algorithm selects these AuPairs in a manner that maximises complementarity and usefulness. We demonstrate the results of our algorithm on 5 LLMs across 7 competitive programming datasets for the code repair task. Our algorithm yields a significant boost in performance compared to best-of-$N$ and self-repair, and also exhibits strong generalisation across datasets and models. Moreover, our approach shows stronger scaling with inference-time compute budget compared to baselines.

Large language models (LLMs) acquire a breadth of information across various domains. However, their computational complexity, cost, and lack of transparency often hinder their direct application for predictive tasks where privacy and interpretability are paramount. In fields such as healthcare, biology, and finance, specialised and interpretable linear models still hold considerable value. In such domains, labelled data may be scarce or expensive to obtain. Well-specified prior distributions over model parameters can reduce the sample complexity of learning through Bayesian inference; however, eliciting expert priors can be time-consuming. We therefore introduce AutoElicit to extract knowledge from LLMs and construct priors for predictive models. We show these priors are informative and can be refined using natural language. We perform a careful study contrasting AutoElicit with in-context learning and demonstrate how to perform model selection between the two methods. We find that AutoElicit yields priors that can substantially reduce error over uninformative priors, using fewer labels, and consistently outperform in-context learning. We show that AutoElicit saves over 6 months of labelling effort when building a new predictive model for urinary tract infections from sensor recordings of people living with dementia.

Time series with missing or irregularly sampled data are a persistent challenge in machine learning. Many methods operate on the frequency-domain, relying on the Fast Fourier Transform (FFT) which assumes uniform sampling, therefore requiring prior interpolation that can distort the spectra. To address this limitation, we introduce a differentiable Lomb--Scargle layer that enables a reliable computation of the power spectrum of irregularly sampled data. We integrate this layer into a novel score-based diffusion model (LSCD) for time series imputation conditioned on the entire signal spectrum. Experiments on synthetic and real-world benchmarks demonstrate that our method recovers missing data more accurately than purely time-domain baselines, while simultaneously producing consistent frequency estimates. Crucially, our method can be easily integrated into learning frameworks, enabling broader adoption of spectral guidance in machine learning approaches involving incomplete or irregular data.

Expert parallelism has emerged as a key strategy for distributing the computational workload of sparsely-gated mixture-of-experts (MoE) models across multiple devices, enabling the processing of increasingly large-scale models. However, the All-to-All communication inherent to expert parallelism poses a significant bottleneck, limiting the efficiency of MoE models. Although existing optimization methods partially mitigate this issue, they remain constrained by the sequential dependency between communication and computation operations. To address this challenge, we propose ScMoE, a novel shortcut-connected MoE architecture integrated with an overlapping parallelization strategy. ScMoE decouples communication from its conventional sequential ordering, enabling up to 100\% overlap with computation. Compared to the prevalent top-2 MoE baseline, ScMoE achieves speedups of $1.49\times$ in training and $1.82\times$ in inference. Moreover, our experiments and analyses indicate that ScMoE not only achieves comparable but in some instances surpasses the model quality of existing approaches.

In this paper, we clarify the effect of noise on common spectrally motivated algorithms such as Diffusion Maps (DM) for dimension reduction. Empirically, these methods are much more robust to noise than current work suggests. Specifically, existing consistency results require that either the noise amplitude or dimensionality must vary with the sample size $n$. We provide new theoretical results demonstrating that low-frequency eigenpairs reliably capture the geometry of the underlying manifold under a constant noise level, up to a dimension independent threshold $O(r^{-2})$, where $r$ is the noise amplitude. Our results rely on a decomposition of the manifold Laplacian in the Sasaki metric, a technique not used before in this area, to our knowledge. We experimentally validate our theoretical predictions. Additionally, we observe similar robust behavior for other manifold learning algorithms which are not based on computing the Laplacian, namely LTSA and VAE.

In this paper, we propose an improved online confidence bound for multinomial logistic (MNL) models and apply this result to MNL bandits, achieving variance-dependent optimal regret. Recently, Lee & Oh (2024) established an online confidence bound for MNL models and achieved nearly minimax-optimal regret in MNL bandits. However, their results still depend on the norm-boundedness of the unknown parameter $B$ and the maximum size of possible outcomes $K$. To address this, we first derive an online confidence bound of $\mathcal{O} (\sqrt{d \log t} + B )$, which is a significant improvement over the previous bound of $\mathcal{O} (B \sqrt{d} \log t \log K )$ (Lee & Oh, 2024). This is mainly achieved by establishing tighter self-concordant properties of the MNL loss and introducing a novel intermediary term to bound the estimation error. Using this new online confidence bound, we propose a constant-time algorithm, **OFU-MNL++**, which achieves a variance-dependent regret bound of $\mathcal{O} \Big( d \log T \sqrt{ \sum_{t=1}^T \sigma_t^2 } \Big) $ for sufficiently large $T$, where $\sigma_t^2$ denotes the variance of the rewards at round $t$, $d$ is the dimension of the contexts, and $T$ is the total number of rounds. Furthermore, we introduce an Maximum Likelihood Estimation (MLE)-based algorithm that achieves an anytime, **OFU-M$^2$NL**, $\operatorname{poly}(B)$-free regret of $\mathcal{O} \Big( d \log (BT) \sqrt{ \sum_{t=1}^T \sigma_t^2 } \Big) $.

The memory requirements of machine learning (ML) models has been growing quickly. However, the memory capacity of GPUs has not kept pace. Despite significant research on reducing the memory usage of ML models, the larger models do not fit in a single device. A popular solution to the memory capacity issue is to use multiple devices in parallel. In this paper, we focus on a particular form of parallelism called pipelining, as it offers a good balance between cost and performance for many ML models. We present Pfeife, the first tool that integrates with PyTorch to provide automatic pipelining of ML models. Pfeife intercepts the execution of models and parallelizes them transparently, requiring no manual work. We show that Pfeife can execute large models that would otherwise not run due to not fitting in a single device. Moreover, Pfeife can pipeline non-sequential models such as Stable Diffusion, which are not supported by existing pipelining parallelism tools. Pfeife outperforms state-of-the-art tools by up to 22%.

Leveraging long contexts is crucial for advanced AI systems, but attention computation poses a scalability challenge. While scaled dot-product attention (SDPA) exhibits token sparsity, i.e. only a few pivotal tokens significantly contribute to output, exploiting this sparsity remains challenging. Existing methods either suffer from quality degradation or require substantial additional resources. We show that identifying pivotal tokens is a Maximum Inner Product Search (MIPS) problem. However, existing MIPS solutions are not well-suited for SDPA, as they are not GPU-friendly and often underperform due to the separated query and key distributions. This paper introduces HashAttention, framing pivotal token identification as a recommendation problem. Given a query, HashAttention encodes keys and queries in Hamming space, capturing the required semantic similarity, using learned mapping functions. HashAttention efficiently identifies pivotal tokens for a given query using bitwise operations and computes attention using only these tokens, improving the overall attention efficiency. Trained on generic data, HashAttention reduces tokens used by up to $16\times$ with minimal quality loss, requiring only 32 bits of auxiliary memory per token. Sparsity can be further improved to $32\times$ through task-specific fine-tuning. On A100 GPU, at $32\times$ sparsity, incorporating HashAttention reduces attention latency by up to $4.3\times$ in GPT-FAST and $2.54\times$ in FlashDecode, and achieves up to $3.12\times$ higher throughput for GPT-FAST.

Arena-based evaluation is a fundamental yet significant evaluation paradigm for modern AI models, especially large language models (LLMs). Existing framework based on ELO rating system suffers from the inevitable instability problem due to ranking inconsistency and the lack of attention to the varying abilities of annotators. In this paper, we introduce a novel stable arena framework to address these issues by enhancing the ELO Rating System. Specifically, we replace the iterative update method with a Maximum Likelihood Estimation (MLE) approach, m-ELO, and provide theoretical proof of the consistency and stability of the MLE approach for model ranking. Additionally, we proposed the am-ELO, which modify the Elo Rating’s probability function to incorporate annotator abilities, enabling the simultaneous estimation of model scores and annotator reliability. Experiments demonstrate that this method ensures stability, proving that this framework offers a more robust, accurate, and stable evaluation method for LLMs.

Recently, forecasting future abnormal events has emerged as an important scenario to tackle realworld necessities. However, the solution of predicting specific future time points when anomalies will occur, known as Anomaly Prediction (AP), remains under-explored. Existing methods dealing with time series data fail in AP, focusing only on immediate anomalies or failing to provide precise predictions for future anomalies. To address AP, we propose a novel framework called Anomaly to Prompt (A2P), comprised of Anomaly-Aware Forecasting (AAF) and Synthetic Anomaly Prompting (SAP). To enable the forecasting model to forecast abnormal time points, we adopt a strategy to learn the relationships of anomalies. For the robust detection of anomalies, our proposed SAP introduces a learnable Anomaly Prompt Pool (APP) that simulates diverse anomaly patterns using signal-adaptive prompt. Comprehensive experiments on multiple real-world datasets demonstrate the superiority of A2P over state-of-the-art methods, showcasing its ability to predict future anomalies.

Latent space interpolations are a powerful tool for navigating deep generative models in applied settings. An example is single-cell RNA sequencing, where existing methods model cellular state transitions as latent space interpolations with variational autoencoders, often assuming linear shifts and Euclidean geometry. However, unless explicitly enforced, linear interpolations in the latent space may not correspond to geodesic paths on the data manifold, limiting methods that assume Euclidean geometry in the data representations. We introduce FlatVI, a novel training framework that regularises the latent manifold of discrete-likelihood variational autoencoders towards Euclidean geometry, specifically tailored for modelling single-cell count data. By encouraging straight lines in the latent space to approximate geodesic interpolations on the decoded single-cell manifold, FlatVI enhances compatibility with downstream approaches that assume Euclidean latent geometry. Experiments on synthetic data support the theoretical soundness of our approach, while applications to time-resolved single-cell RNA sequencing data demonstrate improved trajectory reconstruction and manifold interpolation.