NeurIPS 2025 Papers

Conference on Neural Information Processing Systems

Decision breakdown

5,812papers

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

  • Oral
    931.6%
  • Spotlight
    73912.7%
  • Poster
    4,98085.7%

Browse all papers

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models

Charles W. J. Pugh, Paulina G. Nuñez-Valencia, Mafalda Dias, Jonathan Frazer

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Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biology. In the zero-shot setting, variant impact is estimated by comparing the likelihoods of sequences, under the assumption that likelihood serves as a proxy for fitness. However, this assumption often breaks down in practice: sequence likelihood reflects not only evolutionary fitness constraints, but also phylogenetic structure and sampling biases, especially as model capacity increases. We introduce Likelihood-Fitness Bridging (LFB), a simple and general strategy that improves variant effect prediction by averaging model scores across sequences subject to similar selective pressures. Assuming an Ornstein-Uhlenbeck model of evolution, LFB can be viewed as a way to marginalize the effects of genetic drift, although its benefits appear to extend more broadly. LFB applies to existing protein and genomic language models without requiring retraining, and incurs only modest computational overhead. Evaluated on large-scale deep mutational scans and clinical benchmarks, LFB consistently improves predictive performance across model families and sizes. Notably, it reverses the performance plateau observed in larger protein language models, making the largest models the most accurate when combined with LFB. These results suggest that accounting for phylogenetic and sampling biases is essential to realizing the full potential of large sequence models in variant effect prediction.

Poster
Estimation of Treatment Effects in Extreme and Unobserved Data

Jiyuan Tan, Vasilis Syrgkanis, Jose Blanchet

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Causal effect estimation seeks to determine the impact of an intervention from observational data. However, the existing causal inference literature primarily addresses treatment effects on frequently occurring events. But what if we are interested in estimating the effects of a policy intervention whose benefits, while potentially important, can only be observed and measured in rare yet impactful events, such as extreme climate events? The standard causal inference methodology is not designed for this type of inference since the events of interest may be scarce in the observed data and some degree of extrapolation is necessary. Extreme Value Theory (EVT) provides methodologies for analyzing statistical phenomena in such extreme regimes. We introduce a novel framework for assessing treatment effects in extreme data to capture the causal effect at the occurrence of rare events of interest. In particular, we employ the theory of multivariate regular variation to model extremities. We develop a consistent estimator for extreme treatment effects and present a rigorous non-asymptotic analysis of its performance. We illustrate the performance of our estimator using both synthetic and semi-synthetic data.

Poster
It’s Hard to Be Normal: The Impact of Noise on Structure-agnostic Estimation

Jikai Jin, Lester Mackey, Vasilis Syrgkanis

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Structure-agnostic causal inference studies the statistical limits of treatment effect estimation, when given access to black-box ML models that estimate nuisance components of the data generating process, such as estimates of the outcome regression and the treatment propensity. Here, we find that the answer depends in a surprising way on the distribution of the treatment noise. Focusing on the partially linear outcome model of \citet{robinson1988root}, we first show that the widely adopted double machine learning (DML) estimator is minimax rate-optimal for Gaussian treatment noise, resolving an open problem of \citet{mackey2018orthogonal}. Meanwhile, for independent non-Gaussian treatment noise, we show that DML is always suboptimal by constructing new practical procedures with higher-order robustness to nuisance errors. These *ACE* procedures use structure-agnostic cumulant estimators to achieve $r$-th order insensitivity to nuisance errors whenever the $(r+1)$-st treatment cumulant is non-zero. We complement these core results with novel minimax guarantees for binary treatments in the partially linear outcome model. Finally, using synthetic demand estimation experiments, we demonstrate the practical benefits of our higher-order robust estimators.

Poster
Born a Transformer -- Always a Transformer? On the Effect of Pretraining on Architectural Abilities

Mayank Jobanputra, Yana Veitsman, Yash Sarrof, Aleksandra Bakalova, Vera Demberg, Ellie Pavlick, Michael Hahn

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Transformers have theoretical limitations in modeling certain sequence-to-sequence tasks, yet it remains largely unclear if these limitations play a role in large-scale pretrained LLMs, or whether LLMs might effectively overcome these constraints in practice due to the scale of both the models themselves and their pretraining data. We explore how these architectural constraints manifest after pretraining by studying a family of *retrieval* and *copying* tasks inspired by Liu et al. [2024a]. We use a recently proposed framework for studying length generalization [Huang et al., 2025] to provide guarantees for each of our settings. Empirically, we observe an *induction-versus-anti-induction asymmetry*, where pretrained models are better at retrieving tokens to the right (induction) rather than the left (anti-induction) of a query token. This asymmetry disappears upon targeted fine-tuning if length-generalization is guaranteed by theory. Mechanistic analysis reveals that this asymmetry is connected to the differences in the strength of induction versus anti-induction circuits within pretrained transformers. We validate our findings through practical experiments on real-world tasks demonstrating reliability risks. Our results highlight that pretraining selectively enhances certain transformer capabilities, but does not overcome fundamental length-generalization limits.

Poster
Neural Mutual Information Estimation with Vector Copulas

Yanzhi Chen, Zijing Ou, Adrian Weller, Michael U. Gutmann

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Estimating mutual information (MI) is a fundamental task in data science and machine learning. Existing estimators mainly rely on either highly flexible models (e.g., neural networks), which require large amounts of data, or overly simplified models (e.g., Gaussian copula), which fail to capture complex distributions. Drawing upon recent vector copula theory, we propose a principled interpolation between these two extremes to achieve a better trade-off between complexity and capacity. Experiments on state-of-the-art synthetic benchmarks and real-world data with diverse modalities demonstrate the advantages of the proposed method.

Poster
Beyond the Average: Distributional Causal Inference under Imperfect Compliance

Undral Byambadalai, Tomu Hirata, Tatsushi Oka, Shota Yasui

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We study the estimation of distributional treatment effects in randomized experiments with imperfect compliance. When participants do not adhere to their assigned treatments, we leverage treatment assignment as an instrumental variable to identify the local distributional treatment effect—the difference in outcome distributions between treatment and control groups for the subpopulation of compliers. We propose a regression-adjusted estimator based on a distribution regression framework with Neyman-orthogonal moment conditions, enabling robustness and flexibility with high-dimensional covariates. Our approach accommodates continuous, discrete, and mixed discrete-continuous outcomes, and applies under a broad class of covariate-adaptive randomization schemes, including stratified block designs and simple random sampling. We derive the estimator’s asymptotic distribution and show that it achieves the semiparametric efficiency bound. Simulation results demonstrate favorable finite-sample performance, and we demonstrate the method’s practical relevance in an application to the Oregon Health Insurance Experiment.

Poster
Orthogonal Survival Learners for Estimating Heterogeneous Treatment Effects from Time-to-Event Data

Dennis Frauen, Maresa Schröder, Konstantin Hess, Stefan Feuerriegel

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Estimating heterogeneous treatment effects (HTEs) is crucial for personalized decision-making. However, this task is challenging in survival analysis, which includes time-to-event data with censored outcomes (e.g., due to study dropout). In this paper, we propose a toolbox of orthogonal survival learners to estimate HTEs from time-to-event data under censoring. Our learners have three main advantages: (i) we show that learners from our toolbox are guaranteed to be orthogonal and thus robust with respect to nuisance estimation errors; (ii) our toolbox allows for incorporating a custom weighting function, which can lead to robustness against different types of low overlap, and (iii) our learners are \emph{model-agnostic} (i.e., they can be combined with arbitrary machine learning models). We instantiate the learners from our toolbox using several weighting functions and, as a result, propose various neural orthogonal survival learners. Some of these coincide with existing survival learners (including survival versions of the DR- and R-learner), while others are novel and further robust w.r.t. low overlap regimes specific to the survival setting (i.e., survival overlap and censoring overlap). We then empirically verify the effectiveness of our learners for HTE estimation in different low-overlap regimes through numerical experiments. In sum, we provide practitioners with a large toolbox of learners that can be used for randomized and observational studies with censored time-to-event data.

Poster
On Minimax Estimation of Parameters in Softmax-Contaminated Mixture of Experts

Fanqi Yan, Huy Nguyen, Le Quang Dung, Pedram Akbarian, Nhat Ho, Alessandro Rinaldo

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The softmax-contaminated mixture of experts (MoE) model is deployed when a large-scale pre-trained model, which plays the role of a fixed expert, is fine-tuned for learning downstream tasks by including a new contamination part, or prompt, functioning as a new, trainable expert. Despite its popularity and relevance, the theoretical properties of the softmax-contaminated MoE have remained unexplored in the literature. In the paper, we study the convergence rates of the maximum likelihood estimator of gating and prompt parameters in order to gain insights into the statistical properties and potential challenges of fine-tuning with a new prompt. We find that the estimability of these parameters is compromised when the prompt acquires overlapping knowledge with the pre-trained model, in the sense that we make precise by formulating a novel analytic notion of distinguishability. Under distinguishability of the pre-trained and prompt models, we derive minimax optimal estimation rates for all the gating and prompt parameters. By contrast, when the distinguishability condition is violated, these estimation rates become significantly slower due to their dependence on the prompt convergence rate to the pre-trained model. Finally, we empirically corroborate our theoretical findings through several numerical experiments.

Poster
An Analysis of Causal Effect Estimation using Outcome Invariant Data Augmentation

UZAIR AKBAR, Niki Kilbertus, Hao Shen, Krikamol Muandet, Bo Dai

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The technique of data augmentation (DA) is often used in machine learning for regularization purposes to better generalize under i.i.d. settings. In this work, we present a unifying framework with topics in causal inference to make a case for the use of DA beyond just the i.i.d. setting, but for generalization across interventions as well. Specifically, we argue that when the outcome generating mechanism is invariant to our choice of DA, then such augmentations can effectively be thought of as interventions on the treatment generating mechanism itself. This can potentially help to reduce bias in causal effect estimation arising from hidden confounders. In the presence of such unobserved confounding we typically make use of instrumental variables (IVs)—sources of treatment randomization that are conditionally independent of the outcome. However, IVs may not be as readily available as DA for many applications, which is the main motivation behind this work. By appropriately regularizing IV based estimators, we introduce the concept of *IV-like (IVL)* regression for mitigating confounding bias and improving predictive performance across interventions even when certain IV properties are relaxed. Finally, we cast parameterized DA as an IVL regression problem and show that when used in composition can simulate a worst-case application of such DA, further improving performance on causal estimation and generalization tasks beyond what simple DA may offer. This is shown both theoretically for the population case and via simulation experiments for the finite sample case using a simple linear example. We also present real data experiments to support our case.

Spotlight
Treatment Effect Estimation for Optimal Decision-Making

Dennis Frauen, Valentyn Melnychuk, Jonas Schweisthal, Mihaela van der Schaar, Stefan Feuerriegel

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Decision-making across various fields, such as medicine, heavily relies on conditional average treatment effects (CATEs). Practitioners commonly make decisions by checking whether the estimated CATE is positive, even though the decision-making performance of modern CATE estimators is poorly understood from a theoretical perspective. In this paper, we study optimal decision-making based on two-stage CATE estimators (e.g., DR-learner), which are considered state-of-the-art and widely used in practice. We prove that, while such estimators may be optimal for estimating CATE, they can be suboptimal when used for decision-making. Intuitively, this occurs because such estimators prioritize CATE accuracy in regions far away from the decision boundary, which is ultimately irrelevant to decision-making. As a remedy, we propose a novel two-stage learning objective that retargets the CATE to balance CATE estimation error and decision performance. We then propose a neural method that optimizes an adaptively-smoothed approximation of our learning objective. Finally, we confirm the effectiveness of our method both empirically and theoretically. In sum, our work is the first to show how state-of-the-art CATE estimators can be adapted for optimal decision-making.

Poster
Pool Me Wisely: On the Effect of Pooling in Transformer-Based Models

Sofiane ENNADIR, Levente Zólyomi, Oleg Smirnov, Tianze Wang, John Pertoft, Filip Cornell, Lele Cao

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Transformer models have become the dominant backbone for sequence modeling, leveraging self-attention to produce contextualized token representations. These are typically aggregated into fixed-size vectors via pooling operations for downstream tasks. While much of the literature has focused on attention mechanisms, the role of pooling remains underexplored despite its critical impact on model behavior. In this paper, we introduce a theoretical framework that rigorously characterizes the expressivity of Transformer-based models equipped with widely used pooling methods by deriving closed-form bounds on their representational capacity and the ability to distinguish similar inputs. Our analysis extends to different variations of attention formulations, demonstrating that these bounds hold across diverse architectural variants. We empirically evaluate pooling strategies across tasks requiring both global and local contextual understanding, spanning three major modalities: computer vision, natural language processing, and time-series analysis. Results reveal consistent trends in how pooling choices affect accuracy, sensitivity, and optimization behavior. Our findings unify theoretical and empirical perspectives, providing practical guidance for selecting or designing pooling mechanisms suited to specific tasks. This work positions pooling as a key architectural component in Transformer models and lays the foundation for more principled model design beyond attention alone.

Poster
Transferring Causal Effects using Proxies

Manuel Iglesias-Alonso, Felix Schur, Julius Von Kügelgen, Jonas Peters

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We consider the problem of estimating a causal effect in a multi-domain setting. The causal effect of interest is confounded by an unobserved confounder and can change between the different domains. We assume that we have access to a proxy of the hidden confounder and that all variables are discrete or categorical. We propose methodology to estimate the causal effect in the target domain, where we assume to observe only the proxy variable. Under these conditions, we prove identifiability (even when treatment and response variables are continuous). We introduce two estimation techniques, prove consistency, and derive confidence intervals. The theoretical results are supported by simulation studies and a real-world example studying the causal effect of website rankings on consumer choices.

Poster
DoseSurv: Predicting Personalized Survival Outcomes under Continuous-Valued Treatments

Moritz Gögl, Yu Liu, Christopher Yau, Peter Watkinson, Tingting Zhu

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Estimating heterogeneous treatment effects (HTEs) of continuous-valued interventions on survival, that is, time-to-event (TTE) outcomes, is crucial in various fields, notably in clinical decision-making and in driving the advancement of next-generation clinical trials. However, while HTE estimation for continuous-valued (i.e., dosage-dependent) interventions and for TTE outcomes have been separately explored, their combined application remains largely overlooked in the machine learning literature. We propose DoseSurv, a varying-coefficient network designed to estimate HTEs for different dosage-dependent and non-dosage treatment options from TTE data. DoseSurv uses radial basis functions to model continuity in dose-response relationships and learns balanced representations to address covariate shifts arising in HTE estimation from observational TTE data. We present experiments across various treatment scenarios on both simulated and real-world data, demonstrating DoseSurv's superior performance over existing baseline models.

Poster
Refinement Methods for Distributed Distribution Estimation under $\ell^p$-Losses

Deheng Yuan, Tao Guo, Zhongyi Huang

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Consider the communication-constrained estimation of discrete distributions under $\ell^p$ losses, where each distributed terminal holds multiple independent samples and uses limited number of bits to describe the samples. We obtain the minimax optimal rates of the problem for most parameter regimes. As a result, an elbow effect of the optimal rates at $p=2$ is clearly identified. In order to achieve the optimal rates for different parameter regimes, we introduce refinement methods and develop additional customized techniques in the estimation protocols. The general idea of the refinement methods is to first generate rough estimate by partial information and then establish refined estimate in subsequent steps guided by the rough estimate. Then customized techniques such as successive refinement, sample compression, thresholding and random hashing are leveraged to achieve the optimal rates in different parameter regimes. The optimality of the estimation protocols is shown by deriving compatible minimax lower bounds.

Spotlight