LGOct 17, 2023Code
From Alexnet to Transformers: Measuring the Non-linearity of Deep Neural Networks with Affine Optimal TransportQuentin Bouniot, Ievgen Redko, Anton Mallasto et al.
In the last decade, we have witnessed the introduction of several novel deep neural network (DNN) architectures exhibiting ever-increasing performance across diverse tasks. Explaining the upward trend of their performance, however, remains difficult as different DNN architectures of comparable depth and width -- common factors associated with their expressive power -- may exhibit a drastically different performance even when trained on the same dataset. In this paper, we introduce the concept of the non-linearity signature of DNN, the first theoretically sound solution for approximately measuring the non-linearity of deep neural networks. Built upon a score derived from closed-form optimal transport mappings, this signature provides a better understanding of the inner workings of a wide range of DNN architectures and learning paradigms, with a particular emphasis on the computer vision task. We provide extensive experimental results that highlight the practical usefulness of the proposed non-linearity signature and its potential for long-reaching implications. The code for our work is available at https://github.com/qbouniot/AffScoreDeep
LGMay 27
Bridging Chemists and AI: An Expert-Augmented Framework for Interpretable Route EvaluationYujia Guo, Mikhail Kabeshov, Tat Hong Duong Le et al.
Selecting efficient multi-step synthetic routes is a central challenge in organic synthesis, particularly in medicinal and process chemistry, where route choice directly impacts feasibility, cost, and development efficiency. Data-driven assessment systems often oversimplify the multi-objective nature of synthesis design and rely on proxy datasets, such as patent routes, rather than universally grounded criteria. To address this, we introduce an expert-augmented, data-driven scoring framework that integrates machine learning with chemists' domain knowledge for both numerical and explainable route assessment. A DeepSets-based model is trained using tree edit distance between reference and machine-generated routes, and then fine-tuned with expert evaluations to produce both quantitative scores and interpretable qualitative categories: Good, Plausible, and Bad. The resulting system achieves a Spearman correlation coefficient of 0.78 and a Pearson correlation of 0.77 for category assessment prediction, and 60.2% top-1 ranking accuracy for score prediction, substantially outperforming the previous baseline of 17.5%.
LGSep 29, 2022
Provably expressive temporal graph networksAmauri H. Souza, Diego Mesquita, Samuel Kaski et al.
Temporal graph networks (TGNs) have gained prominence as models for embedding dynamic interactions, but little is known about their theoretical underpinnings. We establish fundamental results about the representational power and limits of the two main categories of TGNs: those that aggregate temporal walks (WA-TGNs), and those that augment local message passing with recurrent memory modules (MP-TGNs). Specifically, novel constructions reveal the inadequacy of MP-TGNs and WA-TGNs, proving that neither category subsumes the other. We extend the 1-WL (Weisfeiler-Leman) test to temporal graphs, and show that the most powerful MP-TGNs should use injective updates, as in this case they become as expressive as the temporal WL. Also, we show that sufficiently deep MP-TGNs cannot benefit from memory, and MP/WA-TGNs fail to compute graph properties such as girth. These theoretical insights lead us to PINT -- a novel architecture that leverages injective temporal message passing and relative positional features. Importantly, PINT is provably more expressive than both MP-TGNs and WA-TGNs. PINT significantly outperforms existing TGNs on several real-world benchmarks.
LGSep 28, 2023
Compositional Sculpting of Iterative Generative ProcessesTimur Garipov, Sebastiaan De Peuter, Ge Yang et al.
High training costs of generative models and the need to fine-tune them for specific tasks have created a strong interest in model reuse and composition. A key challenge in composing iterative generative processes, such as GFlowNets and diffusion models, is that to realize the desired target distribution, all steps of the generative process need to be coordinated, and satisfy delicate balance conditions. In this work, we propose Compositional Sculpting: a general approach for defining compositions of iterative generative processes. We then introduce a method for sampling from these compositions built on classifier guidance. We showcase ways to accomplish compositional sculpting in both GFlowNets and diffusion models. We highlight two binary operations $\unicode{x2014}$ the harmonic mean ($p_1 \otimes p_2$) and the contrast ($p_1 \unicode{x25D1}\,p_2$) between pairs, and the generalization of these operations to multiple component distributions. We offer empirical results on image and molecular generation tasks.
LGOct 25, 2022
Multi-Fidelity Bayesian Optimization with Unreliable Information SourcesPetrus Mikkola, Julien Martinelli, Louis Filstroff et al.
Bayesian optimization (BO) is a powerful framework for optimizing black-box, expensive-to-evaluate functions. Over the past decade, many algorithms have been proposed to integrate cheaper, lower-fidelity approximations of the objective function into the optimization process, with the goal of converging towards the global optimum at a reduced cost. This task is generally referred to as multi-fidelity Bayesian optimization (MFBO). However, MFBO algorithms can lead to higher optimization costs than their vanilla BO counterparts, especially when the low-fidelity sources are poor approximations of the objective function, therefore defeating their purpose. To address this issue, we propose rMFBO (robust MFBO), a methodology to make any GP-based MFBO scheme robust to the addition of unreliable information sources. rMFBO comes with a theoretical guarantee that its performance can be bound to its vanilla BO analog, with high controllable probability. We demonstrate the effectiveness of the proposed methodology on a number of numerical benchmarks, outperforming earlier MFBO methods on unreliable sources. We expect rMFBO to be particularly useful to reliably include human experts with varying knowledge within BO processes.
LGOct 12, 2022
Modular Flows: Differential Molecular GenerationYogesh Verma, Samuel Kaski, Markus Heinonen et al.
Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.
MLJun 19, 2023
Practical Equivariances via Relational Conditional Neural ProcessesDaolang Huang, Manuel Haussmann, Ulpu Remes et al.
Conditional Neural Processes (CNPs) are a class of metalearning models popular for combining the runtime efficiency of amortized inference with reliable uncertainty quantification. Many relevant machine learning tasks, such as in spatio-temporal modeling, Bayesian Optimization and continuous control, inherently contain equivariances -- for example to translation -- which the model can exploit for maximal performance. However, prior attempts to include equivariances in CNPs do not scale effectively beyond two input dimensions. In this work, we propose Relational Conditional Neural Processes (RCNPs), an effective approach to incorporate equivariances into any neural process model. Our proposed method extends the applicability and impact of equivariant neural processes to higher dimensions. We empirically demonstrate the competitive performance of RCNPs on a large array of tasks naturally containing equivariances.
AIApr 3, 2022
Best-Response Bayesian Reinforcement Learning with Bayes-adaptive POMDPs for CentaursMustafa Mert Çelikok, Frans A. Oliehoek, Samuel Kaski
Centaurs are half-human, half-AI decision-makers where the AI's goal is to complement the human. To do so, the AI must be able to recognize the goals and constraints of the human and have the means to help them. We present a novel formulation of the interaction between the human and the AI as a sequential game where the agents are modelled using Bayesian best-response models. We show that in this case the AI's problem of helping bounded-rational humans make better decisions reduces to a Bayes-adaptive POMDP. In our simulated experiments, we consider an instantiation of our framework for humans who are subjectively optimistic about the AI's future behaviour. Our results show that when equipped with a model of the human, the AI can infer the human's bounds and nudge them towards better decisions. We discuss ways in which the machine can learn to improve upon its own limitations as well with the help of the human. We identify a novel trade-off for centaurs in partially observable tasks: for the AI's actions to be acceptable to the human, the machine must make sure their beliefs are sufficiently aligned, but aligning beliefs might be costly. We present a preliminary theoretical analysis of this trade-off and its dependence on task structure.
LGSep 21, 2023
Expert-Aided Causal Discovery of Ancestral GraphsTiago da Silva, Bruna Bazaluk, Eliezer de Souza da Silva et al.
Causal discovery (CD) algorithms are notably brittle when data is scarce, inferring unreliable causal relations that may contradict expert knowledge, especially when considering latent confounders. Furthermore, the lack of uncertainty quantification in most CD methods hinders users from diagnosing and refining results. To address these issues, we introduce Ancestral GFlowNets (AGFNs). AGFN samples ancestral graphs (AGs) proportionally to a score-based belief distribution representing our epistemic uncertainty over the causal relationships. Building upon this distribution, we propose an elicitation framework for expert-driven assessment. This framework comprises an optimal experimental design to probe the expert and a scheme to incorporate the obtained feedback into AGFN. Our experiments show that: i) AGFN is competitive against other methods that address latent confounding on both synthetic and real-world datasets; and ii) our design for incorporating feedback from a (simulated) human expert or a Large Language Model (LLM) improves inference quality.
LGJun 23, 2022
Human-in-the-Loop Large-Scale Predictive Maintenance of WorkstationsAlexander Nikitin, Samuel Kaski
Predictive maintenance (PdM) is the task of scheduling maintenance operations based on a statistical analysis of the system's condition. We propose a human-in-the-loop PdM approach in which a machine learning system predicts future problems in sets of workstations (computers, laptops, and servers). Our system interacts with domain experts to improve predictions and elicit their knowledge. In our approach, domain experts are included in the loop not only as providers of correct labels, as in traditional active learning, but as a source of explicit decision rule feedback. The system is automated and designed to be easily extended to novel domains, such as maintaining workstations of several organizations. In addition, we develop a simulator for reproducible experiments in a controlled environment and deploy the system in a large-scale case of real-life workstations PdM with thousands of workstations for dozens of companies.
MLJun 6, 2022
Tackling covariate shift with node-based Bayesian neural networksTrung Trinh, Markus Heinonen, Luigi Acerbi et al.
Bayesian neural networks (BNNs) promise improved generalization under covariate shift by providing principled probabilistic representations of epistemic uncertainty. However, weight-based BNNs often struggle with high computational complexity of large-scale architectures and datasets. Node-based BNNs have recently been introduced as scalable alternatives, which induce epistemic uncertainty by multiplying each hidden node with latent random variables, while learning a point-estimate of the weights. In this paper, we interpret these latent noise variables as implicit representations of simple and domain-agnostic data perturbations during training, producing BNNs that perform well under covariate shift due to input corruptions. We observe that the diversity of the implicit corruptions depends on the entropy of the latent variables, and propose a straightforward approach to increase the entropy of these variables during training. We evaluate the method on out-of-distribution image classification benchmarks, and show improved uncertainty estimation of node-based BNNs under covariate shift due to input perturbations. As a side effect, the method also provides robustness against noisy training labels.
LGAug 18, 2022
Bayesian Optimization Augmented with Actively Elicited Expert KnowledgeDaolang Huang, Louis Filstroff, Petrus Mikkola et al.
Bayesian optimization (BO) is a well-established method to optimize black-box functions whose direct evaluations are costly. In this paper, we tackle the problem of incorporating expert knowledge into BO, with the goal of further accelerating the optimization, which has received very little attention so far. We design a multi-task learning architecture for this task, with the goal of jointly eliciting the expert knowledge and minimizing the objective function. In particular, this allows for the expert knowledge to be transferred into the BO task. We introduce a specific architecture based on Siamese neural networks to handle the knowledge elicitation from pairwise queries. Experiments on various benchmark functions with both simulated and actual human experts show that the proposed method significantly speeds up BO even when the expert knowledge is biased compared to the objective function.
MLJun 5, 2023
Input-gradient space particle inference for neural network ensemblesTrung Trinh, Markus Heinonen, Luigi Acerbi et al.
Deep Ensembles (DEs) demonstrate improved accuracy, calibration and robustness to perturbations over single neural networks partly due to their functional diversity. Particle-based variational inference (ParVI) methods enhance diversity by formalizing a repulsion term based on a network similarity kernel. However, weight-space repulsion is inefficient due to over-parameterization, while direct function-space repulsion has been found to produce little improvement over DEs. To sidestep these difficulties, we propose First-order Repulsive Deep Ensemble (FoRDE), an ensemble learning method based on ParVI, which performs repulsion in the space of first-order input gradients. As input gradients uniquely characterize a function up to translation and are much smaller in dimension than the weights, this method guarantees that ensemble members are functionally different. Intuitively, diversifying the input gradients encourages each network to learn different features, which is expected to improve the robustness of an ensemble. Experiments on image classification datasets and transfer learning tasks show that FoRDE significantly outperforms the gold-standard DEs and other ensemble methods in accuracy and calibration under covariate shift due to input perturbations.
LGMar 3, 2023
Online simulator-based experimental design for cognitive model selectionAlexander Aushev, Aini Putkonen, Gregoire Clarte et al.
The problem of model selection with a limited number of experimental trials has received considerable attention in cognitive science, where the role of experiments is to discriminate between theories expressed as computational models. Research on this subject has mostly been restricted to optimal experiment design with analytically tractable models. However, cognitive models of increasing complexity, with intractable likelihoods, are becoming more commonplace. In this paper, we propose BOSMOS: an approach to experimental design that can select between computational models without tractable likelihoods. It does so in a data-efficient manner, by sequentially and adaptively generating informative experiments. In contrast to previous approaches, we introduce a novel simulator-based utility objective for design selection, and a new approximation of the model likelihood for model selection. In simulated experiments, we demonstrate that the proposed BOSMOS technique can accurately select models in up to 2 orders of magnitude less time than existing LFI alternatives for three cognitive science tasks: memory retention, sequential signal detection and risky choice.
LGNov 29, 2022
Differentiable User ModelsAlex Hämäläinen, Mustafa Mert Çelikok, Samuel Kaski
Probabilistic user modeling is essential for building machine learning systems in the ubiquitous cases with humans in the loop. However, modern advanced user models, often designed as cognitive behavior simulators, are incompatible with modern machine learning pipelines and computationally prohibitive for most practical applications. We address this problem by introducing widely-applicable differentiable surrogates for bypassing this computational bottleneck; the surrogates enable computationally efficient inference with modern cognitive models. We show experimentally that modeling capabilities comparable to the only available solution, existing likelihood-free inference methods, are achievable with a computational cost suitable for online applications. Finally, we demonstrate how AI-assistants can now use cognitive models for online interaction in a menu-search task, which has so far required hours of computation during interaction.
MLOct 28, 2022
DPVIm: Differentially Private Variational Inference ImprovedJoonas Jälkö, Lukas Prediger, Antti Honkela et al.
Differentially private (DP) release of multidimensional statistics typically considers an aggregate sensitivity, e.g. the vector norm of a high-dimensional vector. However, different dimensions of that vector might have widely different magnitudes and therefore DP perturbation disproportionately affects the signal across dimensions. We observe this problem in the gradient release of the DP-SGD algorithm when using it for variational inference (VI), where it manifests in poor convergence as well as high variance in outputs for certain variational parameters, and make the following contributions: (i) We mathematically isolate the cause for the difference in magnitudes between gradient parts corresponding to different variational parameters. Using this as prior knowledge we establish a link between the gradients of the variational parameters, and propose an efficient while simple fix for the problem to obtain a less noisy gradient estimator, which we call $\textit{aligned}$ gradients. This approach allows us to obtain the updates for the covariance parameter of a Gaussian posterior approximation without a privacy cost. We compare this to alternative approaches for scaling the gradients using analytically derived preconditioning, e.g. natural gradients. (ii) We suggest using iterate averaging over the DP parameter traces recovered during the training, to reduce the DP-induced noise in parameter estimates at no additional cost in privacy. Finally, (iii) to accurately capture the additional uncertainty DP introduces to the model parameters, we infer the DP-induced noise from the parameter traces and include that in the learned posteriors to make them $\textit{noise aware}$. We demonstrate the efficacy of our proposed improvements through various experiments on real data.
MLMay 28, 2022
Noise-Aware Statistical Inference with Differentially Private Synthetic DataOssi Räisä, Joonas Jälkö, Samuel Kaski et al.
While generation of synthetic data under differential privacy (DP) has received a lot of attention in the data privacy community, analysis of synthetic data has received much less. Existing work has shown that simply analysing DP synthetic data as if it were real does not produce valid inferences of population-level quantities. For example, confidence intervals become too narrow, which we demonstrate with a simple experiment. We tackle this problem by combining synthetic data analysis techniques from the field of multiple imputation (MI), and synthetic data generation using noise-aware (NA) Bayesian modeling into a pipeline NA+MI that allows computing accurate uncertainty estimates for population-level quantities from DP synthetic data. To implement NA+MI for discrete data generation using the values of marginal queries, we develop a novel noise-aware synthetic data generation algorithm NAPSU-MQ using the principle of maximum entropy. Our experiments demonstrate that the pipeline is able to produce accurate confidence intervals from DP synthetic data. The intervals become wider with tighter privacy to accurately capture the additional uncertainty stemming from DP noise.
LGAug 9, 2023
Collaborative Learning From Distributed Data With Differentially Private Synthetic Twin DataLukas Prediger, Joonas Jälkö, Antti Honkela et al.
Consider a setting where multiple parties holding sensitive data aim to collaboratively learn population level statistics, but pooling the sensitive data sets is not possible. We propose a framework in which each party shares a differentially private synthetic twin of their data. We study the feasibility of combining such synthetic twin data sets for collaborative learning on real-world health data from the UK Biobank. We discover that parties engaging in the collaborative learning via shared synthetic data obtain more accurate estimates of target statistics compared to using only their local data. This finding extends to the difficult case of small heterogeneous data sets. Furthermore, the more parties participate, the larger and more consistent the improvements become. Finally, we find that data sharing can especially help parties whose data contain underrepresented groups to perform better-adjusted analysis for said groups. Based on our results we conclude that sharing of synthetic twins is a viable method for enabling learning from sensitive data without violating privacy constraints even if individual data sets are small or do not represent the overall population well. The setting of distributed sensitive data is often a bottleneck in biomedical research, which our study shows can be alleviated with privacy-preserving collaborative learning methods.
MLMay 26
Constrained Bayesian Experimental Design via Online PlanningYujia Guo, Daolang Huang, Xinyu Zhang et al.
Bayesian experimental design (BED) is a principled framework for data-efficient design of sequential experiments. However, existing BED methods are unable to adapt to dynamic constraints inherent in real-world tasks due to budget limitations, varying costs, or physical constraints that restrict how designs evolve over time. In this paper, we introduce a novel approach to BED that enables constrained optimization of experimental designs by combining offline pre-training of an amortized policy and a posterior network with online multi-step lookahead planning using scenario trees. We empirically demonstrate that our method yields substantially more informative design sequences than existing methods across a range of constrained BED tasks, while incurring only a modest additional computational overhead.
LGNov 6, 2023
Estimating treatment effects from single-arm trials via latent-variable modelingManuel Haussmann, Tran Minh Son Le, Viivi Halla-aho et al.
Randomized controlled trials (RCTs) are the accepted standard for treatment effect estimation but they can be infeasible due to ethical reasons and prohibitive costs. Single-arm trials, where all patients belong to the treatment group, can be a viable alternative but require access to an external control group. We propose an identifiable deep latent-variable model for this scenario that can also account for missing covariate observations by modeling their structured missingness patterns. Our method uses amortized variational inference to learn both group-specific and identifiable shared latent representations, which can subsequently be used for {\em (i)} patient matching if treatment outcomes are not available for the treatment group, or for {\em (ii)} direct treatment effect estimation assuming outcomes are available for both groups. We evaluate the model on a public benchmark as well as on a data set consisting of a published RCT study and real-world electronic health records. Compared to previous methods, our results show improved performance both for direct treatment effect estimation as well as for effect estimation via patient matching.
LGAug 12, 2024Code
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?Rafał Karczewski, Samuel Kaski, Markus Heinonen et al.
Several generative models with elaborate training and sampling procedures have been proposed to accelerate structure-based drug design (SBDD); however, their empirical performance turns out to be suboptimal. We seek to better understand this phenomenon from both theoretical and empirical perspectives. Since most of these models apply graph neural networks (GNNs), one may suspect that they inherit the representational limitations of GNNs. We analyze this aspect, establishing the first such results for protein-ligand complexes. A plausible counterview may attribute the underperformance of these models to their excessive parameterizations, inducing expressivity at the expense of generalization. We investigate this possibility with a simple metric-aware approach that learns an economical surrogate for affinity to infer an unlabelled molecular graph and optimizes for labels conditioned on this graph and molecular properties. The resulting model achieves state-of-the-art results using 100x fewer trainable parameters and affords up to 1000x speedup. Collectively, our findings underscore the need to reassess and redirect the existing paradigm and efforts for SBDD. Code is available at https://github.com/rafalkarczewski/SimpleSBDD.
LGFeb 7, 2023
Uncoupled Learning of Differential Stackelberg Equilibria with CommitmentsRobert Loftin, Mustafa Mert Çelikok, Herke van Hoof et al.
In multi-agent problems requiring a high degree of cooperation, success often depends on the ability of the agents to adapt to each other's behavior. A natural solution concept in such settings is the Stackelberg equilibrium, in which the ``leader'' agent selects the strategy that maximizes its own payoff given that the ``follower'' agent will choose their best response to this strategy. Recent work has extended this solution concept to two-player differentiable games, such as those arising from multi-agent deep reinforcement learning, in the form of the \textit{differential} Stackelberg equilibrium. While this previous work has presented learning dynamics which converge to such equilibria, these dynamics are ``coupled'' in the sense that the learning updates for the leader's strategy require some information about the follower's payoff function. As such, these methods cannot be applied to truly decentralised multi-agent settings, particularly ad hoc cooperation, where each agent only has access to its own payoff function. In this work we present ``uncoupled'' learning dynamics based on zeroth-order gradient estimators, in which each agent's strategy update depends only on their observations of the other's behavior. We analyze the convergence of these dynamics in general-sum games, and prove that they converge to differential Stackelberg equilibria under the same conditions as previous coupled methods. Furthermore, we present an online mechanism by which symmetric learners can negotiate leader-follower roles. We conclude with a discussion of the implications of our work for multi-agent reinforcement learning and ad hoc collaboration more generally.
LGMar 16
Point-Identification of a Robust Predictor Under Latent Shift with Imperfect ProxiesZahra Rahiminasab, Reza Soumi, Arto Klami et al.
Addressing the domain adaptation problem becomes more challenging when distribution shifts across domains stem from latent confounders that affect both covariates and outcomes. Existing proxy-based approaches that address latent shift rely on a strong completeness assumption to uniquely determine (point-identify) a robust predictor. Completeness requires that proxies have sufficient information about variations in latent confounders. For imperfect proxies the mapping from confounders to the space of proxy distributions is non-injective, and multiple latent confounder values can generate the same proxy distribution. This breaks the completeness assumption and observed data are consistent with multiple potential predictors (set-identified). To address this, we introduce latent equivalent classes (LECs). LECs are defined as groups of latent confounders that induce the same conditional proxy distribution. We show that point-identification for the robust predictor remains achievable as long as multiple domains differ sufficiently in how they mix proxy-induced LECs to form the robust predictor. This domain diversity condition is formalized as a cross-domain rank condition on the mixture weights, which is substantially weaker assumption than completeness. We introduce the Proximal Quasi-Bayesian Active learning (PQAL) framework, which actively queries a minimal set of diverse domains that satisfy this rank condition. PQAL can efficiently recover the point-identified predictor, demonstrates robustness to varying degrees of shift and outperforms previous methods on synthetic data and semi-synthetic dSprites dataset.
LGJan 26
Rank-1 Approximation of Inverse Fisher for Natural Policy Gradients in Deep Reinforcement LearningYingxiao Huo, Satya Prakash Dash, Radu Stoican et al.
Natural gradients have long been studied in deep reinforcement learning due to their fast convergence properties and covariant weight updates. However, computing natural gradients requires inversion of the Fisher Information Matrix (FIM) at each iteration, which is computationally prohibitive in nature. In this paper, we present an efficient and scalable natural policy optimization technique that leverages a rank-1 approximation to full inverse-FIM. We theoretically show that under certain conditions, a rank-1 approximation to inverse-FIM converges faster than policy gradients and, under some conditions, enjoys the same sample complexity as stochastic policy gradient methods. We benchmark our method on a diverse set of environments and show that it achieves superior performance to standard actor-critic and trust-region baselines.
LGJan 26
Gradient Regularized Natural GradientsSatya Prakash Dash, Hossein Abdi, Wei Pan et al.
Gradient regularization (GR) has been shown to improve the generalizability of trained models. While Natural Gradient Descent has been shown to accelerate optimization in the initial phase of training, little attention has been paid to how the training dynamics of second-order optimizers can benefit from GR. In this work, we propose Gradient-Regularized Natural Gradients (GRNG), a family of scalable second-order optimizers that integrate explicit gradient regularization with natural gradient updates. Our framework provides two complementary algorithms: a frequentist variant that avoids explicit inversion of the Fisher Information Matrix (FIM) via structured approximations, and a Bayesian variant based on a Regularized-Kalman formulation that eliminates the need for FIM inversion entirely. We establish convergence guarantees for GRNG, showing that gradient regularization improves stability and enables convergence to global minima. Empirically, we demonstrate that GRNG consistently enhances both optimization speed and generalization compared to first-order methods (SGD, AdamW) and second-order baselines (K-FAC, Sophia), with strong results on vision and language benchmarks. Our findings highlight gradient regularization as a principled and practical tool to unlock the robustness of natural gradient methods for large-scale deep learning.
LGOct 23, 2023
Bayesian Active Learning in the Presence of Nuisance ParametersSabina J. Sloman, Ayush Bharti, Julien Martinelli et al.
In many settings, such as scientific inference, optimization, and transfer learning, the learner has a well-defined objective, which can be treated as estimation of a target parameter, and no intrinsic interest in characterizing the entire data-generating process. Usually, the learner must also contend with additional sources of uncertainty or variables -- with nuisance parameters. Bayesian active learning, or sequential optimal experimental design, can straightforwardly accommodate the presence of nuisance parameters, and so is a natural active learning framework for such problems. However, the introduction of nuisance parameters can lead to bias in the Bayesian learner's estimate of the target parameters, a phenomenon we refer to as negative interference. We characterize the threat of negative interference and how it fundamentally changes the nature of the Bayesian active learner's task. We show that the extent of negative interference can be extremely large, and that accurate estimation of the nuisance parameters is critical to reducing it. The Bayesian active learner is confronted with a dilemma: whether to spend a finite acquisition budget in pursuit of estimation of the target or of the nuisance parameters. Our setting encompasses Bayesian transfer learning as a special case, and our results shed light on the phenomenon of negative transfer between learning environments.
LGMay 18
Decoupled Conformal Optimisation: Efficient Prediction Sets via Independent Tuning and CalibrationFanyi Wu, Lihua Niu, Samuel Kaski et al.
Bayesian conformal optimisation methods often use the same held-out data both to search for efficient prediction sets and to certify coverage or risk. This coupling is natural for high-probability risk-control guarantees, but it is not necessary when the target is standard finite-sample marginal conformal coverage. We propose Decoupled Conformal Optimisation (DCO), a train-tune-calibrate design principle that uses an independent tuning split for efficiency-oriented structural selection and a fresh calibration split for the final conformal quantile. Conditional on the tuned structure, standard split-conformal exchangeability yields finite-sample marginal coverage for any candidate class, without a confidence parameter or multiple-testing correction. DCO therefore targets a different finite-sample guarantee from PAC-style methods: marginal conformal coverage rather than high-probability risk control. Under consistency assumptions on the coupled risk bound, the two approaches nevertheless converge to the same population threshold. Across classification and regression benchmarks, including ImageNet-A, CIFAR-100, Diabetes, California Housing, and Concrete, DCO tracks the nominal coverage level closely while often reducing average prediction-set size or interval width relative to PAC-style calibration. On ImageNet-A, for example, the average set size decreases from $26.52$ to $25.26$ and the 95th-percentile set size from $58.95$ to $53.73$; on Diabetes, the average interval width decreases from $2.098$ to $1.914$.
MAFeb 23, 2024Code
Open Ad Hoc Teamwork with Cooperative Game TheoryJianhong Wang, Yang Li, Yuan Zhang et al.
Ad hoc teamwork poses a challenging problem, requiring the design of an agent to collaborate with teammates without prior coordination or joint training. Open ad hoc teamwork (OAHT) further complicates this challenge by considering environments with a changing number of teammates, referred to as open teams. One promising solution in practice to this problem is leveraging the generalizability of graph neural networks to handle an unrestricted number of agents with various agent-types, named graph-based policy learning (GPL). However, its joint Q-value representation over a coordination graph lacks convincing explanations. In this paper, we establish a new theory to understand the representation of the joint Q-value for OAHT and its learning paradigm, through the lens of cooperative game theory. Building on our theory, we propose a novel algorithm named CIAO, based on GPL's framework, with additional provable implementation tricks that can facilitate learning. The demos of experimental results are available on https://sites.google.com/view/ciao2024, and the code of experiments is published on https://github.com/hsvgbkhgbv/CIAO.
LGMar 30
Mixture-Model Preference Learning for Many-Objective Bayesian OptimizationManisha Dubey, Sebastiaan De Peuter, Wanrong Wang et al.
Preference-based many-objective optimization faces two obstacles: an expanding space of trade-offs and heterogeneous, context-dependent human value structures. Towards this, we propose a Bayesian framework that learns a small set of latent preference archetypes rather than assuming a single fixed utility function, modelling them as components of a Dirichlet-process mixture with uncertainty over both archetypes and their weights. To query efficiently, we designing hybrid queries that target information about (i) mode identity and (ii) within-mode trade-offs. Under mild assumptions, we provide a simple regret guarantee for the resulting mixture-aware Bayesian optimization procedure. Empirically, our method outperforms standard baselines on synthetic and real-world many-objective benchmarks, and mixture-aware diagnostics reveal structure that regret alone fails to capture.
LGOct 19, 2023
Bayesian Meta-Learning for Improving Generalizability of Health Prediction Models With Similar Causal MechanismsSophie Wharrie, Lisa Eick, Lotta Mäkinen et al.
Machine learning strategies like multi-task learning, meta-learning, and transfer learning enable efficient adaptation of machine learning models to specific applications in healthcare, such as prediction of various diseases, by leveraging generalizable knowledge across large datasets and multiple domains. In particular, Bayesian meta-learning methods pool data across related prediction tasks to learn prior distributions for model parameters, which are then used to derive models for specific tasks. However, inter- and intra-task variability due to disease heterogeneity and other patient-level differences pose challenges of negative transfer during shared learning and poor generalizability to new patients. We introduce a novel Bayesian meta-learning approach that aims to address this in two key settings: (1) predictions for new patients (same population as the training set) and (2) adapting to new patient populations. Our main contribution is in modeling similarity between causal mechanisms of the tasks, for (1) mitigating negative transfer during training and (2) fine-tuning that pools information from tasks that are expected to aid generalizability. We propose an algorithm for implementing this approach for Bayesian deep learning, and apply it to a case study for stroke prediction tasks using electronic health record data. Experiments for the UK Biobank dataset as the training population demonstrated significant generalizability improvements compared to standard meta-learning, non-causal task similarity measures, and local baselines (separate models for each task). This was assessed for a variety of tasks that considered both new patients from the training population (UK Biobank) and a new population (FinnGen).
LGApr 17
Multi-Objective Bayesian Optimization via Adaptive \varepsilon-Constraints DecompositionYaohong Yang, Sammie Katt, Samuel Kaski
Multi-objective Bayesian optimization (MOBO) provides a principled framework for optimizing expensive black-box functions with multiple objectives. However, existing MOBO methods often struggle with coverage, scalability with respect to the number of objectives, and integrating constraints and preferences. In this work, we propose \textit{STAGE-BO, Sequential Targeting Adaptive Gap-Filling $\varepsilon$-Constraint Bayesian Optimization}, that explicitly targets under-explored regions of the Pareto front. By analyzing the coverage of the approximate Pareto front, our method identifies the largest geometric gaps. These gaps are then used as constraints, which transforms the problem into a sequence of inequality-constrained subproblems, efficiently solved via constrained expected improvement acquisition. Our approach provides a uniform Pareto coverage without hypervolume computation and naturally applies to constrained and preference-based settings. Experiments on synthetic and real-world benchmarks demonstrate superior coverage and competitive hypervolume performance against state-of-the-art baselines.
LGMay 12
Elicitation-Augmented Bayesian OptimizationAlvar Haltia, Ville Hyvönen, Samuel Kaski
Human-in-the-loop Bayesian optimization (HITL BO) methods utilize human expertise to improve the sample-efficiency of BO. Most HITL BO methods assume that a domain expert can quantify their knowledge, for instance by pinpointing query locations or specifying their prior beliefs about the location of the maximum as a probability distribution. However, since human expertise is often tacit and cannot be explicitly quantified, we consider a setting where domain knowledge of an expert is elicited via pairwise comparisons of designs. We interpret the expert's pairwise judgements as noisy evidence about the values of the observable objective function and develop a principled method for combining the information obtained via direct observations and pairwise queries. Specifically, we derive a cost-aware value-of-information acquisition function that balances direct observations against pairwise queries. The proposed method approaches the convex hull of the trajectories of the individual information sources: when pairwise queries are cheap it substantially improves sample-efficiency over observation-only BO, and when pairwise queries are costly or noisy, it recovers the performance of standard BO by relying on direct observations alone.
MLNov 10, 2025
Robust Experimental Design via Generalised Bayesian InferenceYasir Zubayr Barlas, Sabina J. Sloman, Samuel Kaski
Bayesian optimal experimental design is a principled framework for conducting experiments that leverages Bayesian inference to quantify how much information one can expect to gain from selecting a certain design. However, accurate Bayesian inference relies on the assumption that one's statistical model of the data-generating process is correctly specified. If this assumption is violated, Bayesian methods can lead to poor inference and estimates of information gain. Generalised Bayesian (or Gibbs) inference is a more robust probabilistic inference framework that replaces the likelihood in the Bayesian update by a suitable loss function. In this work, we present Generalised Bayesian Optimal Experimental Design (GBOED), an extension of Gibbs inference to the experimental design setting which achieves robustness in both design and inference. Using an extended information-theoretic framework, we derive a new acquisition function, the Gibbs expected information gain (Gibbs EIG). Our empirical results demonstrate that GBOED enhances robustness to outliers and incorrect assumptions about the outcome noise distribution.
LGMay 11
Online Sharp-Calibrated Bayesian OptimizationMarshal Arijona Sinaga, Julien Martinelli, Teemu Turpeinen et al.
Bayesian optimization (BO) is a widely used framework for optimizing expensive black-box functions, commonly based on Gaussian process (GP) surrogate models. Its effectiveness relies on uncertainty quantification that is both sharp (informative) and well-calibrated along the BO trajectory. In practice, GP kernel hyperparameters are unknown and are refit online from sequentially collected (non-i.i.d.) data, which can yield miscalibrated or overly conservative uncertainty and lies outside the fixed-kernel assumptions of standard BO regret theory. We propose Online Sharp-Calibrated Bayesian Optimization (OSCBO), a BO algorithm that adaptively balances GP sharpness and calibration by casting hyperparameter selection as a constrained online-learning problem. We also show that OSCBO preserves sublinear regret bounds by leveraging the theoretical guarantees of the underlying online learning algorithm. Empirically, OSCBO performs competitively across synthetic and real-world benchmarks, ranking among the strongest methods in final simple regret while maintaining robust cumulative-regret behavior.
LGFeb 23
Bayesian Meta-Learning with Expert Feedback for Task-Shift Adaptation through Causal EmbeddingsLotta Mäkinen, Jorge Loría, Samuel Kaski
Meta-learning methods perform well on new within-distribution tasks but often fail when adapting to out-of-distribution target tasks, where transfer from source tasks can induce negative transfer. We propose a causally-aware Bayesian meta-learning method, by conditioning task-specific priors on precomputed latent causal task embeddings, enabling transfer based on mechanistic similarity rather than spurious correlations. Our approach explicitly considers realistic deployment settings where access to target-task data is limited, and adaptation relies on noisy (expert-provided) pairwise judgments of causal similarity between source and target tasks. We provide a theoretical analysis showing that conditioning on causal embeddings controls prior mismatch and mitigates negative transfer under task shift. Empirically, we demonstrate reductions in negative transfer and improved out-of-distribution adaptation in both controlled simulations and a large-scale real-world clinical prediction setting for cross-disease transfer, where causal embeddings align with underlying clinical mechanisms.
CVOct 23, 2025Code
Attentive Convolution: Unifying the Expressivity of Self-Attention with Convolutional EfficiencyHao Yu, Haoyu Chen, Yan Jiang et al.
Self-attention (SA) has become the cornerstone of modern vision backbones for its powerful expressivity over traditional Convolutions (Conv). However, its quadratic complexity remains a critical bottleneck for practical applications. Given that Conv offers linear complexity and strong visual priors, continuing efforts have been made to promote the renaissance of Conv. However, a persistent performance chasm remains, highlighting that these modernizations have not yet captured the intrinsic expressivity that defines SA. In this paper, we re-examine the design of the CNNs, directed by a key question: what principles give SA its edge over Conv? As a result, we reveal two fundamental insights that challenge the long-standing design intuitions in prior research (e.g., Receptive field). The two findings are: (1) \textit{Adaptive routing}: SA dynamically regulates positional information flow according to semantic content, whereas Conv employs static kernels uniformly across all positions. (2) \textit{Lateral inhibition}: SA induces score competition among token weighting, effectively suppressing redundancy and sharpening representations, whereas Conv filters lack such inhibitory dynamics and exhibit considerable redundancy. Based on this, we propose \textit{Attentive Convolution} (ATConv), a principled reformulation of the convolutional operator that intrinsically injects these principles. Interestingly, with only $3\times3$ kernels, ATConv consistently outperforms various SA mechanisms in fundamental vision tasks. Building on ATConv, we introduce AttNet, a CNN family that can attain \textbf{84.4\%} ImageNet-1K Top-1 accuracy with only 27M parameters. In diffusion-based image generation, replacing all SA with the proposed $3\times 3$ ATConv in SiT-XL/2 reduces ImageNet FID by 0.15 in 400k steps with faster sampling. Code is available at: github.com/price112/Attentive-Convolution.
LGMay 19, 2023Code
TSGM: A Flexible Framework for Generative Modeling of Synthetic Time SeriesAlexander Nikitin, Letizia Iannucci, Samuel Kaski
Temporally indexed data are essential in a wide range of fields and of interest to machine learning researchers. Time series data, however, are often scarce or highly sensitive, which precludes the sharing of data between researchers and industrial organizations and the application of existing and new data-intensive ML methods. A possible solution to this bottleneck is to generate synthetic data. In this work, we introduce Time Series Generative Modeling (TSGM), an open-source framework for the generative modeling of synthetic time series. TSGM includes a broad repertoire of machine learning methods: generative models, probabilistic, and simulator-based approaches. The framework enables users to evaluate the quality of the produced data from different angles: similarity, downstream effectiveness, predictive consistency, diversity, and privacy. The framework is extensible, which allows researchers to rapidly implement their own methods and compare them in a shareable environment. TSGM was tested on open datasets and in production and proved to be beneficial in both cases. Additionally to the library, the project allows users to employ command line interfaces for synthetic data generation which lowers the entry threshold for those without a programming background.
MLApr 18, 2018Code
Bayesian Metabolic Flux Analysis reveals intracellular flux couplingsMarkus Heinonen, Maria Osmala, Henrik Mannerström et al.
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic assumptions on fluxes due to the convenience of formulating the problem as a linear programming model, and most methods ignore the notable uncertainty in flux estimates. We introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and target function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as flux balance analysis (FBA). Our experiments indicate that we can characterise the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in C. acetobutylicum from 13C data than flux variability analysis. The COBRA compatible software is available at github.com/markusheinonen/bamfa
GNAug 28, 2013Code
Exploration and retrieval of whole-metagenome sequencing samplesSohan Seth, Niko Välimäki, Samuel Kaski et al.
Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation. In this paper, we develop a content-based exploration and retrieval method for whole metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence $k$-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome data sets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and very high accuracy in discriminating between different body sites even though the method is unsupervised. A software implementation of the DSM framework is available at https://github.com/HIITMetagenomics/dsm-framework
AINov 15, 2025
More Than Irrational: Modeling Belief-Biased AgentsYifan Zhu, Sammie Katt, Samuel Kaski
Despite the explosive growth of AI and the technologies built upon it, predicting and inferring the sub-optimal behavior of users or human collaborators remains a critical challenge. In many cases, such behaviors are not a result of irrationality, but rather a rational decision made given inherent cognitive bounds and biased beliefs about the world. In this paper, we formally introduce a class of computational-rational (CR) user models for cognitively-bounded agents acting optimally under biased beliefs. The key novelty lies in explicitly modeling how a bounded memory process leads to a dynamically inconsistent and biased belief state and, consequently, sub-optimal sequential decision-making. We address the challenge of identifying the latent user-specific bound and inferring biased belief states from passive observations on the fly. We argue that for our formalized CR model family with an explicit and parameterized cognitive process, this challenge is tractable. To support our claim, we propose an efficient online inference method based on nested particle filtering that simultaneously tracks the user's latent belief state and estimates the unknown cognitive bound from a stream of observed actions. We validate our approach in a representative navigation task using memory decay as an example of a cognitive bound. With simulations, we show that (1) our CR model generates intuitively plausible behaviors corresponding to different levels of memory capacity, and (2) our inference method accurately and efficiently recovers the ground-truth cognitive bounds from limited observations ($\le 100$ steps). We further demonstrate how this approach provides a principled foundation for developing adaptive AI assistants, enabling adaptive assistance that accounts for the user's memory limitations.
LGMay 7
In-Context Black-Box Optimization with Unreliable FeedbackNicolas Samuel Blumer, Julien Martinelli, Samuel Kaski
Black-box optimization in science and engineering often comes with side information: experts, simulators, pretrained predictors, or heuristics can suggest which candidates look promising. This information can accelerate search, but it can also be biased, input-dependent, or misleading. Feedback-aware BO methods typically handle one task at a time, limiting their ability to generalize over multiple sources of feedback. In-context optimizers address cross-task adaptation, but usually assume that optimization history is the only available signal at test time. We study feedback-informed in-context black-box optimization (FICBO), where a pretrained optimizer conditions on both the observed history and cheap auxiliary feedback for the current candidate set. We introduce a structured feedback prior that models how feedback sources vary in their access, relevance, and distortion relative to the true objective, and use it to pretrain a feedback-aware transformer. At test time, the model estimates source reliability in context by comparing observed objective values with auxiliary signals, improving query selection. On synthetic and real-world tasks, FICBO effectively exploits informative feedback while remaining robust to weak or misleading sources, improving over other baselines. Empirical investigations further illustrate how the model perceives test-time sources, offering insights into its interpretability and decision-making process.
MLOct 20, 2024
Amortized Probabilistic Conditioning for Optimization, Simulation and InferencePaul E. Chang, Nasrulloh Loka, Daolang Huang et al.
Amortized meta-learning methods based on pre-training have propelled fields like natural language processing and vision. Transformer-based neural processes and their variants are leading models for probabilistic meta-learning with a tractable objective. Often trained on synthetic data, these models implicitly capture essential latent information in the data-generation process. However, existing methods do not allow users to flexibly inject (condition on) and extract (predict) this probabilistic latent information at runtime, which is key to many tasks. We introduce the Amortized Conditioning Engine (ACE), a new transformer-based meta-learning model that explicitly represents latent variables of interest. ACE affords conditioning on both observed data and interpretable latent variables, the inclusion of priors at runtime, and outputs predictive distributions for discrete and continuous data and latents. We show ACE's modeling flexibility and performance in diverse tasks such as image completion and classification, Bayesian optimization, and simulation-based inference.
MLNov 4, 2024
Amortized Bayesian Experimental Design for Decision-MakingDaolang Huang, Yujia Guo, Luigi Acerbi et al.
Many critical decisions, such as personalized medical diagnoses and product pricing, are made based on insights gained from designing, observing, and analyzing a series of experiments. This highlights the crucial role of experimental design, which goes beyond merely collecting information on system parameters as in traditional Bayesian experimental design (BED), but also plays a key part in facilitating downstream decision-making. Most recent BED methods use an amortized policy network to rapidly design experiments. However, the information gathered through these methods is suboptimal for down-the-line decision-making, as the experiments are not inherently designed with downstream objectives in mind. In this paper, we present an amortized decision-aware BED framework that prioritizes maximizing downstream decision utility. We introduce a novel architecture, the Transformer Neural Decision Process (TNDP), capable of instantly proposing the next experimental design, whilst inferring the downstream decision, thus effectively amortizing both tasks within a unified workflow. We demonstrate the performance of our method across several tasks, showing that it can deliver informative designs and facilitate accurate decision-making.
LGMar 7, 2024
Cooperative Bayesian Optimization for Imperfect AgentsAli Khoshvishkaie, Petrus Mikkola, Pierre-Alexandre Murena et al.
We introduce a cooperative Bayesian optimization problem for optimizing black-box functions of two variables where two agents choose together at which points to query the function but have only control over one variable each. This setting is inspired by human-AI teamwork, where an AI-assistant helps its human user solve a problem, in this simplest case, collaborative optimization. We formulate the solution as sequential decision-making, where the agent we control models the user as a computationally rational agent with prior knowledge about the function. We show that strategic planning of the queries enables better identification of the global maximum of the function as long as the user avoids excessive exploration. This planning is made possible by using Bayes Adaptive Monte Carlo planning and by endowing the agent with a user model that accounts for conservative belief updates and exploratory sampling of the points to query.
LGFeb 3, 2025
Memento No More: Coaching AI Agents to Master Multiple Tasks via Hints InternalizationMinttu Alakuijala, Ya Gao, Georgy Ananov et al.
As the general capabilities of artificial intelligence (AI) agents continue to evolve, their ability to learn to master multiple complex tasks through experience remains a key challenge. Current LLM agents, particularly those based on proprietary language models, typically rely on prompts to incorporate knowledge about the target tasks. This approach does not allow the agent to internalize this information and instead relies on ever-expanding prompts to sustain its functionality in diverse scenarios. This resembles a system of notes used by a person affected by anterograde amnesia, the inability to form new memories. In this paper, we propose a novel method to train AI agents to incorporate knowledge and skills for multiple tasks without the need for either cumbersome note systems or prior high-quality demonstration data. Our approach employs an iterative process where the agent collects new experiences, receives corrective feedback from humans in the form of hints, and integrates this feedback into its weights via a context distillation training procedure. We demonstrate the efficacy of our approach by implementing it in a Llama-3-based agent that, after only a few rounds of feedback, outperforms advanced models GPT-4o and DeepSeek-V3 in tasksets requiring correct sequencing of information retrieval, tool use, and question answering.
MLMar 31
Representative, Informative, and De-Amplifying: Requirements for Robust Bayesian Active Learning under Model MisspecificationRoubing Tang, Sabina J. Sloman, Samuel Kaski
In many science and industry settings, a central challenge is designing experiments under time and budget constraints. Bayesian Optimal Experimental Design (BOED) is a paradigm to pick maximally informative designs that has been widely applied to such problems. During training, BOED selects inputs according to a pre-determined acquisition criterion to target informativeness. During testing, the model learned during training encounters a naturally occurring distribution of test samples. This leads to an instance of covariate shift, where the train and test samples are drawn from different distributions (the training samples are not representative of the test distribution). Prior work has shown that in the presence of model misspecification, covariate shift amplifies generalization error. Our first contribution is to provide a mathematical analysis of generalization error in the presence of model misspecification, revealing that, beyond covariate shift, generalization error is also driven by a previously unidentified phenomenon we term error (de-)amplification. We then develop a new acquisition function that mitigates the effects of model misspecification by including terms for representativeness, informativeness, and de-amplification (R-IDeA). Our experimental results demonstrate that the proposed method performs better than methods that target only informativeness, only representativeness, or both.
MLMar 2, 2025
PABBO: Preferential Amortized Black-Box OptimizationXinyu Zhang, Daolang Huang, Samuel Kaski et al.
Preferential Bayesian Optimization (PBO) is a sample-efficient method to learn latent user utilities from preferential feedback over a pair of designs. It relies on a statistical surrogate model for the latent function, usually a Gaussian process, and an acquisition strategy to select the next candidate pair to get user feedback on. Due to the non-conjugacy of the associated likelihood, every PBO step requires a significant amount of computations with various approximate inference techniques. This computational overhead is incompatible with the way humans interact with computers, hindering the use of PBO in real-world cases. Building on the recent advances of amortized BO, we propose to circumvent this issue by fully amortizing PBO, meta-learning both the surrogate and the acquisition function. Our method comprises a novel transformer neural process architecture, trained using reinforcement learning and tailored auxiliary losses. On a benchmark composed of synthetic and real-world datasets, our method is several orders of magnitude faster than the usual Gaussian process-based strategies and often outperforms them in accuracy.
MLOct 10, 2025
Efficient Autoregressive Inference for Transformer Probabilistic ModelsConor Hassan, Nasrulloh Loka, Cen-You Li et al.
Transformer-based models for amortized probabilistic inference, such as neural processes, prior-fitted networks, and tabular foundation models, excel at single-pass marginal prediction. However, many real-world applications, from signal interpolation to multi-column tabular predictions, require coherent joint distributions that capture dependencies between predictions. While purely autoregressive architectures efficiently generate such distributions, they sacrifice the flexible set-conditioning that makes these models powerful for meta-learning. Conversely, the standard approach to obtain joint distributions from set-based models requires expensive re-encoding of the entire augmented conditioning set at each autoregressive step. We introduce a causal autoregressive buffer that preserves the advantages of both paradigms. Our approach decouples context encoding from updating the conditioning set. The model processes the context once and caches it. A dynamic buffer then captures target dependencies: as targets are incorporated, they enter the buffer and attend to both the cached context and previously buffered targets. This enables efficient batched autoregressive generation and one-pass joint log-likelihood evaluation. A unified training strategy allows seamless integration of set-based and autoregressive modes at minimal additional cost. Across synthetic functions, EEG signals, cognitive models, and tabular data, our method matches predictive accuracy of strong baselines while delivering up to 20 times faster joint sampling. Our approach combines the efficiency of autoregressive generative models with the representational power of set-based conditioning, making joint prediction practical for transformer-based probabilistic models.
LGMay 29, 2025
Epistemic Errors of Imperfect Multitask Learners When Distributions ShiftSabina J. Sloman, Michele Caprio, Samuel Kaski
Uncertainty-aware machine learners, such as Bayesian neural networks, output a quantification of uncertainty instead of a point prediction. In this work, we provide uncertainty-aware learners with a principled framework to characterize, and identify ways to eliminate, errors that arise from reducible (epistemic) uncertainty. We introduce a principled definition of epistemic error, and provide a decompositional epistemic error bound which operates in the very general setting of imperfect multitask learning under distribution shift. In this setting, the training (source) data may arise from multiple tasks, the test (target) data may differ systematically from the source data tasks, and/or the learner may not arrive at an accurate characterization of the source data. Our bound separately attributes epistemic errors to each of multiple aspects of the learning procedure and environment. As corollaries of the general result, we provide epistemic error bounds specialized to the settings of Bayesian transfer learning and distribution shift within $ε$-neighborhoods. We additionally leverage the terms in our bound to provide a novel definition of negative transfer.
LGNov 5, 2024
Proxy-informed Bayesian transfer learning with unknown sourcesSabina J. Sloman, Julien Martinelli, Samuel Kaski
Generalization outside the scope of one's training data requires leveraging prior knowledge about the effects that transfer, and the effects that don't, between different data sources. Transfer learning is a framework for specifying and refining this knowledge about sets of source (training) and target (prediction) data. A challenging open problem is addressing the empirical phenomenon of negative transfer, whereby the transfer learner performs worse on the target data after taking the source data into account than before. We first introduce a Bayesian perspective on negative transfer, and then a method to address it. The key insight from our formulation is that negative transfer can stem from misspecified prior information about non-transferable causes of the source data. Our proposed method, proxy-informed robust method for probabilistic transfer learning (PROMPT), does not require prior knowledge of the source data (the data sources may be "unknown"). PROMPT is thus applicable when differences between tasks are unobserved, such as in the presence of latent confounders. Moreover, the learner need not have access to observations in the target task (may not have the ability to "fine-tune"), and instead makes use of proxy (indirect) information. Our theoretical results show that the threat of negative transfer does not depend on the informativeness of the proxy information, highlighting the usefulness of PROMPT in cases where only noisy indirect information, such as human feedback, is available.