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Willem Waegeman

Willem Waegeman appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Machine LearningArtificial IntelligenceComputational Engineering, Finance, and ScienceQuantitative Methods

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Published work

9 published item(s)

preprint2026arXiv

Position: agentic AI orchestration should be Bayes-consistent

LLMs excel at predictive tasks and complex reasoning tasks, but many high-value deployments rely on decisions under uncertainty, for example, which tool to call, which expert to consult, or how many resources to invest. While the usefulness and feasibility of Bayesian approaches remain unclear for LLM inference, this position paper argues that the control layer of an agentic AI system (that orchestrates LLMs and tools) is a clear case where Bayesian principles should shine. Bayesian decision theory provides a framework for agentic systems that can help to maintain beliefs over task-relevant latent quantities, to update these beliefs from observed agentic and human-AI interactions, and to choose actions. Making LLMs themselves explicitly Bayesian belief-updating engines remains computationally intensive and conceptually nontrivial as a general modeling target. In contrast, this paper argues that coherent decision-making requires Bayesian principles at the orchestration level of the agentic system, not necessarily the LLM agent parameters. This paper articulates practical properties for Bayesian control that fit modern agentic AI systems and human-AI collaboration, and provides concrete examples and design patterns to illustrate how calibrated beliefs and utility-aware policies can improve agentic AI orchestration.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Set-valued prediction in hierarchical classification with constrained representation complexity

Set-valued prediction is a well-known concept in multi-class classification. When a classifier is uncertain about the class label for a test instance, it can predict a set of classes instead of a single class. In this paper, we focus on hierarchical multi-class classification problems, where valid sets (typically) correspond to internal nodes of the hierarchy. We argue that this is a very strong restriction, and we propose a relaxation by introducing the notion of representation complexity for a predicted set. In combination with probabilistic classifiers, this leads to a challenging inference problem for which specific combinatorial optimization algorithms are needed. We propose three methods and evaluate them on benchmark datasets: a naïve approach that is based on matrix-vector multiplication, a reformulation as a knapsack problem with conflict graph, and a recursive tree search method. Experimental results demonstrate that the last method is computationally more efficient than the other two approaches, due to a hierarchical factorization of the conditional class distribution.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Efficient Set-Valued Prediction in Multi-Class Classification

In cases of uncertainty, a multi-class classifier preferably returns a set of candidate classes instead of predicting a single class label with little guarantee. More precisely, the classifier should strive for an optimal balance between the correctness (the true class is among the candidates) and the precision (the candidates are not too many) of its prediction. We formalize this problem within a general decision-theoretic framework that unifies most of the existing work in this area. In this framework, uncertainty is quantified in terms of conditional class probabilities, and the quality of a predicted set is measured in terms of a utility function. We then address the problem of finding the Bayes-optimal prediction, i.e., the subset of class labels with highest expected utility. For this problem, which is computationally challenging as there are exponentially (in the number of classes) many predictions to choose from, we propose efficient algorithms that can be applied to a broad family of utility functions. Our theoretical results are complemented by experimental studies, in which we analyze the proposed algorithms in terms of predictive accuracy and runtime efficiency.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Efficient Pairwise Learning Using Kernel Ridge Regression: an Exact Two-Step Method

Pairwise learning or dyadic prediction concerns the prediction of properties for pairs of objects. It can be seen as an umbrella covering various machine learning problems such as matrix completion, collaborative filtering, multi-task learning, transfer learning, network prediction and zero-shot learning. In this work we analyze kernel-based methods for pairwise learning, with a particular focus on a recently-suggested two-step method. We show that this method offers an appealing alternative for commonly-applied Kronecker-based methods that model dyads by means of pairwise feature representations and pairwise kernels. In a series of theoretical results, we establish correspondences between the two types of methods in terms of linear algebra and spectral filtering, and we analyze their statistical consistency. In addition, the two-step method allows us to establish novel algorithmic shortcuts for efficient training and validation on very large datasets. Putting those properties together, we believe that this simple, yet powerful method can become a standard tool for many problems. Extensive experimental results for a range of practical settings are reported.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

On the Bayes-optimality of F-measure maximizers

The F-measure, which has originally been introduced in information retrieval, is nowadays routinely used as a performance metric for problems such as binary classification, multi-label classification, and structured output prediction. Optimizing this measure is a statistically and computationally challenging problem, since no closed-form solution exists. Adopting a decision-theoretic perspective, this article provides a formal and experimental analysis of different approaches for maximizing the F-measure. We start with a Bayes-risk analysis of related loss functions, such as Hamming loss and subset zero-one loss, showing that optimizing such losses as a surrogate of the F-measure leads to a high worst-case regret. Subsequently, we perform a similar type of analysis for F-measure maximizing algorithms, showing that such algorithms are approximate, while relying on additional assumptions regarding the statistical distribution of the binary response variables. Furthermore, we present a new algorithm which is not only computationally efficient but also Bayes-optimal, regardless of the underlying distribution. To this end, the algorithm requires only a quadratic (with respect to the number of binary responses) number of parameters of the joint distribution. We illustrate the practical performance of all analyzed methods by means of experiments with multi-label classification problems.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Spectral Analysis of Symmetric and Anti-Symmetric Pairwise Kernels

We consider the problem of learning regression functions from pairwise data when there exists prior knowledge that the relation to be learned is symmetric or anti-symmetric. Such prior knowledge is commonly enforced by symmetrizing or anti-symmetrizing pairwise kernel functions. Through spectral analysis, we show that these transformations reduce the kernel's effective dimension. Further, we provide an analysis of the approximation properties of the resulting kernels, and bound the regularization bias of the kernels in terms of the corresponding bias of the original kernel.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

A two-step learning approach for solving full and almost full cold start problems in dyadic prediction

Dyadic prediction methods operate on pairs of objects (dyads), aiming to infer labels for out-of-sample dyads. We consider the full and almost full cold start problem in dyadic prediction, a setting that occurs when both objects in an out-of-sample dyad have not been observed during training, or if one of them has been observed, but very few times. A popular approach for addressing this problem is to train a model that makes predictions based on a pairwise feature representation of the dyads, or, in case of kernel methods, based on a tensor product pairwise kernel. As an alternative to such a kernel approach, we introduce a novel two-step learning algorithm that borrows ideas from the fields of pairwise learning and spectral filtering. We show theoretically that the two-step method is very closely related to the tensor product kernel approach, and experimentally that it yields a slightly better predictive performance. Moreover, unlike existing tensor product kernel methods, the two-step method allows closed-form solutions for training and parameter selection via cross-validation estimates both in the full and almost full cold start settings, making the approach much more efficient and straightforward to implement.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Identification of functionally related enzymes by learning-to-rank methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data

In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. We propose efficient algorithms for conditional ranking by optimizing squared regression and ranking loss functions. We show theoretically, that learning with the ranking loss is likely to generalize better than with the regression loss. Further, we prove that symmetry or reciprocity properties of relations can be efficiently enforced in the learned models. Experiments on synthetic and real-world data illustrate that the proposed methods deliver state-of-the-art performance in terms of predictive power and computational efficiency. Moreover, we also show empirically that incorporating symmetry or reciprocity properties can improve the generalization performance.

0 citations0 reviewsNo code linkedOpen access