Thomas D. Nielsen

Luis A. Ortega, Andrés R. Masegosa, Thomas D. Nielsen

Implicit-process priors define distributions over functions through flexible generative mechanisms, making them attractive for Bayesian function-space modelling. However, performing posterior inference with such priors is challenging because their induced function-space distributions are typically not available in closed form. One practical strategy is to approximate the prior using a finite collection of sampled functions, and then represent posterior functions as learned combinations of these samples. Existing approaches commonly place a Gaussian variational distribution over the combination weights. While tractable, this choice limits the shapes of posterior uncertainty that can be represented, especially when the true posterior is asymmetric, heavy-tailed, or multimodal. We propose Flow-Transformed Implicit Processes (FTIP), a variational inference method that makes this finite-dimensional function-space approximation more expressive. Instead of using a Gaussian distribution over the combination weights, FTIP uses a normalizing flow to define a richer variational distribution. This induces a flexible posterior distribution over functions while preserving tractable optimization. We train the model using a Black-Box α objective, allowing us to compare mass-covering and mode-seeking variational behaviour. Experiments show that FTIP captures asymmetric and multimodal posterior structure in function space that Gaussian coefficient approximations tend to smooth or collapse.

Andrés R. Masegosa, Ana M. Martínez, Darío Ramos-López et al.

The AMIDST Toolbox is a software for scalable probabilistic machine learning with a spe- cial focus on (massive) streaming data. The toolbox supports a flexible modeling language based on probabilistic graphical models with latent variables and temporal dependencies. The specified models can be learnt from large data sets using parallel or distributed implementa- tions of Bayesian learning algorithms for either streaming or batch data. These algorithms are based on a flexible variational message passing scheme, which supports discrete and continu- ous variables from a wide range of probability distributions. AMIDST also leverages existing functionality and algorithms by interfacing to software tools such as Flink, Spark, MOA, Weka, R and HUGIN. AMIDST is an open source toolbox written in Java and available at http://www.amidsttoolbox.com under the Apache Software License version 2.0.

Abdulkadir Celikkanat, Andres R. Masegosa, Thomas D. Nielsen

Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of determining their microbial compositions. In this paper, we revisit k-mer-based representations of genomes and provide a theoretical analysis of their use in representation learning. Based on the analysis, we propose a lightweight and scalable model for performing metagenomic binning at the genome read level, relying only on the k-mer compositions of the DNA fragments. We compare the model to recent genome foundation models and demonstrate that while the models are comparable in performance, the proposed model is significantly more effective in terms of scalability, a crucial aspect for performing metagenomic binning of real-world datasets.

Abdulkadir Celikkanat, Andres R. Masegosa, Mads Albertsen et al.

Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as k-mer profiles or embeddings from large language models, which fail to capture the uncertainty inherent in DNA sequences arising from inter-species DNA sharing and from fragments with highly similar representations. We present the first probabilistic embedding approach, UncertainGen, for metagenomic binning, representing each DNA fragment as a probability distribution in latent space. Our approach naturally models sequence-level uncertainty, and we provide theoretical guarantees on embedding distinguishability. This probabilistic embedding framework expands the feasible latent space by introducing a data-adaptive metric, which in turn enables more flexible separation of bins/clusters. Experiments on real metagenomic datasets demonstrate the improvements over deterministic k-mer and LLM-based embeddings for the binning task by offering a scalable and lightweight solution for large-scale metagenomic analysis.

Andrés R. Masegosa, Rafael Cabañas, Helge Langseth et al.

Recent advances in statistical inference have significantly expanded the toolbox of probabilistic modeling. Historically, probabilistic modeling has been constrained to (i) very restricted model classes where exact or approximate probabilistic inference were feasible, and (ii) small or medium-sized data sets which fit within the main memory of the computer. However, developments in variational inference, a general form of approximate probabilistic inference originated in statistical physics, are allowing probabilistic modeling to overcome these restrictions: (i) Approximate probabilistic inference is now possible over a broad class of probabilistic models containing a large number of parameters, and (ii) scalable inference methods based on stochastic gradient descent and distributed computation engines allow to apply probabilistic modeling over massive data sets. One important practical consequence of these advances is the possibility to include deep neural networks within a probabilistic model to capture complex non-linear stochastic relationships between random variables. These advances in conjunction with the release of novel probabilistic modeling toolboxes have greatly expanded the scope of application of probabilistic models, and allow these models to take advantage of the recent strides made by the deep learning community. In this paper we review the main concepts, methods and tools needed to use deep neural networks within a probabilistic modeling framework.

Andres Masegosa, Thomas D. Nielsen, Helge Langseth et al.

Making inferences from data streams is a pervasive problem in many modern data analysis applications. But it requires to address the problem of continuous model updating and adapt to changes or drifts in the underlying data generating distribution. In this paper, we approach these problems from a Bayesian perspective covering general conjugate exponential models. Our proposal makes use of non-conjugate hierarchical priors to explicitly model temporal changes of the model parameters. We also derive a novel variational inference scheme which overcomes the use of non-conjugate priors while maintaining the computational efficiency of variational methods over conjugate models. The approach is validated on three real data sets over three latent variable models.

Thomas D. Nielsen, Finn Verner Jensen

Influence diagrams serve as a powerful tool for modelling symmetric decision problems. When solving an influence diagram we determine a set of strategies for the decisions involved. A strategy for a decision variable is in principle a function over its past. However, some of the past may be irrelevant for the decision, and for computational reasons it is important not to deal with redundant variables in the strategies. We show that current methods (e.g. the "Decision Bayes-ball" algorithm by Shachter UAI98) do not determine the relevant past, and we present a complete algorithm. Actually, this paper takes a more general outset: When formulating a decision scenario as an influence diagram, a linear temporal ordering of the decisions variables is required. This constraint ensures that the decision scenario is welldefined. However, the structure of a decision scenario often yields certain decisions conditionally independent, and it is therefore unnecessary to impose a linear temporal ordering on the decisions. In this paper we deal with partial influence diagrams i.e. influence diagrams with only a partial temporal ordering specified. We present a set of conditions which are necessary and sufficient to ensure that a partial influence diagram is welldefined. These conditions are used as a basis for the construction of an algorithm for determining whether or not a partial influence diagram is welldefined.

Thomas D. Nielsen, Pierre-Henri Wuillemin, Finn Verner Jensen et al.

When using Bayesian networks for modelling the behavior of man-made machinery, it usually happens that a large part of the model is deterministic. For such Bayesian networks deterministic part of the model can be represented as a Boolean function, and a central part of belief updating reduces to the task of calculating the number of satisfying configurations in a Boolean function. In this paper we explore how advances in the calculation of Boolean functions can be adopted for belief updating, in particular within the context of troubleshooting. We present experimental results indicating a substantial speed-up compared to traditional junction tree propagation.

Thomas D. Nielsen, Finn Verner Jensen

This paper deals with the representation and solution of asymmetric Bayesian decision problems. We present a formal framework, termed asymmetric influence diagrams, that is based on the influence diagram and allows an efficient representation of asymmetric decision problems. As opposed to existing frameworks, the asymmetric influece diagram primarily encodes asymmetry at the qualitative level and it can therefore be read directly from the model. We give an algorithm for solving asymmetric influence diagrams. The algorithm initially decomposes the asymmetric decision problem into a structure of symmetric subproblems organized as a tree. A solution to the decision problem can then be found by propagating from the leaves toward the root using existing evaluation methods to solve the sub-problems.