arXiv subjects

Morten Mørup

Publications and source records attributed to Morten Mørup.

At least 19 recordsLinked to original sources

arXiv2026

Exploiting chemical shift variability enables recovery of overlapping metabolites from 1H nuclear magnetic resonance spectra

Overlapping peaks and sample-dependent chemical shift variability prevent reliable metabolite recovery from complex biological spectra. This problem is critical in one-dimensional proton (1D 1H) NMR which has become the standard method providing fast acquisition and information-rich spectra in metabolomics and foodomics. This study demonstrates how chemical shifts can be utilised as a strength in 1D 1H NMR, when suitably modeled through the proposed Bayesian Shift-Invariant Non-negative Matrix Factorization (BSI-NMF) procedure. We find that BSI-NMF accurately recovers the underlying chemical signals in 1D 1H NMR spectra missed by existing analyses approaches across simulations, laboratory created datasets, and a large urine dataset obtained from 2439 people across Europe. Our study highlights how shifts in the chemical signatures - until now perceived as a nuisance - can in fact when suitably modelled be instrumental for unique recovery of metabolites. This creates an opportunity to experimentally induce chemical shifts changes to facilitate unique recovery of spectra.

q-bio.QM↗

arXiv2026

E$^2$M: Double Bounded $α$-Divergence Optimization for Tensor-based Discrete Density Estimation

Tensor-based discrete density estimation requires flexible modeling and proper divergence criteria to enable effective learning; however, traditional approaches using $α$-divergence face analytical challenges due to the $α$-power terms in the objective function, which hinder the derivation of closed-form update rules. We present a generalization of the expectation-maximization (EM) algorithm, called the E$^2$M algorithm. It circumvents this issue by first relaxing the optimization into the minimization of a surrogate objective based on the Kullback-Leibler (KL) divergence, which is tractable via the standard EM algorithm, and subsequently applying a tensor many-body approximation in the M-step to enable simultaneous closed-form updates of all parameters. Our approach offers flexible modeling for not only a variety of low-rank structures, including the CP, Tucker, and Tensor Train formats, but also their mixtures, thus allowing us to leverage the strengths of different low-rank structures. We evaluate the effectiveness of our approach on synthetic and real datasets, highlighting its comparable convergence to gradient-based procedures, robustness to outliers, and favorable density estimation performance compared to prominent existing tensor-based methods.

stat.ML↗

arXiv2026

(MPO)$^2$: Multivariate Polynomial Optimization based on Matrix Product Operators

Central to machine learning and signal processing is the ability to perform universal function approximation and learn complex input-output relationships from limited numbers of observations. Multivariate polynomial models offer a natural way to express such relationships through multiplicative feature interactions, but their coefficient tensors grow exponentially in size with the polynomial degree. Existing tensorized polynomial models reduce this cost, yet canonical polyadic decompositions have rank-limited expressivity, and tensor train formulations are feature order dependent. We introduce Multivariate Polynomial Optimization based on Matrix Product Operators (MPO)$^2$, a framework that combines learned MPO feature embeddings with compact polynomial weight tensors. This yields feature order independent polynomial representations that can incorporate structured operators such as projections, convolutions, and masks for weight tensor symmetries. Across regression and classification benchmarks, (MPO)$^2$ improves over existing tensor decomposition based polynomial models and provides a flexible alternative for efficient polynomial function approximation.

cs.LG↗

arXiv2026

Shift- and stretch-invariant non-negative matrix factorization with an application to brain tissue delineation in emission tomography data

Dynamic neuroimaging data, such as emission tomography measurements of radiotracer transport in blood or cerebrospinal fluid, often exhibit diffusion-like properties. These introduce distance-dependent temporal delays, scale-differences, and stretching effects that limit the effectiveness of conventional linear modeling and decomposition methods. To address this, we present the shift- and stretch-invariant non-negative matrix factorization framework. Our approach estimates both integer and non-integer temporal shifts as well as temporal stretching, all implemented in the frequency domain, where shifts correspond to phase modifications, and where stretching is handled via zero-padding or truncation. The model is implemented in PyTorch (https://github.com/anders-s-olsen/shiftstretchNMF). We demonstrate on synthetic data and brain emission tomography data that the model is able to account for stretching to provide more detailed characterization of brain tissue structure.

cs.LG↗

arXiv2026

Knowing When to Quit: Probabilistic Early Exits for Speech Separation

In recent years, deep learning-based single-channel speech separation has improved considerably, in large part driven by increasingly compute- and parameter-efficient neural network architectures. Most such architectures are, however, designed with a fixed compute and parameter budget and consequently cannot scale to varying compute demands or resources, which limits their use in embedded and heterogeneous devices such as mobile phones and hearables. To enable such use-cases we design a neural network architecture for speech separation and enhancement capable of early-exit, and we propose an uncertainty-aware probabilistic framework to jointly model the clean speech signal and error variance which we use to derive probabilistic early-exit conditions in terms of desired signal-to-noise ratios. We evaluate our methods on both speech separation and enhancement tasks where we demonstrate that early-exit capabilities can be introduced without compromising reconstruction, and that when trained on variable-length audio our early-exit conditions are well-calibrated and lead to considerable compute savings when used to dynamically scale compute at test time while remaining directly interpretable.

cs.LG↗

arXiv2025

A Survey on Archetypal Analysis

Archetypal analysis (AA) was originally proposed in 1994 by Adele Cutler and Leo Breiman as a computational procedure for extracting distinct aspects, so-called archetypes, from observations, with each observational record approximated as a mixture (i.e., convex combination) of these archetypes. AA thereby provides straightforward, interpretable, and explainable representations for feature extraction and dimensionality reduction, facilitating the understanding of the structure of high-dimensional data and enabling wide applications across the sciences. However, AA also faces challenges, particularly as the associated optimization problem is non-convex. This is the first survey that provides researchers and data mining practitioners with an overview of the methodologies and opportunities that AA offers, surveying the many applications of AA across disparate fields of science, as well as best practices for modeling data with AA and its limitations. The survey concludes by explaining crucial future research directions concerning AA.

stat.ME↗

arXiv2025

Estimating the Event-Related Potential from Few EEG Trials

Event-related potentials (ERP) are measurements of brain activity with wide applications in basic and clinical neuroscience, that are typically estimated using the average of many trials of electroencephalography signals (EEG) to sufficiently reduce noise and signal variability. We introduce EEG2ERP, a novel uncertainty-aware autoencoder approach that maps an arbitrary number of EEG trials to their associated ERP. To account for the ERP uncertainty we use bootstrapped training targets and introduce a separate variance decoder to model the uncertainty of the estimated ERP. We evaluate our approach in the challenging zero-shot scenario of generalizing to new subjects considering three different publicly available data sources; i) the comprehensive ERP CORE dataset that includes over 50,000 EEG trials across six ERP paradigms from 40 subjects, ii) the large P300 Speller BCI dataset, and iii) a neuroimaging dataset on face perception consisting of both EEG and magnetoencephalography (MEG) data. We consistently find that our method in the few trial regime provides substantially better ERP estimates than commonly used conventional and robust averaging procedures. EEG2ERP is the first deep learning approach to map EEG signals to their associated ERP, moving toward reducing the number of trials necessary for ERP research. Code is available at https://github.com/andersxa/EEG2ERP

cs.LG↗

arXiv2025

Modeling roles and trade-offs in multiplex networks

A multiplex social network captures multiple types of social relations among the same set of people, with each layer representing a distinct type of relationship. Understanding the structure of such systems allows us to identify how social exchanges may be driven by a person's own attributes and actions (independence), the status or resources of others (dependence), and mutual influence between entities (interdependence). Characterizing structure in multiplex networks is challenging, as the distinct layers can reflect different yet complementary roles, with interdependence emerging across multiple scales. Here, we introduce the Multiplex Latent Trade-off Model (MLT), a framework for extracting roles in multiplex social networks that accounts for independence, dependence, and interdependence. MLT defines roles as trade-offs, requiring each node to distribute its source and target roles across layers while simultaneously distributing community memberships within hierarchical, multi-scale structures. Applying the MLT approach to 176 real-world multiplex networks, composed of social, health, and economic layers, from villages in western Honduras, we see core social exchange principles emerging, while also revealing local, layer-specific, and multi-scale communities. Link prediction analyses reveal that modeling interdependence yields the greatest performance gains in the social layer, with subtler effects in health and economic layers. This suggests that social ties are structurally embedded, whereas health and economic ties are primarily shaped by individual status and behavioral engagement. Our findings offer new insights into the structure of human social systems.

cs.SI↗

arXiv2025

How Low Can You Go? Searching for the Intrinsic Dimensionality of Complex Networks using Metric Node Embeddings

Low-dimensional embeddings are essential for machine learning tasks involving graphs, such as node classification, link prediction, community detection, network visualization, and network compression. Although recent studies have identified exact low-dimensional embeddings, the limits of the required embedding dimensions remain unclear. We presently prove that lower dimensional embeddings are possible when using Euclidean metric embeddings as opposed to vector-based Logistic PCA (LPCA) embeddings. In particular, we provide an efficient logarithmic search procedure for identifying the exact embedding dimension and demonstrate how metric embeddings enable inference of the exact embedding dimensions of large-scale networks by exploiting that the metric properties can be used to provide linearithmic scaling. Empirically, we show that our approach extracts substantially lower dimensional representations of networks than previously reported for small-sized networks. For the first time, we demonstrate that even large-scale networks can be effectively embedded in very low-dimensional spaces, and provide examples of scalable, exact reconstruction for graphs with up to a million nodes. Our approach highlights that the intrinsic dimensionality of networks is substantially lower than previously reported and provides a computationally efficient assessment of the exact embedding dimension also of large-scale networks. The surprisingly low dimensional representations achieved demonstrate that networks in general can be losslessly represented using very low dimensional feature spaces, which can be used to guide existing network analysis tasks from community detection and node classification to structure revealing exact network visualizations.

cs.LG↗

arXiv2025

Archetypal Analysis for Binary Data

Archetypal analysis (AA) is a matrix decomposition method that identifies distinct patterns using convex combinations of the data points denoted archetypes with each data point in turn reconstructed as convex combinations of the archetypes. AA thereby forms a polytope representing trade-offs of the distinct aspects in the data. Most existing methods for AA are designed for continuous data and do not exploit the structure of the data distribution. In this paper, we propose two new optimization frameworks for archetypal analysis for binary data. i) A second order approximation of the AA likelihood based on the Bernoulli distribution with efficient closed-form updates using an active set procedure for learning the convex combinations defining the archetypes, and a sequential minimal optimization strategy for learning the observation specific reconstructions. ii) A Bernoulli likelihood based version of the principal convex hull analysis (PCHA) algorithm originally developed for least squares optimization. We compare these approaches with the only existing binary AA procedure relying on multiplicative updates and demonstrate their superiority on both synthetic and real binary data. Notably, the proposed optimization frameworks for AA can easily be extended to other data distributions providing generic efficient optimization frameworks for AA based on tailored likelihood functions reflecting the underlying data distribution.

cs.LG↗

arXiv2024

SepMamba: State-space models for speaker separation using Mamba

Deep learning-based single-channel speaker separation has improved significantly in recent years largely due to the introduction of the transformer-based attention mechanism. However, these improvements come at the expense of intense computational demands, precluding their use in many practical applications. As a computationally efficient alternative with similar modeling capabilities, Mamba was recently introduced. We propose SepMamba, a U-Net-based architecture composed primarily of bidirectional Mamba layers. We find that our approach outperforms similarly-sized prominent models - including transformer-based models - on the WSJ0 2-speaker dataset while enjoying a significant reduction in computational cost, memory usage, and forward pass time. We additionally report strong results for causal variants of SepMamba. Our approach provides a computationally favorable alternative to transformer-based architectures for deep speech separation.

cs.SD↗

arXiv2024

Modeling Human Responses by Ordinal Archetypal Analysis

This paper introduces a novel framework for Archetypal Analysis (AA) tailored to ordinal data, particularly from questionnaires. Unlike existing methods, the proposed method, Ordinal Archetypal Analysis (OAA), bypasses the two-step process of transforming ordinal data into continuous scales and operates directly on the ordinal data. We extend traditional AA methods to handle the subjective nature of questionnaire-based data, acknowledging individual differences in scale perception. We introduce the Response Bias Ordinal Archetypal Analysis (RBOAA), which learns individualized scales for each subject during optimization. The effectiveness of these methods is demonstrated on synthetic data and the European Social Survey dataset, highlighting their potential to provide deeper insights into human behavior and perception. The study underscores the importance of considering response bias in cross-national research and offers a principled approach to analyzing ordinal data through Archetypal Analysis.

cs.LG↗

arXiv2024

Evaluating the Influence of Temporal Context on Automatic Mouse Sleep Staging through the Application of Human Models

In human sleep staging models, augmenting the temporal context of the input to the range of tens of minutes has recently demonstrated performance improvement. In contrast, the temporal context of mouse sleep staging models is typically in the order of tens of seconds. While long-term time patterns are less clear in mouse sleep, increasing the temporal context further than that of the current mouse sleep staging models might still result in a performance increase, given that the current methods only model very short term patterns. In this study, we examine the influence of increasing the temporal context in mouse sleep staging up to 15 minutes in three mouse cohorts using two recent and high-performing human sleep staging models that account for long-term dependencies. These are compared to two prominent mouse sleep staging models that use a local context of 12 s and 20 s, respectively. An increase in context up to 28 s is observed to have a positive impact on sleep stage classification performance, especially in REM sleep. However, the impact is limited for longer context windows. One of the human sleep scoring models, L-SeqSleepNet, outperforms both mouse models in all cohorts. This suggests that mouse sleep staging can benefit from more temporal context than currently used.

q-bio.NC↗

arXiv2024

Coupled generator decomposition for fusion of electro- and magnetoencephalography data

Data fusion modeling can identify common features across diverse data sources while accounting for source-specific variability. Here we introduce the concept of a \textit{coupled generator decomposition} and demonstrate how it generalizes sparse principal component analysis (SPCA) for data fusion. Leveraging data from a multisubject, multimodal (electro- and magnetoencephalography (EEG and MEG)) neuroimaging experiment, we demonstrate the efficacy of the framework in identifying common features in response to face perception stimuli, while accommodating modality- and subject-specific variability. Through split-half cross-validation of EEG/MEG trials, we investigate the optimal model order and regularization strengths for models of varying complexity, comparing these to a group-level model assuming shared brain responses to stimuli. Our findings reveal altered $\sim170ms$ fusiform face area activation for scrambled faces, as opposed to real faces, particularly evident in the multimodal, multisubject model. Model parameters were inferred using stochastic optimization in PyTorch, demonstrating comparable performance to conventional quadratic programming inference for SPCA but with considerably faster execution. We provide an easily accessible toolbox for coupled generator decomposition that includes data fusion for SPCA, archetypal analysis and directional archetypal analysis. Overall, our approach offers a promising new avenue for data fusion.

eess.SP↗

arXiv2024

Time to Cite: Modeling Citation Networks using the Dynamic Impact Single-Event Embedding Model

Understanding the structure and dynamics of scientific research, i.e., the science of science (SciSci), has become an important area of research in order to address imminent questions including how scholars interact to advance science, how disciplines are related and evolve, and how research impact can be quantified and predicted. Central to the study of SciSci has been the analysis of citation networks. Here, two prominent modeling methodologies have been employed: one is to assess the citation impact dynamics of papers using parametric distributions, and the other is to embed the citation networks in a latent space optimal for characterizing the static relations between papers in terms of their citations. Interestingly, citation networks are a prominent example of single-event dynamic networks, i.e., networks for which each dyad only has a single event (i.e., the point in time of citation). We presently propose a novel likelihood function for the characterization of such single-event networks. Using this likelihood, we propose the Dynamic Impact Single-Event Embedding model (DISEE). The \textsc{\modelabbrev} model characterizes the scientific interactions in terms of a latent distance model in which random effects account for citation heterogeneity while the time-varying impact is characterized using existing parametric representations for assessment of dynamic impact. We highlight the proposed approach on several real citation networks finding that the DISEE well reconciles static latent distance network embedding approaches with classical dynamic impact assessments.

cs.SI↗

arXiv2023

Continuous-time Graph Representation with Sequential Survival Process

Over the past two decades, there has been a tremendous increase in the growth of representation learning methods for graphs, with numerous applications across various fields, including bioinformatics, chemistry, and the social sciences. However, current dynamic network approaches focus on discrete-time networks or treat links in continuous-time networks as instantaneous events. Therefore, these approaches have limitations in capturing the persistence or absence of links that continuously emerge and disappear over time for particular durations. To address this, we propose a novel stochastic process relying on survival functions to model the durations of links and their absences over time. This forms a generic new likelihood specification explicitly accounting for intermittent edge-persistent networks, namely GraSSP: Graph Representation with Sequential Survival Process. We apply the developed framework to a recent continuous time dynamic latent distance model characterizing network dynamics in terms of a sequence of piecewise linear movements of nodes in latent space. We quantitatively assess the developed framework in various downstream tasks, such as link prediction and network completion, demonstrating that the developed modeling framework accounting for link persistence and absence well tracks the intrinsic trajectories of nodes in a latent space and captures the underlying characteristics of evolving network structure.

cs.LG↗

arXiv2023

CSLP-AE: A Contrastive Split-Latent Permutation Autoencoder Framework for Zero-Shot Electroencephalography Signal Conversion

Electroencephalography (EEG) is a prominent non-invasive neuroimaging technique providing insights into brain function. Unfortunately, EEG data exhibit a high degree of noise and variability across subjects hampering generalizable signal extraction. Therefore, a key aim in EEG analysis is to extract the underlying neural activation (content) as well as to account for the individual subject variability (style). We hypothesize that the ability to convert EEG signals between tasks and subjects requires the extraction of latent representations accounting for content and style. Inspired by recent advancements in voice conversion technologies, we propose a novel contrastive split-latent permutation autoencoder (CSLP-AE) framework that directly optimizes for EEG conversion. Importantly, the latent representations are guided using contrastive learning to promote the latent splits to explicitly represent subject (style) and task (content). We contrast CSLP-AE to conventional supervised, unsupervised (AE), and self-supervised (contrastive learning) training and find that the proposed approach provides favorable generalizable characterizations of subject and task. Importantly, the procedure also enables zero-shot conversion between unseen subjects. While the present work only considers conversion of EEG, the proposed CSLP-AE provides a general framework for signal conversion and extraction of content (task activation) and style (subject variability) components of general interest for the modeling and analysis of biological signals.

cs.LG↗

arXiv2023

Probabilistic Block Term Decomposition for the Modelling of Higher-Order Arrays

Tensors are ubiquitous in science and engineering and tensor factorization approaches have become important tools for the characterization of higher order structure. Factorizations includes the outer-product rank Canonical Polyadic Decomposition (CPD) as well as the multi-linear rank Tucker decomposition in which the Block-Term Decomposition (BTD) is a structured intermediate interpolating between these two representations. Whereas CPD, Tucker, and BTD have traditionally relied on maximum-likelihood estimation, Bayesian inference has been use to form probabilistic CPD and Tucker. We propose, an efficient variational Bayesian probabilistic BTD, which uses the von-Mises Fisher matrix distribution to impose orthogonality in the multi-linear Tucker parts forming the BTD. On synthetic and two real datasets, we highlight the Bayesian inference procedure and demonstrate using the proposed pBTD on noisy data and for model order quantification. We find that the probabilistic BTD can quantify suitable multi-linear structures providing a means for robust inference of patterns in multi-linear data.

stat.ML↗