arXiv subjects

Christian Holm

Publications and source records attributed to Christian Holm.

At least 19 recordsLinked to original sources

arXiv2026

Multi-modal transformer for signal classification in nanopore blockade experiments

Nanopore devices have emerged as powerful tools for single-molecule sensing, with potential for rapid, portable diagnostics. They detect changes in ionic current as analytes enter nanometer-scale pores, providing a means of identifying diverse biomarkers from their characteristic signal patterns. However, these signals are highly complex, and reliably assigning them to specific molecules remains a major challenge. Here, we address this by introducing a multi-modal deep learning architecture that jointly processes multiple signal representations, including raw time-series data, wavelet-based images, and static feature vectors. Our approach surpasses existing methods by more than 10 percentage points on a 42-peptide benchmark and transfers to a 20-amino-acid dataset with near-perfect accuracy. The model integrates complementary information from these representations, with attention analysis showing that the time-series and wavelet-image inputs emphasize different features of the same event. Together, these results demonstrate the potential of machine learning to enable robust, high-accuracy molecular identification with nanopore sensors.

cs.LG↗

arXiv2026

How Topology Shapes the Phase Behavior of Polyelectrolytes

We develop a topology-specific theory of polyelectrolyte coacervation using the random phase approximation and apply it to both simple and complex coacervation. Our results for stars and dendrimers show that more compact chain topologies display a greater propensity for liquid-liquid phase separation, as a function of both Bjerrum length and salt concentration. For mixtures of different topologies, we demonstrate that differences in polymer topology alone are sufficient to drive multiphase coacervation of polyelectrolytes, which we rationalize in terms of an effective $\chi$ parameter. Analysis of a simplified global phase diagram reveals that the propensity for such topology-driven phase separation is largest at a finite molecular weight. Overall, our results establish polymer topology as a powerful design lever for tuning the phase diagram of charged macromolecules independently of molecular weight, net charge, and monomer chemistry, since changes in topology enable fine-tuning of the effective charge density without altering these molecular characteristics.

cond-mat.soft↗

arXiv2026

Reinforcement Learning Enables Autonomous Microrobot Navigation and Intervention in Simulated Blood Capillaries

Autonomous microrobots navigating biological vasculature could enable targeted drug delivery and thrombolysis, yet training control policies for realistic environments remains an open challenge. Prior reinforcement learning (RL) studies of microrobotic navigation have been limited to idealized geometries that omit complex hydrodynamic flow fields, confined branching structures, and dense cellular obstacles found in vivo. Here, we develop a physically grounded simulation of a blood capillary network, incorporating realistic hydrodynamic flow fields, explicit red blood cell dynamics, and anatomically derived branching geometry, and train deep RL agents to navigate it via chemotaxis. We systematically map the physical limits of navigation across robot size and swimming speed, revealing a forbidden regime where Brownian motion and flow overcome propulsion. Successful agents independently discover multiple universal strategy types, including run-and-rotate and energy-efficient search-and-sit policies, regardless of robot parameters. Without retraining, these agents perform targeted blocking and unblocking of capillary flow, restoring throughput to healthy baseline levels. These results establish RL as a viable framework for developing autonomous microrobotic intervention strategies in complex biological environments.

cs.RO↗

arXiv2026

Spectral Reach: Understanding Neural Scaling as Progress into the Spectral Tail

Neural scaling laws describe predictable power-law relationships between model size, dataset size, compute, and performance. While these laws guide the development of modern foundation models, the mechanisms underpinning them remain poorly understood, in part due to the absence of scalable analysis tools. To close this gap, we introduce "spectral position": a scalable measure of which eigenvalues of the empirical neural tangent kernel (eNTK) currently drive loss reduction. Applying this measure to scaling experiments, we find that spectral position decreases throughout training: learning shifts from dominant eigenmodes into the spectral tail. Larger models reach further into the tail than smaller models, revealing a size-dependent capacity we call "spectral reach". This suggests why larger models achieve lower losses: they sustain learning on weak spectral signals inaccessible to smaller models. We further identify feature learning as a key enabler of spectral reach. It adaptively amplifies gradient magnitudes as learning advances, sustaining progress where frozen representations stall. This points to concrete interventions through architecture and optimizer design.

cs.LG↗

arXiv2026

Multivariate quantum reservoir computing with discrete and continuous variable systems

Quantum reservoir computing is a promising paradigm for processing temporal data. So far, the primary focus has been on univariate time series. However, the most relevant and complex real-world data is multidimensional. In this paper, we establish an extensive framework for multivariate data processing in quantum reservoir computing. We propose and evaluate three multivariate encoding schemes and introduce the mixing capacity as a novel metric to evaluate the effectiveness with which a reservoir combines independent data streams. The computational performance of these proposed schemes is systematically assessed using this metric, as well as on the chaotic Lorenz-63 system prediction task, for two quantum reservoirs based on discrete and continuous-variable quantum systems. Furthermore, we relate the computational performance on these tasks to the underlying quantum properties of the reservoir. Our findings reveal that the optimal encoding method is highly dependent on the reservoir system and the specific task, underlining the importance of a task-specific input design. Moreover, we observe that peak computational performance coincides with the presence of non-classical effects, which indicates that quantum resources play a role in processing multivariate data.

quant-ph↗

arXiv2025

Deep Learning-Driven Peptide Classification in Biological Nanopores

Nanopore-based single-molecule sensing is a promising route to fast, low-cost disease diagnosis and protein sequencing: as an analyte such as a peptide or protein traverses a nanoscale pore, it modulates the ionic current, producing a resistive pulse whose signature is determined by the analyte's structure and its interactions with the pore. Translating these signatures into reliable molecular identities, however, is an open problem well suited for machine learning, as the signals are noisy, suffer from variations due to experimental conditions, and are difficult to featurize, which has so far limited classification accuracy. Here we translate the peptide identification problem into an image-classification task by transforming each resistive pulse into a scaleogram via the continuous wavelet transform, a representation that jointly encodes amplitude, frequency, and time in a form well suited for deep convolutional models. On a dataset of 42 peptides, recorded as six separate peptide ladders, this approach reaches a macro-averaged classification accuracy of $82\,\%$ on held-out events, an improvement of $8.6$ percentage points over the descriptor-based approach previously reported for the same dataset. We further show that the trained models tolerate substantial compression, retaining their accuracy with half of their weights set to zero and under 8-bit quantization, a prerequisite for deploying trained classifiers on embedded sensing hardware. Our results demonstrate how physically motivated signal representations can make complex single-molecule data tractable for modern learning algorithms, a step on the path towards point-of-care peptide and protein diagnostics.

cs.LG↗

arXiv2025

Robustness of quantum algorithms: Worst-case fidelity bounds and implications for design

Errors occurring on noisy hardware pose a key challenge to reliable quantum computing. Existing techniques such as error correction, mitigation, or suppression typically separate the error handling from the algorithm analysis and design. In this paper, we develop an alternative, algorithm-centered framework for understanding and improving the robustness against errors. For a given quantum algorithm and error model, we derive worst-case fidelity bounds which can be efficiently computed to certify the robustness. We consider general error models including coherent and (Markovian) incoherent errors and allowing for set-based error descriptions to address uncertainty or time-dependence in the errors. Our results give rise to guidelines for robust algorithm design and compilation by optimizing our theoretical robustness measure. We demonstrate the practicality of the framework with numerical results on algorithm analysis and robust optimization, including the robustness analysis of a 50-qubit modular adder circuit.

quant-ph↗

arXiv2025

Beyond Scaling Curves: Internal Dynamics of Neural Networks Through the NTK Lens

Scaling laws offer valuable insights into the relationship between neural network performance and computational cost, yet their underlying mechanisms remain poorly understood. In this work, we empirically analyze how neural networks behave under data and model scaling through the lens of the neural tangent kernel (NTK). This analysis establishes a link between performance scaling and the internal dynamics of neural networks. Our findings of standard vision tasks show that similar performance scaling exponents can occur even though the internal model dynamics show opposite behavior. This demonstrates that performance scaling alone is insufficient for understanding the underlying mechanisms of neural networks. We also address a previously unresolved issue in neural scaling: how convergence to the infinite-width limit affects scaling behavior in finite-width models. To this end, we investigate how feature learning is lost as the model width increases and quantify the transition between kernel-driven and feature-driven scaling regimes. We identify the maximum model width that supports feature learning, which, in our setups, we find to be more than ten times smaller than typical large language model widths.

cs.LG↗

arXiv2025

The interplay of robustness and generalization in quantum machine learning

While adversarial robustness and generalization have individually received substantial attention in the recent literature on quantum machine learning, their interplay is much less explored. In this chapter, we address this interplay for variational quantum models, which were recently proposed as function approximators in supervised learning. We discuss recent results quantifying both robustness and generalization via Lipschitz bounds, which explicitly depend on model parameters. Thus, they give rise to a regularization-based training approach for robust and generalizable quantum models, highlighting the importance of trainable data encoding strategies. The practical implications of the theoretical results are demonstrated with an application to time series analysis.

quant-ph↗

arXiv2025

Apax: A Flexible and Performant Framework For The Development of Machine-Learned Interatomic Potentials

We introduce Atomistic learned potentials in JAX (apax), a flexible and efficient open source software package for training and inference of machine-learned interatomic potentials. Built on the JAX framework, apax supports GPU acceleration and implements flexible model abstractions for fast development. With features such as kernel-based data selection, well-calibrated uncertainty estimation, and enhanced sampling, it is tailored to active learning applications and ease of use. The features and design decisions made in apax are discussed before demonstrating some of its capabilities. First, a data set for the room-temperature ionic liquid EMIM+BF4- is created using active learning. It is highlighted how continuously learning models between iterations can reduce training times up to 85 % with only a minor reduction of the models' accuracy. Second, we show good scalability in a data-parallel training setting. We report that a Gaussian Moment Neural Network model, as implemented in apax, achieves higher accuracy and up to 10 times faster inference times than a performance-optimized Allegro model. A recently published Li3PO4 dataset, reported with comparable accuracy and inference performance metrics, is used as a point of comparison. Moreover, the inference speeds of the available simulation engines are compared. Finally, to highlight the modularity of apax, an equivariant message-passing model is trained as a shallow ensemble and used to perform uncertainty-driven dynamics.

physics.chem-ph↗

arXiv2025

Quantum vs. classical: A comprehensive benchmark study for predicting time series with variational quantum machine learning

Variational quantum machine learning algorithms have been proposed as promising tools for time series prediction, with the potential to handle complex sequential data more effectively than classical approaches. However, their practical advantage over established classical methods remains uncertain. In this work, we present a comprehensive benchmark study comparing a range of variational quantum algorithms and classical machine learning models for time series forecasting. We evaluate their predictive performance on three chaotic systems across 27 time series prediction tasks of varying complexity, and ensure a fair comparison through extensive hyperparameter optimization. Our results indicate that, in many cases, quantum models struggle to match the accuracy of simple classical counterparts of comparable complexity. Furthermore, we analyze the predictive performance relative to the model complexity and discuss the practical limitations of variational quantum algorithms for time series forecasting.

quant-ph↗

arXiv2025

Intermittent flow paths in biofilms grown in a microfluidic channel

Biofilms exposed to flow experience shear stress, which leads to a competitive interaction between the growth and development of a biofilm and shearing. In this study, Pseudonomas fluorescene biofilm was grown in a microfluidic channel and exposed to forced flow of an aqueous solution of variable velocity. It can be observed that under certain conditions preferential flow paths form with a dynamic, but quasi-steady state interaction of growth, detachment, and re-attachment. We find that the regimes for preferential flow path development are determined by nutrient availability and the ratio of shear stress versus the biofilm's ability to resist shear forces. The intermittent regime of flow paths is mainly driven by the supply with nutrients, which we confirm by comparison with a numerical model based on coarse-grained molecular dynamics and Lattice Boltzmann hydrodynamics.

physics.flu-dyn↗

arXiv2025

Intermittent molecular motion and first passage statistics for the NMR relaxation of confined water

The structure and dynamics of fluids confined in nanoporous media differ from those in bulk, which can be probed using NMR relaxation measurements. We here show, using atomistic molecular dynamics simulations of water in a slit nanopore, that the behavior of the NMR relaxation rate, R1, with varying surface interaction and confinement strength can be estimated from the exchange statistics of fluid molecules between the adsorbed surface layer and the bulk region, where molecules undergo intermittent dynamics. We employ first return passage time calculations to quantify the molecular exchange statistics, thereby linking microscopic parameters of the confined fluid-such as adsorption time, pore size, and diffusion coefficient-to the NMR relaxation rate. This approach allows to predict and interpret the molecular relaxation of fluids at interfaces using merely concepts of statistical mechanics and can be generalized to closed and open geometries.

cond-mat.soft↗

arXiv2024

Collective variables of neural networks: empirical time evolution and scaling laws

This work presents a novel means for understanding learning dynamics and scaling relations in neural networks. We show that certain measures on the spectrum of the empirical neural tangent kernel, specifically entropy and trace, yield insight into the representations learned by a neural network and how these can be improved through architecture scaling. These results are demonstrated first on test cases before being shown on more complex networks, including transformers, auto-encoders, graph neural networks, and reinforcement learning studies. In testing on a wide range of architectures, we highlight the universal nature of training dynamics and further discuss how it can be used to understand the mechanisms behind learning in neural networks. We identify two such dominant mechanisms present throughout machine learning training. The first, information compression, is seen through a reduction in the entropy of the NTK spectrum during training, and occurs predominantly in small neural networks. The second, coined structure formation, is seen through an increasing entropy and thus, the creation of structure in the neural network representations beyond the prior established by the network at initialization. Due to the ubiquity of the latter in deep neural network architectures and its flexibility in the creation of feature-rich representations, we argue that this form of evolution of the network's entropy be considered the onset of a deep learning regime.

cs.LG↗

arXiv2024

CO2-induced Drastic Decharging of Dielectric Surfaces in Aqueous Suspensions

We study the influence of airborne CO2 on the charge state of carboxylate stabilized polymer latex particles suspended in aqueous electrolytes. We combine conductometric experiments interpreted in terms of Hessinger's conductivity model with Poisson-Boltzmann cell (PBC) model calculations with charge regulation boundary conditions. Without CO2, a minority of the weakly acidic surface groups are dissociated and only a fraction of the total number of counter-ions actually contribute to conductivity. The remaining counter-ions exchange freely with added other ions like Na+, K+ or Cs+. From the PBC-calculations we infer a corresponding pKa of 4.26 as well as a renormalized charge in reasonably good agreement with the number of freely mobile counter-ions. Equilibration of salt- and CO2-free suspensions against ambient air leads to a drastic de-charging, which exceeds by far the expected effects of to dissolved CO2 and its dissociation products. Further, no counter-ion-exchange is observed. To reproduce the experimental findings, we have to assume an effective pKa of 6.48. This direct influence of CO2 on the state of surface group dissociation explains our recent finding of a CO2-induced decrease of the {\zeta}-potential and supports the suggestion of an additional charge regulation caused by molecular CO2. Given the importance of charged surfaces in contact with aqueous electrolytes, we anticipate that our observations bear substantial theoretical challenges and important implications for applications ranging from desalination to bio-membranes.

cond-mat.soft↗

arXiv2024

Peptide Classification from Statistical Analysis of Nanopore Translocation Experiments

Protein characterization using nanopore-based devices promises to be a breakthrough method in basic research, diagnostics, and analytics. Current research includes the use of machine learning to achieve this task. In this work, a comprehensive statistical analysis of nanopore current signals is performed and demonstrated to be sufficient for classifying up to 42 peptides with over 70 % accuracy. Two sets of features, the statistical moments and the catch22 set, are compared both in their representations and after training small classifier neural networks. We demonstrate that complex features of the events, captured in both the catch22 set and the central moments, are key in classifying peptides with otherwise similar mean currents. These results highlight the efficacy of purely statistical analysis of nanopore data and suggest a path forward for more sophisticated classification techniques.

physics.bio-ph↗

arXiv2024

SwarmRL: Building the Future of Smart Active Systems

This work introduces SwarmRL, a Python package designed to study intelligent active particles. SwarmRL provides an easy-to-use interface for developing models to control microscopic colloids using classical control and deep reinforcement learning approaches. These models may be deployed in simulations or real-world environments under a common framework. We explain the structure of the software and its key features and demonstrate how it can be used to accelerate research. With SwarmRL, we aim to streamline research into micro-robotic control while bridging the gap between experimental and simulation-driven sciences. SwarmRL is available open-source on GitHub at https://github.com/SwarmRL/SwarmRL.

cs.RO↗

arXiv2024

Generating Quantum Reservoir State Representations with Random Matrices

We demonstrate a novel approach to reservoir computation measurements using random matrices. We do so to motivate how atomic-scale devices could be used for real-world computational applications. Our approach uses random matrices to construct reservoir measurements, introducing a simple, scalable means of generating state representations. In our studies, two reservoirs, a five-atom Heisenberg spin chain and a five-qubit quantum circuit, perform time series prediction and data interpolation. The performance of the measurement technique and current limitations are discussed in detail, along with an exploration of the diversity of measurements provided by the random matrices. In addition, we explore the role of reservoir parameters such as coupling strength and measurement dimension, providing insight into how these learning machines could be automatically tuned for different problems. This research highlights the use of random matrices to measure simple quantum reservoirs for natural learning devices, and outlines a path forward for improving their performance and experimental realization.

quant-ph↗