Agnieszka Pregowska

Agnieszka Pregowska, Hazem M. Kalaji

Reconstructing continuous environmental fields from sparse and irregular observations remains a central challenge in environmental modelling and biodiversity informatics. Many ecological datasets are heterogeneous in space and time, making grid-based approaches difficult to scale or generalise across domains. Here, we evaluate implicit neural representations (INRs) as a coordinate-based modelling framework for learning continuous spatial and spatio-temporal fields directly from coordinate inputs. We analyse their behaviour across three representative modelling scenarios: species distribution reconstruction, phenological dynamics, and morphological segmentation derived from open biodiversity data. Beyond predictive performance, we examine interpolation behaviour, spatial coherence, and computational characteristics relevant for environmental modelling workflows, including scalability, resolution-independent querying, and architectural inductive bias. Results show that neural fields provide stable continuous representations with predictable computational cost, complementing classical smoothers and tree-based approaches. These findings position coordinate-based neural fields as a flexible representation layer that can be integrated into environmental modelling pipelines and exploratory analysis frameworks for large, irregularly sampled datasets.

Agnieszka Pregowska, Stefan Marynowicz

Accurate assessment of lithium-ion battery ageing is challenged by cell-to-cell variability, heterogeneous cycling protocols, and limited transferability of data-driven models across datasets. In particular, robust identification of degradation transitions, such as the knee point, and reliable early-life prediction of remaining useful life (RUL) remain open problems. This study proposes a unified framework for battery ageing analysis based on continuous representations of voltage-capacity and capacity-cycle trajectories learned from heterogeneous public datasets (NASA, CALCE, ISU-ILCC). The continuous formulation enables consistent extraction of degradation descriptors, including curvature, plateau length and knee-related metrics, while reducing sensitivity to dataset-specific discretisation. Across more than 250 cells, statistically significant correlations between knee onset and end-of-life (Pearson 0.75-0.84) are observed. Additional early-life analysis confirms that knee-related features retain predictive value when estimated from partial trajectories. Early-life models provide increasingly stable RUL predictions as the number of observed cycles increases, with meaningful predictive performance emerging within the first 5-20 cycles and remain robust under cross-dataset domain shift. The framework integrates continuous modelling, feature extraction and uncertainty-aware prediction, providing an interpretable and dataset-consistent approach demonstrating robustness across heterogeneous dataset types. Compared with conventional discrete or feature-based methods, the proposed representation reduces sensitivity to sampling resolution and improves cross-dataset consistency. The study is limited to laboratory-scale datasets and capacity-based end-of-life definitions.

Agnieszka Pregowska

Implicit neural representations (INRs) offer continuous coordinate-based encodings for atlas registration, cross-modality resampling, sparse-view completion, and compact sharing of neuroanatomical data. Yet reproducible evaluation is lacking for high-resolution larval zebrafish microscopy, where preserving neuropil boundaries and fine neuronal processes is critical. We present a reproducible INR benchmark for the MapZebrain larval zebrafish brain atlas. Using a unified, seed-controlled protocol, we compare SIREN, Fourier features, Haar positional encoding, and a multi-resolution grid on 950 grayscale microscopy images, including atlas slices and single-neuron projections. Images are normalized with per-image (1,99) percentiles estimated from 10% of pixels in non-held-out columns, and spatial generalization is tested with a deterministic 40% column-wise hold-out along the X-axis. Haar and Fourier achieve the strongest macro-averaged reconstruction fidelity on held-out columns (about 26 dB), while the grid is moderately behind. SIREN performs worse in macro averages but remains competitive on area-weighted micro averages in the all-in-one regime. SSIM and edge-focused error further show that Haar and Fourier preserve boundaries more accurately. These results indicate that explicit spectral and multiscale encodings better capture high-frequency neuroanatomical detail than smoother-bias alternatives. For MapZebrain workflows, Haar and Fourier are best suited to boundary-sensitive tasks such as atlas registration, label transfer, and morphology-preserving sharing, while SIREN remains a lightweight baseline for background modelling or denoising.

Agnieszka Pregowska, Agata Roszkiewicz, Magdalena Osial et al.

We focus on the potential possibilities for supporting Scanning Probe Microscopy measurements, emphasizing the application of Artificial Intelligence, especially Machine Learning as well as quantum computing. It turned out that Artificial Intelligence can be helpful in the experimental processes automation in routine operations, the algorithmic search for good sample regions, and shed light on the structure property relationships. Thus, it contributes to increasing the efficiency and accuracy of optical nanoscopy scanning probes. Moreover, the combination of Artificial Intelligence based algorithms and quantum computing may have a huge potential to increase the practical application of Scanning Probe Microscopy. The limitations were also discussed. Finally, we outline a research path for the improvement of the proposed approach.

Marcin Podhajski, Jan Dubiński, Franziska Boenisch et al.

Graph Neural Networks (GNNs) are recognized as potent tools for processing real-world data organized in graph structures. Especially inductive GNNs, which allow for the processing of graph-structured data without relying on predefined graph structures, are becoming increasingly important in a wide range of applications. As such these networks become attractive targets for model-stealing attacks where an adversary seeks to replicate the functionality of the targeted network. Significant efforts have been devoted to developing model-stealing attacks that extract models trained on images and texts. However, little attention has been given to stealing GNNs trained on graph data. This paper identifies a new method of performing unsupervised model-stealing attacks against inductive GNNs, utilizing graph contrastive learning and spectral graph augmentations to efficiently extract information from the targeted model. The new type of attack is thoroughly evaluated on six datasets and the results show that our approach outperforms the current state-of-the-art by Shen et al. (2021). In particular, our attack surpasses the baseline across all benchmarks, attaining superior fidelity and downstream accuracy of the stolen model while necessitating fewer queries directed toward the target model.

Zofia Rudnicka, Janusz Szczepanski, Agnieszka Pregowska

This study explores how the selection of neuron models and learning rules impacts the classification performance of Spiking Neural Networks (SNNs), with a focus on applications in bio-signal processing. We compare biologically inspired neuron models, including Leaky Integrate-and-Fire (LIF), metaneurons, and probabilistic Levy-Baxter (LB) neurons, across multiple learning rules, including spike-timing-dependent plasticity (STDP), tempotron, and reward-modulated updates. A novel element of this work is the integration of a complexity-based decision mechanism into the evaluation pipeline. Using Lempel-Ziv Complexity (LZC), a measure related to entropy rate, we quantify the structural regularity of spike trains and assess classification outcomes in a consistent and interpretable manner across different SNN configurations. To investigate neural dynamics and assess algorithm performance, we employed synthetic datasets with varying temporal dependencies and stochasticity levels. These included Markov and Poisson processes, well-established models to simulate neuronal spike trains and capture the stochastic firing behavior of biological neurons.Validation of synthetic Poisson and Markov-modeled data reveals clear performance trends: classification accuracy depends on the interaction between neuron model, network size, and learning rule, with the LZC-based evaluation highlighting configurations that remain robust to weak or noisy signals. This work delivers a systematic analysis of how neuron model selection interacts with network parameters and learning strategies, supported by a novel complexity-based evaluation approach that offers a consistent benchmark for SNN performance.

Zofia Rudnicka, Janusz Szczepanski, Agnieszka Pregowska

Purpose: Spiking neural networks (SNNs) have recently gained attention as energy-efficient, biologically plausible alternatives to conventional deep learning models. Their application in high-stakes biomedical imaging remains almost entirely unexplored. Methods: This study introduces SNNDeep, the first tailored SNN specifically optimized for binary classification of liver health status from computed tomography (CT) features. To ensure clinical relevance and broad generalizability, the model was developed and evaluated using the Task03\Liver dataset from the Medical Segmentation Decathlon (MSD), a standardized benchmark widely used for assessing performance across diverse medical imaging tasks. We benchmark three fundamentally different learning algorithms, namely Surrogate Gradient Learning, the Tempotron rule, and Bio-Inspired Active Learning across three architectural variants: a fully customized low-level model built from scratch, and two implementations using leading SNN frameworks, i.e., snnTorch and SpikingJelly. Hyperparameter optimization was performed using Optuna. Results: Our results demonstrate that the custom-built SNNDeep consistently outperforms framework-based implementations, achieving a maximum validation accuracy of 98.35%, superior adaptability across learning rules, and significantly reduced training overhead. Conclusion:This study provides the first empirical evidence that low-level, highly tunable SNNs can surpass standard frameworks in medical imaging, especially in data-limited, temporally constrained diagnostic settings, thereby opening a new pathway for neuro-inspired AI in precision medicine.

Zofia Rudnicka, Janusz Szczepanski, Agnieszka Pregowska

This study introduces a novel approach by replacing the traditional perceptron neuron model with a biologically inspired probabilistic meta neuron, where the internal neuron parameters are jointly learned, leading to improved classification accuracy of spiking neural networks (SNNs). To validate this innovation, we implement and compare two SNN architectures: one based on standard leaky integrate-and-fire (LIF) neurons and another utilizing the proposed probabilistic meta neuron model. As a second key contribution, we present a new biologically inspired classification framework that uniquely integrates SNNs with Lempel-Ziv complexity (LZC) a measure closely related to entropy rate. By combining the temporal precision and biological plausibility of SNNs with the capacity of LZC to capture structural regularity, the proposed approach enables efficient and interpretable classification of spatiotemporal neural data, an aspect not addressed in existing works. We consider learning algorithms such as backpropagation, spike-timing-dependent plasticity (STDP), and the Tempotron learning rule. To explore neural dynamics, we use Poisson processes to model neuronal spike trains, a well-established method for simulating the stochastic firing behavior of biological neurons. Our results reveal that depending on the training method, the classifier's efficiency can improve by up to 11.00%, highlighting the advantage of learning additional neuron parameters beyond the traditional focus on weighted inputs alone.