arXiv subjects

Bogdan Gabrys

Publications and source records attributed to Bogdan Gabrys.

At least 19 recordsLinked to original sources

arXiv2026

Multipath Adaptive Gated Bottleneck Latent ODE with Raman Data Fusion for Cell Culture Process Forecasting

Mammalian cell-culture processes underpin the manufacture of many biopharmaceuticals, yet keeping a run on track is hard: critical process parameters drift over days, and an off-specification trend is often confirmed too late to intervene. Early-stage, multi-day forecasts could enable timely adjustment of feeding, sampling, and control, but bioprocess forecasting is challenging because measurements are sparse and irregularly sampled, operating conditions are heterogeneous across cell lines and media, and runs with near-identical early behaviour can diverge into different futures. We propose an adaptive framework combining a Gated Bottleneck Latent Ordinary Differential Equation (GB-Latent ODE) with Multi-Path Just-In-Time Fine Tuning (MP-JIT-FT). The GB-Latent ODE augments the stan dard Latent ODE with learnable variable-wise gating and a mask-aware bottleneck that compress high-dimensional sparse inputs, improving learning under limited data. Given a partially observed run, MP-JIT-FT retrieves similar historical trajectories, clusters the local neighbourhood into candidate regimes, and fine-tunes a separate model per regime to produce multiple plausible paths, each with a reconstruction-based confidence score, not a single averaged forecast. We further fuse Raman spectroscopy data: a machine-learning soft sensor turns dense Raman spectra into pseudo-observations that enrich the sparse offline measurements for more robust training. On 38 fed-batch 5L bioreactor runs spanning 14 conditions, MP-JIT-FT with Raman fusion achieves the best average rank and outperforms a global Latent ODE baseline on 8 of 9 target variables. Using local-divergence metrics, we show the multi-path gains are largest when locally similar prefixes diverge, whereas Raman fusion helps most when early dynamics are representative of later behaviour.

cs.LG↗

arXiv2025

Learning From Limited Data and Feedback for Cell Culture Process Monitoring: A Comparative Study

In cell culture bioprocessing, real-time batch process monitoring (BPM) refers to the continuous tracking and analysis of key process variables such as viable cell density, nutrient levels, metabolite concentrations, and product titer throughout the duration of a batch run. This enables early detection of deviations and supports timely control actions to ensure optimal cell growth and product quality. BPM plays a critical role in ensuring the quality and regulatory compliance of biopharmaceutical manufacturing processes. However, the development of accurate soft sensors for BPM is hindered by key challenges, including limited historical data, infrequent feedback, heterogeneous process conditions, and high-dimensional sensory inputs. This study presents a comprehensive benchmarking analysis of machine learning (ML) methods designed to address these challenges, with a focus on learning from historical data with limited volume and relevance in the context of bioprocess monitoring. We evaluate multiple ML approaches including feature dimensionality reduction, online learning, and just-in-time learning across three datasets, one in silico dataset and two real-world experimental datasets. Our findings highlight the importance of training strategies in handling limited data and feedback, with batch learning proving effective in homogeneous settings, while just-in-time learning and online learning demonstrate superior adaptability in cold-start scenarios. Additionally, we identify key meta-features, such as feed media composition and process control strategies, that significantly impact model transferability. The results also suggest that integrating Raman-based predictions with lagged offline measurements enhances monitoring accuracy, offering a promising direction for future bioprocess soft sensor development.

q-bio.QM↗

arXiv2025

Lessons Learned from Deploying Adaptive Machine Learning Agents with Limited Data for Real-time Cell Culture Process Monitoring

This study explores the deployment of three machine learning (ML) approaches for real-time prediction of glucose, lactate, and ammonium concentrations in cell culture processes, using Raman spectroscopy as input features. The research addresses challenges associated with limited data availability and process variability, providing a comparative analysis of pretrained models, just-in-time learning (JITL), and online learning algorithms. Two industrial case studies are presented to evaluate the impact of varying bioprocess conditions on model performance. The findings highlight the specific conditions under which pretrained models demonstrate superior predictive accuracy and identify scenarios where JITL or online learning approaches are more effective for adaptive process monitoring. This study also highlights the critical importance of updating the deployed models/agents with the latest offline analytical measurements during bioreactor operations to maintain the model performance against the changes in cell growth behaviours and operating conditions throughout the bioreactor run. Additionally, the study confirms the usefulness of a simple mixture-of-experts framework in achieving enhanced accuracy and robustness for real-time predictions of metabolite concentrations based on Raman spectral data. These insights contribute to the development of robust strategies for the efficient deployment of ML models in dynamic and changing biomanufacturing environments.

q-bio.QM↗

arXiv2025

The Illusion of Progress: Re-evaluating Hallucination Detection in LLMs

Large language models (LLMs) have revolutionized natural language processing, yet their tendency to hallucinate poses serious challenges for reliable deployment. Despite numerous hallucination detection methods, their evaluations often rely on ROUGE, a metric based on lexical overlap that misaligns with human judgments. Through comprehensive human studies, we demonstrate that while ROUGE exhibits high recall, its extremely low precision leads to misleading performance estimates. In fact, several established detection methods show performance drops of up to 45.9\% when assessed using human-aligned metrics like LLM-as-Judge. Moreover, our analysis reveals that simple heuristics based on response length can rival complex detection techniques, exposing a fundamental flaw in current evaluation practices. We argue that adopting semantically aware and robust evaluation frameworks is essential to accurately gauge the true performance of hallucination detection methods, ultimately ensuring the trustworthiness of LLM outputs.

cs.CL↗

arXiv2025

Machine Learning Methods for Small Data and Upstream Bioprocessing Applications: A Comprehensive Review

Data is crucial for machine learning (ML) applications, yet acquiring large datasets can be costly and time-consuming, especially in complex, resource-intensive fields like biopharmaceuticals. A key process in this industry is upstream bioprocessing, where living cells are cultivated and optimised to produce therapeutic proteins and biologics. The intricate nature of these processes, combined with high resource demands, often limits data collection, resulting in smaller datasets. This comprehensive review explores ML methods designed to address the challenges posed by small data and classifies them into a taxonomy to guide practical applications. Furthermore, each method in the taxonomy was thoroughly analysed, with a detailed discussion of its core concepts and an evaluation of its effectiveness in tackling small data challenges, as demonstrated by application results in the upstream bioprocessing and other related domains. By analysing how these methods tackle small data challenges from different perspectives, this review provides actionable insights, identifies current research gaps, and offers guidance for leveraging ML in data-constrained environments.

cs.LG↗

arXiv2025

FactSelfCheck: Fact-Level Black-Box Hallucination Detection for LLMs

Large Language Models (LLMs) frequently generate hallucinated content, posing significant challenges for applications where factuality is crucial. While existing hallucination detection methods typically operate at the sentence level or passage level, we propose FactSelfCheck, a novel zero-resource black-box sampling-based method that enables fine-grained fact-level detection. Our approach represents text as interpretable knowledge graphs consisting of facts in the form of triples, providing clearer insights into content factuality than traditional approaches. Through analyzing factual consistency across multiple LLM responses, we compute fine-grained hallucination scores without requiring external resources or training data. Our evaluation demonstrates that FactSelfCheck performs competitively with leading sentence-level sampling-based methods while providing more detailed and interpretable insights. Most notably, our fact-level approach significantly improves hallucination correction, achieving a 35.5% increase in factual content compared to the baseline, while sentence-level SelfCheckGPT yields only a 10.6% improvement. The granular nature of our detection enables more precise identification and correction of hallucinated content. Additionally, we contribute FavaMultiSamples, a novel dataset that addresses a gap in the field by providing the research community with a second dataset for evaluating sampling-based methods.

cs.LG↗

arXiv2025

Hallucination Detection in LLMs Using Spectral Features of Attention Maps

Large Language Models (LLMs) have demonstrated remarkable performance across various tasks but remain prone to hallucinations. Detecting hallucinations is essential for safety-critical applications, and recent methods leverage attention map properties to this end, though their effectiveness remains limited. In this work, we investigate the spectral features of attention maps by interpreting them as adjacency matrices of graph structures. We propose the $\text{LapEigvals}$ method, which utilises the top-$k$ eigenvalues of the Laplacian matrix derived from the attention maps as an input to hallucination detection probes. Empirical evaluations demonstrate that our approach achieves state-of-the-art hallucination detection performance among attention-based methods. Extensive ablation studies further highlight the robustness and generalisation of $\text{LapEigvals}$, paving the way for future advancements in the hallucination detection domain.

cs.LG↗

arXiv2024

Deep Reinforcement Learning for Digital Twin-Oriented Complex Networked Systems

The Digital Twin Oriented Complex Networked System (DT-CNS) aims to build and extend a Complex Networked System (CNS) model with progressively increasing dynamics complexity towards an accurate reflection of reality -- a Digital Twin of reality. Our previous work proposed evolutionary DT-CNSs to model the long-term adaptive network changes in an epidemic outbreak. This study extends this framework by proposeing the temporal DT-CNS model, where reinforcement learning-driven nodes make decisions on temporal directed interactions in an epidemic outbreak. We consider cooperative nodes, as well as egocentric and ignorant "free-riders" in the cooperation. We describe this epidemic spreading process with the Susceptible-Infected-Recovered ($SIR$) model and investigate the impact of epidemic severity on the epidemic resilience for different types of nodes. Our experimental results show that (i) the full cooperation leads to a higher reward and lower infection number than a cooperation with egocentric or ignorant "free-riders"; (ii) an increasing number of "free-riders" in a cooperation leads to a smaller reward, while an increasing number of egocentric "free-riders" further escalate the infection numbers and (iii) higher infection rates and a slower recovery weakens networks' resilience to severe epidemic outbreaks. These findings also indicate that promoting cooperation and reducing "free-riders" can improve public health during epidemics.

cs.AI↗

arXiv2024

Hyperbox Mixture Regression for Process Performance Prediction in Antibody Production

This paper addresses the challenges of predicting bioprocess performance, particularly in monoclonal antibody (mAb) production, where conventional statistical methods often fall short due to time-series data's complexity and high dimensionality. We propose a novel Hyperbox Mixture Regression (HMR) model which employs hyperbox-based input space partitioning to enhance predictive accuracy while managing uncertainty inherent in bioprocess data. The HMR model is designed to dynamically generate hyperboxes for input samples in a single-pass process, thereby improving learning speed and reducing computational complexity. Our experimental study utilizes a dataset that contains 106 bioreactors. This study evaluates the model's performance in predicting critical quality attributes in monoclonal antibody manufacturing over a 15-day cultivation period. The results demonstrate that the HMR model outperforms comparable approximators in accuracy and learning speed and maintains interpretability and robustness under uncertain conditions. These findings underscore the potential of HMR as a powerful tool for enhancing predictive analytics in bioprocessing applications.

cs.LG↗

arXiv2024

Uncertainty Quantification Using Ensemble Learning and Monte Carlo Sampling for Performance Prediction and Monitoring in Cell Culture Processes

Biopharmaceutical products, particularly monoclonal antibodies (mAbs), have gained prominence in the pharmaceutical market due to their high specificity and efficacy. As these products are projected to constitute a substantial portion of global pharmaceutical sales, the application of machine learning models in mAb development and manufacturing is gaining momentum. This paper addresses the critical need for uncertainty quantification in machine learning predictions, particularly in scenarios with limited training data. Leveraging ensemble learning and Monte Carlo simulations, our proposed method generates additional input samples to enhance the robustness of the model in small training datasets. We evaluate the efficacy of our approach through two case studies: predicting antibody concentrations in advance and real-time monitoring of glucose concentrations during bioreactor runs using Raman spectra data. Our findings demonstrate the effectiveness of the proposed method in estimating the uncertainty levels associated with process performance predictions and facilitating real-time decision-making in biopharmaceutical manufacturing. This contribution not only introduces a novel approach for uncertainty quantification but also provides insights into overcoming challenges posed by small training datasets in bioprocess development. The evaluation demonstrates the effectiveness of our method in addressing key challenges related to uncertainty estimation within upstream cell cultivation, illustrating its potential impact on enhancing process control and product quality in the dynamic field of biopharmaceuticals.

q-bio.QM↗

arXiv2024

Transfer Learning and the Early Estimation of Single-Photon Source Quality using Machine Learning Methods

The use of single-photon sources (SPSs) is central to numerous systems and devices proposed amidst a modern surge in quantum technology. However, manufacturing schemes remain imperfect, and single-photon emission purity must often be experimentally verified via interferometry. Such a process is typically slow and costly, which has motivated growing research into whether SPS quality can be more rapidly inferred from incomplete emission statistics. Hence, this study is a sequel to previous work that demonstrated significant uncertainty in the standard method of quality estimation, i.e. the least-squares fitting of a physically motivated function, and asks: can machine learning (ML) do better? The study leverages eight datasets obtained from measurements involving an exemplary quantum emitter, i.e. a single InGaAs/GaAs epitaxial quantum dot; these eight contexts predominantly vary in the intensity of the exciting laser. Specifically, via a form of `transfer learning', five ML models, three linear and two ensemble-based, are trained on data from seven of the contexts and tested on the eighth. Validation metrics quickly reveal that even a linear regressor can outperform standard fitting when it is tested on the same contexts it was trained on, but the success of transfer learning is less assured, even though statistical analysis, made possible by data augmentation, suggests its superiority as an early estimator. Accordingly, the study concludes by discussing future strategies for grappling with the problem of SPS context dissimilarity, e.g. feature engineering and model adaptation.

physics.optics↗

arXiv2023

Network Disruption via Continuous Batch Removal: The Case of Sicilian Mafia

Network disruption is pivotal in understanding the robustness and vulnerability of complex networks, which is instrumental in devising strategies for infrastructure protection, epidemic control, cybersecurity, and combating crime. In this paper, with a particular focus on disrupting criminal networks, we proposed to impose a within-the-largest-connected-component constraint in a continuous batch removal disruption process. Through a series of experiments on a recently released Sicilian Mafia network, we revealed that the constraint would enhance degree-based methods while weakening betweenness-based approaches. Moreover, based on the findings from the experiments using various disruption strategies, we propose a structurally-filtered greedy disruption strategy that integrates the effectiveness of greedy-like methods with the efficiency of structural-metric-based approaches. The proposed strategy significantly outperforms the longstanding state-of-the-art method of betweenness centrality while maintaining the same time complexity.

cs.SI↗

arXiv2023

Applications of Machine Learning in Biopharmaceutical Process Development and Manufacturing: Current Trends, Challenges, and Opportunities

While machine learning (ML) has made significant contributions to the biopharmaceutical field, its applications are still in the early stages in terms of providing direct support for quality-by-design based development and manufacturing of biopharmaceuticals, hindering the enormous potential for bioprocesses automation from their development to manufacturing. However, the adoption of ML-based models instead of conventional multivariate data analysis methods is significantly increasing due to the accumulation of large-scale production data. This trend is primarily driven by the real-time monitoring of process variables and quality attributes of biopharmaceutical products through the implementation of advanced process analytical technologies. Given the complexity and multidimensionality of a bioproduct design, bioprocess development, and product manufacturing data, ML-based approaches are increasingly being employed to achieve accurate, flexible, and high-performing predictive models to address the problems of analytics, monitoring, and control within the biopharma field. This paper aims to provide a comprehensive review of the current applications of ML solutions in a bioproduct design, monitoring, control, and optimisation of upstream, downstream, and product formulation processes. Finally, this paper thoroughly discusses the main challenges related to the bioprocesses themselves, process data, and the use of machine learning models in biopharmaceutical process development and manufacturing. Moreover, it offers further insights into the adoption of innovative machine learning methods and novel trends in the development of new digital biopharma solutions.

cs.LG↗

arXiv2023

Heterogeneous Feature Representation for Digital Twin-Oriented Complex Networked Systems

Building models of Complex Networked Systems (CNS) that can accurately represent reality forms an important research area. To be able to reflect real world systems, the modelling needs to consider not only the intensity of interactions between the entities but also features of all the elements of the system. This study aims to improve the expressive power of node features in Digital Twin-Oriented Complex Networked Systems (DT-CNSs) with heterogeneous feature representation principles. This involves representing features with crisp feature values and fuzzy sets, each describing the objective and the subjective inductions of the nodes' features and feature differences. Our empirical analysis builds DT-CNSs to recreate realistic physical contact networks in different countries from real node feature distributions based on various representation principles and an optimised feature preference. We also investigate their respective disaster resilience to an epidemic outbreak starting from the most popular node. The results suggest that the increasing flexibility of feature representation with fuzzy sets improves the expressive power and enables more accurate modelling. In addition, the heterogeneous features influence the network structure and the speed of the epidemic outbreak, requiring various mitigation policies targeted at different people.

cs.AI↗

arXiv2023

Digital Twin-Oriented Complex Networked Systems based on Heterogeneous Node Features and Interaction Rules

This study proposes an extendable modelling framework for Digital Twin-Oriented Complex Networked Systems (DT-CNSs) with a goal of generating networks that faithfully represent real systems. Modelling process focuses on (i) features of nodes and (ii) interaction rules for creating connections that are built based on individual node's preferences. We conduct experiments on simulation-based DT-CNSs that incorporate various features and rules about network growth and different transmissibilities related to an epidemic spread on these networks. We present a case study on disaster resilience of social networks given an epidemic outbreak by investigating the infection occurrence within specific time and social distance. The experimental results show how different levels of the structural and dynamics complexities, concerned with feature diversity and flexibility of interaction rules respectively, influence network growth and epidemic spread. The analysis revealed that, to achieve maximum disaster resilience, mitigation policies should be targeted at nodes with preferred features as they have higher infection risks and should be the focus of the epidemic control.

cs.SI↗

arXiv2023

Harnessing Data Augmentation to Quantify Uncertainty in the Early Estimation of Single-Photon Source Quality

Novel methods for rapidly estimating single-photon source (SPS) quality have been promoted in recent literature to address the expensive and time-consuming nature of experimental validation via intensity interferometry. However, the frequent lack of uncertainty discussions and reproducible details raises concerns about their reliability. This study investigates the use of data augmentation, a machine learning technique, to supplement experimental data with bootstrapped samples and quantify the uncertainty of such estimates. Eight datasets obtained from measurements involving a single InGaAs/GaAs epitaxial quantum dot serve as a proof-of-principle example. Analysis of one of the SPS quality metrics derived from efficient histogram fitting of the synthetic samples, i.e. the probability of multi-photon emission events, reveals significant uncertainty contributed by stochastic variability in the Poisson processes that describe detection rates. Ignoring this source of error risks severe overconfidence in both early quality estimates and claims for state-of-the-art SPS devices. Additionally, this study finds that standard least-squares fitting is comparable to using a Poisson likelihood, and expanding averages show some promise for early estimation. Also, reducing background counts improves fitting accuracy but does not address the Poisson-process variability. Ultimately, data augmentation demonstrates its value in supplementing physical experiments; its benefit here is to emphasise the need for a cautious assessment of SPS quality.

physics.optics↗

arXiv2023

Review and Assessment of Digital Twin--Oriented Social Network Simulators

The ability to faithfully represent real social networks is critical from the perspective of testing various what-if scenarios which are not feasible to be implemented in a real system as the system's state would be irreversibly changed. High fidelity simulators allow one to investigate the consequences of different actions before introducing them to the real system. For example, in the context of social systems, an accurate social network simulator can be a powerful tool used to guide policy makers, help companies plan their advertising campaigns or authorities to analyse fake news spread. In this study we explore different Social Network Simulators (SNSs) and assess to what extent they are able to mimic the real social networks. We conduct a critical review and assessment of existing Social Network Simulators under the Digital Twin-Oriented Modelling framework proposed in our previous study. We subsequently extend one of the most promising simulators from the evaluated ones, to facilitate generation of social networks of varied structural complexity levels. This extension brings us one step closer to a Digital Twin Oriented SNS (DT Oriented SNS). We also propose an approach to assess the similarity between real and simulated networks with the composite performance indexes based on both global and local structural measures, while taking runtime of the simulator as an indicator of its efficiency. We illustrate various characteristics of the proposed DT Oriented SNS using a well known Karate Club network as an example. While not considered to be of sufficient complexity, the simulator is intended as one of the first steps on a journey towards building a Digital Twin of a social network that perfectly mimics the reality.

cs.SI↗

arXiv2023

A Network Science perspective of Graph Convolutional Networks: A survey

The mining and exploitation of graph structural information have been the focal points in the study of complex networks. Traditional structural measures in Network Science focus on the analysis and modelling of complex networks from the perspective of network structure, such as the centrality measures, the clustering coefficient, and motifs and graphlets, and they have become basic tools for studying and understanding graphs. In comparison, graph neural networks, especially graph convolutional networks (GCNs), are particularly effective at integrating node features into graph structures via neighbourhood aggregation and message passing, and have been shown to significantly improve the performances in a variety of learning tasks. These two classes of methods are, however, typically treated separately with limited references to each other. In this work, aiming to establish relationships between them, we provide a network science perspective of GCNs. Our novel taxonomy classifies GCNs from three structural information angles, i.e., the layer-wise message aggregation scope, the message content, and the overall learning scope. Moreover, as a prerequisite for reviewing GCNs via a network science perspective, we also summarise traditional structural measures and propose a new taxonomy for them. Finally and most importantly, we draw connections between traditional structural approaches and graph convolutional networks, and discuss potential directions for future research.

cs.SI↗