arXiv subjects

Yakub Sebastian

Publications and source records attributed to Yakub Sebastian.

5 recordsLinked to original sources

arXiv2026

A Physics-Informed, Behavior-Aware Digital Twin for Robust Multimodal Forecasting of Core Body Temperature in Precision Livestock Farming

Precision livestock farming requires accurate and timely heat stress prediction to ensure animal welfare and optimize farm management. This study presents a physics-informed digital twin (DT) framework combined with an uncertainty-aware, expert-weighted stacked ensemble for multimodal forecasting of Core Body Temperature (CBT) in dairy cattle. Using the high-frequency, heterogeneous MmCows dataset, the DT integrates an ordinary differential equation (ODE)-based thermoregulation model that simulates metabolic heat production and dissipation, a Gaussian process for capturing cow-specific deviations, a Kalman filter for aligning predictions with real-time sensor data, and a behavioral Markov chain that models activity-state transitions under varying environmental conditions. The DT outputs key physiological indicators, such as predicted CBT, heat stress probability, and behavioral state distributions are fused with raw sensor data and enriched through multi-scale temporal analysis and cross-modal feature engineering to form a comprehensive feature set. The predictive methodology is designed in a three-stage stacked ensemble, where stage 1 trains modality-specific LightGBM 'expert' models on distinct feature groups, stage 2 collects their predictions as meta-features, and at stage 3 Optuna-tuned LightGBM meta-model yields the final CBT forecast. Predictive uncertainty is quantified via bootstrapping and validated using Prediction Interval Coverage Probability (PICP). Ablation analysis confirms that incorporating DT-derived features and multimodal fusion substantially enhances performance. The proposed framework achieves a cross-validated R2 of 0.783, F1 score of 84.25% and PICP of 92.38% for 2-hour ahead forecasting, providing a robust, uncertainty-aware, and physically principled system for early heat stress detection and precision livestock management.

cs.CV↗

arXiv2026

U-FedTomAtt: Ultra-lightweight Federated Learning with Attention for Tomato Disease Recognition

Federated learning has emerged as a privacy-preserving and efficient approach for deploying intelligent agricultural solutions. Accurate edge-based diagnosis across geographically dispersed farms is crucial for recognising tomato diseases in sustainable farming. Traditional centralised training aggregates raw data on a central server, leading to communication overhead, privacy risks and latency. Meanwhile, edge devices require lightweight networks to operate effectively within limited resources. In this paper, we propose U-FedTomAtt, an ultra-lightweight federated learning framework with attention for tomato disease recognition in resource-constrained and distributed environments. The model comprises only 245.34K parameters and 71.41 MFLOPS. First, we propose an ultra-lightweight neural network with dilated bottleneck (DBNeck) modules and a linear transformer to minimise computational and memory overhead. To mitigate potential accuracy loss, a novel local-global residual attention (LoGRA) module is incorporated. Second, we propose the federated dual adaptive weight aggregation (FedDAWA) algorithm that enhances global model accuracy. Third, our framework is validated using three benchmark datasets for tomato diseases under simulated federated settings. Experimental results show that the proposed method achieves 0.9910% and 0.9915% Top-1 accuracy and 0.9923% and 0.9897% F1-scores on SLIF-Tomato and PlantVillage tomato datasets, respectively.

q-bio.QM↗

arXiv2025

Mitigating hallucinations in healthcare LLMs with granular fact-checking and domain-specific adaptation

In healthcare, it is essential for any Large Language Model (LLM)-generated output to be reliable and accurate, particularly in cases involving decision-making and patient safety. However, the outputs are often unreliable in such critical areas due to the risk of hallucinated outputs from the LLMs. To address this issue, we propose a fact-checking module that operates independently of any LLM, along with a domain-specific summarization model designed to minimize hallucination rates. Our model is fine-tuned using Low-Rank Adaptation (LoRA) on the MIMIC-III dataset and is paired with the fact-checking module, which uses numerical tests for correctness and logical checks at a granular level through discrete logic in natural language processing (NLP) to validate facts against electronic health records (EHRs). We trained the LLM on the full MIMIC-III dataset. For evaluation of the fact-checking module, we sampled 104 summaries, extracted them into 3786 propositions, and used these as facts. The fact-checking module achieves a precision of 0.8904, a recall of 0.8234, and an F1-score of 0.8556. Additionally, the LLM summary achieves a ROUGE-1 score of 0.5797 and a BERTScore of 0.9120 for summary quality.

cs.CL↗

arXiv2025

Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances

Generative artificial intelligence (GenAI) is transforming bioinformatics by advancing genomics, proteomics, transcriptomics, structural biology, and drug discovery. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework, this review addresses six research questions to evaluate influential GenAI strategies in terms of methodological innovation, predictive performance, specialization, limitations, and data use. RQ1 shows that GenAI supports sequence analysis, molecular design, and integrative data modelling, often outperforming traditional methods through improved pattern recognition and generation. RQ2 finds that specialized architectures generally outperform general-purpose models because of domain-specific pretraining and context-aware design. RQ3 identifies benefits in molecular analysis and biological data integration, including improved accuracy and reduced analytical error. RQ4 reports advances in structural modelling, functional prediction, and synthetic data generation, supported by established benchmarks. RQ5 highlights key limitations, including poor scalability, data bias, and restricted generalizability, and recommends stronger evaluation and biologically grounded modelling. RQ6 shows that molecular datasets, including UniProtKB and ProteinNet12, cellular datasets, including CELLxGENE and GTEx, and textual resources, including PubMedQA and OMIM, support model training and generalization. Overall, this review demonstrates the growing potential of GenAI to advance computational biology through more accurate, specialized, and integrative bioinformatics analysis.

cs.CL↗

arXiv2021

The Boundary-Spanning Mechanisms of Nobel Prize Winning Papers

The breakthrough potentials of research papers can be explained by their boundary-spanning qualities. Here, for the first time, we apply the structural variation analysis (SVA) model and its affiliated metrics to investigate the extent to which such qualities characterize a group of Nobel Prize winning papers. We find that these papers share remarkable boundary-spanning traits, marked by exceptional abilities to connect disparate and topically-diverse clusters of research papers. Further, their publications exert structural variations on the scale that significantly alters the betweenness centrality distributions of existing intellectual space. Overall, SVA not only provides a set of leading indicators for describing future Nobel Prize winning papers, but also broadens our understanding of the similar prize-winning properties that may have been overlooked among other regular publications.

cs.DL↗