Vahid Farrahi | Searcharxiv

arXiv2026

Resolving Single-Peptide Phosphorylation Dynamics in Plasmonic Nanopores using Physics-Informed Bi-Path Model

Protein phosphorylation provides a dynamic readout of cellular signaling yet remains difficult to detect at low abundance and stoichiometry. Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) using particle-in-pore plasmonic nanopores offers label-free molecular detection with submolecular sensitivity. However, reliable identification of subtle post-translational modifications (PTMs) is hindered by the stochastic nature of SM-SERS signals, partial excitation of peptide residues within the plasmonic hotspot, and background interference. Here, we introduce a physics-informed deep learning framework to decode complex SM-SERS dynamics and identify single-peptide PTMs. The model integrates multiple-instance learning with a temporal encoder combining temporal convolutional networks and bidirectional gated recurrent units to capture both local spectral variability and long-range blinking dynamics. To address diffusion-driven spectral heterogeneity, long spectral trajectories are segmented using Pearson-correlation, enabling weakly supervised training under label ambiguity. This framework robustly distinguishes single peptide phosphorylation despite strong background interference and stochastic signal fluctuations. By coupling nanoplasmonic confinement with spatiotemporal deep learning, our approach enables high-fidelity detection of single-molecule phosphorylation events and advances ultrasensitive phosphoproteomic analysis.

cond-mat.mes-hall↗

arXiv2025

Classification of 24-hour movement behaviors from wrist-worn accelerometer data: from handcrafted features to deep learning techniques

Purpose: We compared the performance of deep learning (DL) and classical machine learning (ML) algorithms for the classification of 24-hour movement behavior into sleep, sedentary, light intensity physical activity (LPA), and moderate-to-vigorous intensity physical activity (MVPA). Methods: Open-access data from 151 adults wearing a wrist-worn accelerometer (Axivity-AX3) was used. Participants were randomly divided into training, validation, and test sets (121, 15, and 15 participants each). Raw acceleration signals were segmented into non-overlapping 10-second windows, and then a total of 104 handcrafted features were extracted. Four DL algorithms-Long Short-Term Memory (LSTM), Bidirectional Long Short-Term Memory (BiLSTM), Gated Recurrent Units (GRU), and One-Dimensional Convolutional Neural Network (1D-CNN)-were trained using raw acceleration signals and with handcrafted features extracted from these signals to predict 24-hour movement behavior categories. The handcrafted features were also used to train classical ML algorithms, namely Random Forest (RF), Support Vector Machine (SVM), Extreme Gradient Boosting (XGBoost), Logistic Regression (LR), Artificial Neural Network (ANN), and Decision Tree (DT) for classifying 24-hour movement behavior intensities. Results: LSTM, BiLSTM, and GRU showed an overall accuracy of approximately 85% when trained with raw acceleration signals, and 1D-CNN an overall accuracy of approximately 80%. When trained on handcrafted features, the overall accuracy for both DL and classical ML algorithms ranged from 70% to 81%. Overall, there was a higher confusion in classification of MVPA and LPA, compared to sleep and sedentary categories. Conclusion: DL methods with raw acceleration signals had only slightly better performance in predicting 24-hour movement behavior intensities, compared to when DL and classical ML were trained with handcrafted features.

cs.LG↗