Navid Ziaei

Navid Ziaei, Reza Saadatifard, Ali Yousefi et al.

Understanding how external stimuli are encoded in distributed neural activity is of significant interest in clinical and basic neuroscience. To address this need, it is essential to develop analytical tools capable of handling limited data and the intrinsic stochasticity present in neural data. In this study, we propose a straightforward Bayesian time series classifier (BTsC) model that tackles these challenges whilst maintaining a high level of interpretability. We demonstrate the classification capabilities of this approach by utilizing neural data to decode colors in a visual task. The model exhibits consistent and reliable average performance of 75.55% on 4 patients' dataset, improving upon state-of-the-art machine learning techniques by about 3.0 percent. In addition to its high classification accuracy, the proposed BTsC model provides interpretable results, making the technique a valuable tool to study neural activity in various tasks and categories. The proposed solution can be applied to neural data recorded in various tasks, where there is a need for interpretable results and accurate classification accuracy.

Ebrahim Pourjafari, Navid Ziaei, Mohammad R. Rezaei et al.

This paper introduces a novel non-parametric deep model for estimating time-to-event (survival analysis) in presence of censored data and competing risks. The model is designed based on the sequence-to-sequence (Seq2Seq) architecture, therefore we name it Survival Seq2Seq. The first recurrent neural network (RNN) layer of the encoder of our model is made up of Gated Recurrent Unit with Decay (GRU-D) cells. These cells have the ability to effectively impute not-missing-at-random values of longitudinal datasets with very high missing rates, such as electronic health records (EHRs). The decoder of Survival Seq2Seq generates a probability distribution function (PDF) for each competing risk without assuming any prior distribution for the risks. Taking advantage of RNN cells, the decoder is able to generate smooth and virtually spike-free PDFs. This is beyond the capability of existing non-parametric deep models for survival analysis. Training results on synthetic and medical datasets prove that Survival Seq2Seq surpasses other existing deep survival models in terms of the accuracy of predictions and the quality of generated PDFs.

Mohammad R. Rezaei, Reza Saadati Fard, Ebrahim Pourjafari et al.

The aim of survival analysis in healthcare is to estimate the probability of occurrence of an event, such as a patient's death in an intensive care unit (ICU). Recent developments in deep neural networks (DNNs) for survival analysis show the superiority of these models in comparison with other well-known models in survival analysis applications. Ensuring the reliability and explainability of deep survival models deployed in healthcare is a necessity. Since DNN models often behave like a black box, their predictions might not be easily trusted by clinicians, especially when predictions are contrary to a physician's opinion. A deep survival model that explains and justifies its decision-making process could potentially gain the trust of clinicians. In this research, we propose the reverse survival model (RSM) framework that provides detailed insights into the decision-making process of survival models. For each patient of interest, RSM can extract similar patients from a dataset and rank them based on the most relevant features that deep survival models rely on for their predictions.

Maryam Ostadsharif Memar, Navid Ziaei, Behzad Nazari et al.

Intracranial electroencephalography (iEEG) is increasingly used for clinical and brain-computer interface applications due to its high spatial and temporal resolution. However, inter-subject variability in electrode implantation poses a challenge for developing generalized neural decoders. To address this, we introduce a novel decoder model that is robust to inter-subject electrode implantation variability. We call this model RISE-iEEG, which stands for Robust to Inter-Subject Electrode Implantation Variability iEEG Classifier. RISE-iEEG employs a deep neural network structure preceded by a participant-specific projection network. The projection network maps the neural data of individual participants onto a common low-dimensional space, compensating for the implantation variability. In other words, we developed an iEEG decoder model that can be applied across multiple participants' data without requiring the coordinates of electrode for each participant. The performance of RISE-iEEG across multiple datasets, including the Music Reconstruction dataset, and AJILE12 dataset, surpasses that of advanced iEEG decoder models such as HTNet and EEGNet. Our analysis shows that the performance of RISE-iEEG is about 7\% higher than that of HTNet and EEGNet in terms of F1 score, with an average F1 score of 0.83, which is the highest result among the evaluation methods defined. Furthermore, Our analysis of the projection network weights reveals that the Superior Temporal and Postcentral lobes are key encoding nodes for the Music Reconstruction and AJILE12 datasets, which aligns with the primary physiological principles governing these regions. This model improves decoding accuracy while maintaining interpretability and generalization.

Navid Ziaei, Behzad Nazari, Uri T. Eden et al.

Extracting meaningful information from high-dimensional data poses a formidable modeling challenge, particularly when the data is obscured by noise or represented through different modalities. This research proposes a novel non-parametric modeling approach, leveraging the Gaussian process (GP), to characterize high-dimensional data by mapping it to a latent low-dimensional manifold. This model, named the latent discriminative generative decoder (LDGD), employs both the data and associated labels in the manifold discovery process. We derive a Bayesian solution to infer the latent variables, allowing LDGD to effectively capture inherent stochasticity in the data. We demonstrate applications of LDGD on both synthetic and benchmark datasets. Not only does LDGD infer the manifold accurately, but its accuracy in predicting data points' labels surpasses state-of-the-art approaches. In the development of LDGD, we have incorporated inducing points to reduce the computational complexity of Gaussian processes for large datasets, enabling batch training for enhanced efficient processing and scalability. Additionally, we show that LDGD can robustly infer manifold and precisely predict labels for scenarios in that data size is limited, demonstrating its capability to efficiently characterize high-dimensional data with limited samples. These collective attributes highlight the importance of developing non-parametric modeling approaches to analyze high-dimensional data.

Navid Ziaei, Joshua J. Stim, Melanie D. Goodman-Keiser et al.

Non-parametric models, such as Gaussian Processes (GP), show promising results in the analysis of complex data. Their applications in neuroscience data have recently gained traction. In this research, we introduce a novel neural decoder model built upon GP models. The core idea is that two GPs generate neural data and their associated labels using a set of low-dimensional latent variables. Under this modeling assumption, the latent variables represent the underlying manifold or essential features present in the neural data. When GPs are trained, the latent variable can be inferred from neural data to decode the labels with a high accuracy. We demonstrate an application of this decoder model in a verbal memory experiment dataset and show that the decoder accuracy in predicting stimulus significantly surpasses the state-of-the-art decoder models. The preceding performance of this model highlights the importance of utilizing non-parametric models in the analysis of neuroscience data.

Pedram Rajaei, Maryam Ostadsharif Memar, Navid Ziaei et al.

The manifold hypothesis suggests that high-dimensional neural time series lie on a low-dimensional manifold shaped by simpler underlying dynamics. To uncover this structure, latent dynamical variable models such as state-space models, recurrent neural networks, neural ordinary differential equations, and Gaussian Process Latent Variable Models are widely used. We propose a novel hierarchical stochastic differential equation (SDE) model that balances computational efficiency and interpretability, addressing key limitations of existing methods. Our model assumes the trajectory of a manifold can be reconstructed from a sparse set of samples from the manifold trajectory. The latent space is modeled using Brownian bridge SDEs, with points - specified in both time and value - sampled from a multivariate marked point process. These Brownian bridges define the drift of a second set of SDEs, which are then mapped to the observed data. This yields a continuous, differentiable latent process capable of modeling arbitrarily complex time series as the number of manifold points increases. We derive training and inference procedures and show that the computational cost of inference scales linearly with the length of the observation data. We then validate our model on both synthetic data and neural recordings to demonstrate that it accurately recovers the underlying manifold structure and scales effectively with data dimensionality.