Mohammad R. Rezaei

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.

Mohammad R. Rezaei, Milos R. Popovic, Milad Lankarany et al.

The state-space models (SSMs) are widely utilized in the analysis of time-series data. SSMs rely on an explicit definition of the state and observation processes. Characterizing these processes is not always easy and becomes a modeling challenge when the dimension of observed data grows or the observed data distribution deviates from the normal distribution. Here, we propose a new formulation of SSM for high-dimensional observation processes. We call this solution the deep direct discriminative decoder (D4). The D4 brings deep neural networks' expressiveness and scalability to the SSM formulation letting us build a novel solution that efficiently estimates the underlying state processes through high-dimensional observation signal. We demonstrate the D4 solutions in simulated and real data such as Lorenz attractors, Langevin dynamics, random walk dynamics, and rat hippocampus spiking neural data and show that the D4 performs better than traditional SSMs and RNNs. The D4 can be applied to a broader class of time-series data where the connection between high-dimensional observation and the underlying latent process is hard to characterize.

Mohammad R. Rezaei

Latent dynamical models are commonly used to learn the distribution of a latent dynamical process that represents a sequence of noisy data samples. However, producing samples from such models with high fidelity is challenging due to the complexity and variability of latent and observation dynamics. Recent advances in diffusion-based generative models, such as DDPM and NCSN, have shown promising alternatives to state-of-the-art latent generative models, such as Neural ODEs, RNNs, and Normalizing flow networks, for generating high-quality sequential samples from a prior distribution. However, their application in modeling sequential data with latent dynamical models is yet to be explored. Here, we propose a novel latent variable model named latent dynamical implicit diffusion processes (LDIDPs), which utilizes implicit diffusion processes to sample from dynamical latent processes and generate sequential observation samples accordingly. We tested LDIDPs on synthetic and simulated neural decoding problems. We demonstrate that LDIDPs can accurately learn the dynamics over latent dimensions. Furthermore, the implicit sampling method allows for the computationally efficient generation of high-quality sequential data samples from the latent and observation spaces.

Mohammad Reza Rezaei, Reza Saadati Fard, Jayson L. Parker et al.

Large Language Models (LLMs) have significantly advanced medical question-answering by leveraging extensive clinical data and medical literature. However, the rapid evolution of medical knowledge and the labor-intensive process of manually updating domain-specific resources pose challenges to the reliability of these systems. To address this, we introduce Agentic Medical Graph-RAG (AMG-RAG), a comprehensive framework that automates the construction and continuous updating of medical knowledge graphs, integrates reasoning, and retrieves current external evidence, such as PubMed and WikiSearch. By dynamically linking new findings and complex medical concepts, AMG-RAG not only improves accuracy but also enhances interpretability in medical queries. Evaluations on the MEDQA and MEDMCQA benchmarks demonstrate the effectiveness of AMG-RAG, achieving an F1 score of 74.1 percent on MEDQA and an accuracy of 66.34 percent on MEDMCQA, outperforming both comparable models and those 10 to 100 times larger. Notably, these improvements are achieved without increasing computational overhead, highlighting the critical role of automated knowledge graph generation and external evidence retrieval in delivering up-to-date, trustworthy medical insights.

Mohammad R. Rezaei

The number of reviews on Amazon has grown significantly over the years. Customers who made purchases on Amazon provide reviews by rating the product from 1 to 5 stars and sharing a text summary of their experience and opinion of the product. The ratings of a product are averaged to provide an overall product rating. We analyzed what ratings score customers give to a specific product (a music track) in order to build a recommender model for digital music tracks on Amazon. We test various traditional models along with our proposed deep neural network (DNN) architecture to predict the reviews rating score. The Amazon review dataset contains 200,000 data samples; we train the models on 70% of the dataset and test the performance of the models on the remaining 30% of the dataset.