Elham Soltanikazemi

Elham Soltanikazemi, Raj S. Roy, Farhan Quadir et al.

Predicted inter-chain residue-residue contacts can be used to build the quaternary structure of protein complexes from scratch. However, only a small number of methods have been developed to reconstruct protein quaternary structures using predicted inter-chain contacts. Here, we present an agent-based self-learning method based on deep reinforcement learning (DRLComplex) to build protein complex structures using inter-chain contacts as distance constraints. We rigorously tested DRLComplex on two standard datasets of homodimeric and heterodimeric protein complexes (i.e., the CASP-CAPRI homodimer and Std_32 heterodimer datasets) using both true and predicted interchain contacts as inputs. Utilizing true contacts as input, DRLComplex achieved high average TM-scores of 0.9895 and 0.9881 and a low average interface RMSD (I_RMSD) of 0.2197 and 0.92 on the two datasets, respectively. When predicted contacts are used, the method achieves TM-scores of 0.73 and 0.76 for homodimers and heterodimers, respectively. Our experiments find that the accuracy of reconstructed quaternary structures depends on the accuracy of the contact predictions. Compared to other optimization methods for reconstructing quaternary structures from inter-chain contacts, DRLComplex performs similar to an advanced gradient descent method and better than a Markov Chain Monte Carlo simulation method and a simulated annealing-based method, validating the effectiveness of DRLComplex for quaternary reconstruction of protein complexes.

Elham Soltanikazemi, Ashwin Dhakal, Bijaya Kumar Hatuwal et al.

This research focuses on real-time surveillance systems as a means for tackling the issue of non-compliance with helmet regulations, a practice that considerably amplifies the risk for motorcycle drivers or riders. Despite the well-established advantages of helmet usage, achieving widespread compliance remains challenging due to diverse contributing factors. To effectively address this concern, real-time monitoring and enforcement of helmet laws have been proposed as a plausible solution. However, previous attempts at real-time helmet violation detection have been hindered by their limited ability to operate in real-time. To overcome this limitation, the current paper introduces a novel real-time helmet violation detection system that utilizes the YOLOv5 single-stage object detection model. This model is trained on the 2023 NVIDIA AI City Challenge 2023 Track 5 dataset. The optimal hyperparameters for training the model are determined using genetic algorithms. Additionally, data augmentation and various sampling techniques are implemented to enhance the model's performance. The efficacy of the models is evaluated using precision, recall, and mean Average Precision (mAP) metrics. The results demonstrate impressive precision, recall, and mAP scores of 0.848, 0.599, and 0.641, respectively for the training data. Furthermore, the model achieves notable mAP score of 0.6667 for the test datasets, leading to a commendable 4th place rank in the public leaderboard. This innovative approach represents a notable breakthrough in the field and holds immense potential to substantially enhance motorcycle safety. By enabling real-time monitoring and enforcement capabilities, this system has the capacity to contribute towards increased compliance with helmet laws, thereby effectively reducing the risks faced by motorcycle riders and passengers.

Sajid Mahmud, Elham Soltanikazemi, Frimpong Boadu et al.

Most children infected with COVID-19 have no or mild symptoms and can recover automatically by themselves, but some pediatric COVID-19 patients need to be hospitalized or even to receive intensive medical care (e.g., invasive mechanical ventilation or cardiovascular support) to recover from the illnesses. Therefore, it is critical to predict the severe health risk that COVID-19 infection poses to children to provide precise and timely medical care for vulnerable pediatric COVID-19 patients. However, predicting the severe health risk for COVID-19 patients including children remains a significant challenge because many underlying medical factors affecting the risk are still largely unknown. In this work, instead of searching for a small number of most useful features to make prediction, we design a novel large-scale bag-of-words like method to represent various medical conditions and measurements of COVID-19 patients. After some simple feature filtering based on logistical regression, the large set of features is used with a deep learning method to predict both the hospitalization risk for COVID-19 infected children and the severe complication risk for the hospitalized pediatric COVID-19 patients. The method was trained and tested the datasets of the Biomedical Advanced Research and Development Authority (BARDA) Pediatric COVID-19 Data Challenge held from Sept. 15 to Dec. 17, 2021. The results show that the approach can rather accurately predict the risk of hospitalization and severe complication for pediatric COVID-19 patients and deep learning is more accurate than other machine learning methods.