Karim Amer

Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins et al.

Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited by the intrinsic instability of RNA molecules to a chemical degradation reaction called in-line hydrolysis. Predicting the degradation of an RNA molecule is a key task in designing more stable RNA-based therapeutics. Here, we describe a crowdsourced machine learning competition ("Stanford OpenVaccine") on Kaggle, involving single-nucleotide resolution measurements on 6043 102-130-nucleotide diverse RNA constructs that were themselves solicited through crowdsourcing on the RNA design platform Eterna. The entire experiment was completed in less than 6 months, and 41% of nucleotide-level predictions from the winning model were within experimental error of the ground truth measurement. Furthermore, these models generalized to blindly predicting orthogonal degradation data on much longer mRNA molecules (504-1588 nucleotides) with improved accuracy compared to previously published models. Top teams integrated natural language processing architectures and data augmentation techniques with predictions from previous dynamic programming models for RNA secondary structure. These results indicate that such models are capable of representing in-line hydrolysis with excellent accuracy, supporting their use for designing stabilized messenger RNAs. The integration of two crowdsourcing platforms, one for data set creation and another for machine learning, may be fruitful for other urgent problems that demand scientific discovery on rapid timescales.

Mohamed Afifi, Yara Ali, Karim Amer et al.

Detection of pedestrians on embedded devices, such as those on-board of robots and drones, has many applications including road intersection monitoring, security, crowd monitoring and surveillance, to name a few. However, the problem can be challenging due to continuously-changing camera viewpoint and varying object appearances as well as the need for lightweight algorithms suitable for embedded systems. This paper proposes a robust framework for pedestrian detection in many footages. The framework performs fine and coarse detections on different image regions and exploits temporal and spatial characteristics to attain enhanced accuracy and real time performance on embedded boards. The framework uses the Yolo-v3 object detection [1] as its backbone detector and runs on the Nvidia Jetson TX2 embedded board, however other detectors and/or boards can be used as well. The performance of the framework is demonstrated on two established datasets and its achievement of the second place in CVPR 2019 Embedded Real-Time Inference (ERTI) Challenge.

Yara Ali Alnaggar, Mohamed Afifi, Karim Amer et al.

Semantic segmentation of 3D point cloud data is essential for enhanced high-level perception in autonomous platforms. Furthermore, given the increasing deployment of LiDAR sensors onboard of cars and drones, a special emphasis is also placed on non-computationally intensive algorithms that operate on mobile GPUs. Previous efficient state-of-the-art methods relied on 2D spherical projection of point clouds as input for 2D fully convolutional neural networks to balance the accuracy-speed trade-off. This paper introduces a novel approach for 3D point cloud semantic segmentation that exploits multiple projections of the point cloud to mitigate the loss of information inherent in single projection methods. Our Multi-Projection Fusion (MPF) framework analyzes spherical and bird's-eye view projections using two separate highly-efficient 2D fully convolutional models then combines the segmentation results of both views. The proposed framework is validated on the SemanticKITTI dataset where it achieved a mIoU of 55.5 which is higher than state-of-the-art projection-based methods RangeNet++ and PolarNet while being 1.6x faster than the former and 3.1x faster than the latter.

Mohamed Afifi, Yara Ali, Karim Amer et al.

Detection of pedestrians in aerial imagery captured by drones has many applications including intersection monitoring, patrolling, and surveillance, to name a few. However, the problem is involved due to continuouslychanging camera viewpoint and object appearance as well as the need for lightweight algorithms to run on on-board embedded systems. To address this issue, the paper proposes a framework for pedestrian detection in videos based on the YOLO object detection network [6] while having a high throughput of more than 5 FPS on the Jetson TX2 embedded board. The framework exploits deep learning for robust operation and uses a pre-trained model without the need for any additional training which makes it flexible to apply on different setups with minimum amount of tuning. The method achieves ~81 mAP when applied on a sample video from the Embedded Real-Time Inference (ERTI) Challenge where pedestrians are monitored by a UAV.

M. Samy, K. Amer, M. Shaker et al.

his paper presents a simple approach for drone navigation to follow a predetermined path using visual input only without reliance on a Global Positioning System (GPS). A Convolutional Neural Network (CNN) is used to output the steering command of the drone in an end-to-end approach. We tested our approach in two simulated environments in the Unreal Engine using the AirSim plugin for drone simulation. Results show that the proposed approach, despite its simplicity, has average cross track distance less than 2.9 meters in the simulated environment. We also investigate the significance of data augmentation in path following. Finally, we conclude by suggesting possible enhancements for extending our approach to more difficult paths in real life, in the hope that one day visual navigation will become the norm in GPS-denied zones.