Evidence of Scaling Regimes in the Hopfield Dynamics of Whole Brain Model

It is shown that a Hopfield recurrent neural network, informed by experimentally derived brain topology, recovers the scaling picture recently introduced by Deco et al., according to which the process of information transfer within the human brain shows spatially correlated patterns qualitatively similar to those displayed by turbulent flows. Although both models employ a coupling strength which decays exponentially with the euclidean distance between the nodes, their mathematical nature is widely different, Hopf oscillators versus Hopfield neural network. Hence, their convergence suggests a remarkable robustness of the aforementioned scaling picture. Furthermore, the present analysis shows that the Hopfield model brain remains functional by removing links above about five decay lengths, corresponding to about one sixth of the size of the global brain. This suggests that, in terms of connectivity decay length, the Hopfield brain functions in a sort of intermediate "turbulent liquid"-like state, whose essential connections are the intermediate ones between the connectivity decay length and the global brain size. This "turbulent-like liquid" appears to be more spiky than actual turbulent fluids, with a scaling exponent around $2/5$ instead of $2/3$.

Benchmarking YOLOv5 and YOLOv7 models with DeepSORT for droplet tracking applications

Tracking droplets in microfluidics is a challenging task. The difficulty arises in choosing a tool to analyze general microfluidic videos to infer physical quantities. The state-of-the-art object detector algorithm You Only Look Once (YOLO) and the object tracking algorithm Simple Online and Realtime Tracking with a Deep Association Metric (DeepSORT) are customizable for droplet identification and tracking. The customization includes training YOLO and DeepSORT networks to identify and track the objects of interest. We trained several YOLOv5 and YOLOv7 models and the DeepSORT network for droplet identification and tracking from microfluidic experimental videos. We compare the performance of the droplet tracking applications with YOLOv5 and YOLOv7 in terms of training time and time to analyze a given video across various hardware configurations. Despite the latest YOLOv7 being 10% faster, the real-time tracking is only achieved by lighter YOLO models on RTX 3070 Ti GPU machine due to additional significant droplet tracking costs arising from the DeepSORT algorithm. This work is a benchmark study for the YOLOv5 and YOLOv7 networks with DeepSORT in terms of the training time and inference time for a custom dataset of microfluidic droplets.

DropTrack -- automatic droplet tracking using deep learning for microfluidic applications

Deep neural networks are rapidly emerging as data analysis tools, often outperforming the conventional techniques used in complex microfluidic systems. One fundamental analysis frequently desired in microfluidic experiments is counting and tracking the droplets. Specifically, droplet tracking in dense emulsions is challenging as droplets move in tightly packed configurations. Sometimes the individual droplets in these dense clusters are hard to resolve, even for a human observer. Here, two deep learning-based cutting-edge algorithms for object detection (YOLO) and object tracking (DeepSORT) are combined into a single image analysis tool, DropTrack, to track droplets in microfluidic experiments. DropTrack analyzes input videos, extracts droplets' trajectories, and infers other observables of interest, such as droplet numbers. Training an object detector network for droplet recognition with manually annotated images is a labor-intensive task and a persistent bottleneck. This work partly resolves this problem by training object detector networks (YOLOv5) with hybrid datasets containing real and synthetic images. We present an analysis of a double emulsion experiment as a case study to measure DropTrack's performance. For our test case, the YOLO networks trained with 60% synthetic images show similar performance in droplet counting as with the one trained using 100% real images, meanwhile saving the image annotation work by 60%. DropTrack's performance is measured in terms of mean average precision (mAP), mean square error in counting the droplets, and inference speed. The fastest configuration of DropTrack runs inference at about 30 frames per second, well within the standards for real-time image analysis.

Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative method that combines both approaches to accelerate drug discovery. The scale of the resulting workflow is such that it is dependent on high performance computing. We have demonstrated the applicability of this workflow on four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead compounds on a variety of supercomputers.