Ankit Gupta

Charlotte Bunne, Yusuf Roohani, Yanay Rosen et al.

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

Ankit Gupta, Ida-Maria Sintorn

Template matching is a fundamental problem in computer vision with applications in fields including object detection, image registration, and object tracking. Current methods rely on nearest-neighbour (NN) matching, where the query feature space is converted to NN space by representing each query pixel with its NN in the template. NN-based methods have been shown to perform better in occlusions, appearance changes, and non-rigid transformations; however, they scale poorly with high-resolution data and high feature dimensions. We present an NN-based method which efficiently reduces the NN computations and introduces filtering in the NN fields (NNFs). A vector quantization step is introduced before the NN calculation to represent the template with $k$ features, and the filter response over the NNFs is used to compare the template and query distributions over the features. We show that state-of-the-art performance is achieved in low-resolution data, and our method outperforms previous methods at higher resolution.

Ankit Gupta, George Tang, Sylesh Suresh

Cardiovascular disease (CD) is the number one leading cause of death worldwide, accounting for more than 17 million deaths in 2015. Critical indicators of CD include heart murmurs, intense sounds emitted by the heart during periods of irregular blood flow. Current diagnosis of heart murmurs relies on echocardiography (ECHO), which costs thousands of dollars and medical professionals to analyze the results, making it very unsuitable for areas with inadequate medical facilities. Thus, there is a need for an accessible alternative. Based on a simple interface and deep learning, HeartFit allows users to administer diagnoses themselves. An inexpensive, custom designed stethoscope in conjunction with a mobile application allows users to record and upload audio of their heart to a database. Using a deep learning network architecture, the database classifies the audio and returns the diagnosis to the user. The model consists of a deep recurrent convolutional neural network trained on 300 prelabeled heartbeat audio samples. After the model was validated on a previously unseen set of 100 heartbeat audio samples, it achieved a f beta score of 0.9545 and an accuracy of 95.5 percent. This value exceeds that of clinical examination accuracy, which is around 83 percent to 91 percent and costs orders of magnitude less than ECHO, demonstrating the effectiveness of the HeartFit platform. Through the platform, users can obtain immediate, accurate diagnosis of heart murmurs without any professional medical assistance, revolutionizing how we combat CD.

Ankit Gupta

According to the WHO, Cerebrovascular Stroke, or CS, is the second largest cause of death worldwide. Current diagnosis of CS relies on labor and cost intensive neuroimaging techniques, unsuitable for areas with inadequate access to quality medical facilities. Thus, there is a great need for an efficient diagnosis alternative. StrokeSave is a platform for users to self-diagnose for prevalence to stroke. The mobile app is continuously updated with heart rate, blood pressure, and blood oxygen data from sensors on the patient wrist. Once these measurements reach a threshold for possible stroke, the patient takes facial images and vocal recordings to screen for paralysis attributed to stroke. A custom designed lens attached to a phone's camera then takes retinal images for the deep learning model to classify based on presence of retinopathy and sends a comprehensive diagnosis. The deep learning model, which consists of a RNN trained on 100 voice slurred audio files, a SVM trained on 410 vascular data points, and a CNN trained on 520 retinopathy images, achieved a holistic accuracy of 95.0 percent when validated on 327 samples. This value exceeds that of clinical examination accuracy, which is around 40 to 89 percent, further demonstrating the vital utility of such a medical device. Through this automated platform, users receive efficient, highly accurate diagnosis without professional medical assistance, revolutionizing medical diagnosis of CS and potentially saving millions of lives.