Ahmed Ashraf

Muhammad Tahir, Shehroz S. Khan, James Davie et al.

In mammalian and vertebrate genomes, the promoter regions of the gene and their distal enhancers may be located millions of base-pairs from each other, while a promoter may not interact with the closest enhancer. Since base-pair proximity is not a good indicator of these interactions, there is considerable work toward developing methods for predicting Enhancer-Promoter Interactions (EPI). Several machine learning methods have reported increasingly higher accuracies for predicting EPI. Typically, these approaches randomly split the dataset of Enhancer-Promoter (EP) pairs into training and testing subsets followed by model training. However, the aforementioned random splitting causes information leakage by assigning EP pairs from the same genomic region to both testing and training sets, leading to performance overestimation. In this paper we propose to use a more thorough training and testing paradigm i.e., Leave-one-chromosome-out (LOCO) cross-validation for EPI-prediction. We demonstrate that a deep learning algorithm, which gives higher accuracies when trained and tested on random-splitting setting, drops drastically in performance under LOCO setting, confirming overestimation of performance. We further propose a novel hybrid deep neural network for EPI-prediction that fuses k-mer features of the nucleotide sequence. We show that the hybrid architecture performs significantly better in the LOCO setting, demonstrating it can learn more generalizable aspects of EP interactions. With this paper we are also releasing the LOCO splitting-based EPI dataset. Research data is available in this public repository: https://github.com/malikmtahir/EPI

Muhammad Tahir, Mahboobeh Norouzi, Shehroz S. Khan et al.

Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA methylation, histone modifications, chromatin conformation, and non-coding RNA. The changes in gene regulation and expression can manifest in the form of various diseases and disorders such as cancer and congenital deformities. Over the last few decades, high throughput experimental approaches have been used to identify and understand epigenetic changes, but these laboratory experimental approaches and biochemical processes are time-consuming and expensive. To overcome these challenges, machine learning and artificial intelligence (AI) approaches have been extensively used for mapping epigenetic modifications to their phenotypic manifestations. In this paper we provide a narrative review of published research on AI models trained on epigenomic data to address a variety of problems such as prediction of disease markers, gene expression, enhancer promoter interaction, and chromatin states. The purpose of this review is twofold as it is addressed to both AI experts and epigeneticists. For AI researchers, we provided a taxonomy of epigenetics research problems that can benefit from an AI-based approach. For epigeneticists, given each of the above problems we provide a list of candidate AI solutions in the literature. We have also identified several gaps in the literature, research challenges, and recommendations to address these challenges.

Shehroz S. Khan, Petar Przulj, Ahmed Ashraf et al.

The global demand for radiologists is increasing rapidly due to a growing reliance on medical imaging services, while the supply of radiologists is not keeping pace. Advances in computer vision and image processing technologies present significant potential to address this gap by enhancing radiologists' capabilities and improving diagnostic accuracy. Large language models (LLMs), particularly generative pre-trained transformers (GPTs), have become the primary approach for understanding and generating textual data. In parallel, vision transformers (ViTs) have proven effective at converting visual data into a format that LLMs can process efficiently. In this paper, we present ChestGPT, a deep-learning framework that integrates the EVA ViT with the Llama 2 LLM to classify diseases and localize regions of interest in chest X-ray images. The ViT converts X-ray images into tokens, which are then fed, together with engineered prompts, into the LLM, enabling joint classification and localization of diseases. This approach incorporates transfer learning techniques to enhance both explainability and performance. The proposed method achieved strong global disease classification performance on the VinDr-CXR dataset, with an F1 score of 0.76, and successfully localized pathologies by generating bounding boxes around the regions of interest. We also outline several task-specific prompts, in addition to general-purpose prompts, for scenarios radiologists might encounter. Overall, this framework offers an assistive tool that can lighten radiologists' workload by providing preliminary findings and regions of interest to facilitate their diagnostic process.

Shehroz S. Khan, Faraz Khoshbakhtian, Ahmed Bilal Ashraf

The current COVID-19 pandemic is now getting contained, albeit at the cost of morethan2.3million human lives. A critical phase in any pandemic is the early detection of cases to develop preventive treatments and strategies. In the case of COVID-19,several studies have indicated that chest radiography images of the infected patients show characteristic abnormalities. However, at the onset of a given pandemic, such asCOVID-19, there may not be sufficient data for the affected cases to train models for their robust detection. Hence, supervised classification is ill-posed for this problem because the time spent in collecting large amounts of data from infected persons could lead to the loss of human lives and delays in preventive interventions. Therefore, we formulate the problem of identifying early cases in a pandemic as an anomaly detection problem, in which the data for healthy patients is abundantly available, whereas no training data is present for the class of interest (COVID-19 in our case). To solve this problem, we present several unsupervised deep learning approaches, including convolutional and adversarially trained autoencoder. We tested two settings on a publicly available dataset (COVIDx)by training the model on chest X-rays from (i) only healthy adults, and (ii) healthy and other non-COVID-19 pneumonia, and detected COVID-19 as an anomaly. Afterperforming3-fold cross validation, we obtain a ROC-AUC of0.765. These results are very encouraging and pave the way towards research for ensuring emergency preparedness in future pandemics, especially the ones that could be detected from chest X-rays

Azin Asgarian, Shun Zhao, Ahmed B. Ashraf et al.

Accurate facial expression analysis is an essential step in various clinical applications that involve physical and mental health assessments of older adults (e.g. diagnosis of pain or depression). Although remarkable progress has been achieved toward developing robust facial landmark detection methods, state-of-the-art methods still face many challenges when encountering uncontrolled environments, different ranges of facial expressions, and different demographics of the population. A recent study has revealed that the health status of individuals can also affect the performance of facial landmark detection methods on front views of faces. In this work, we investigate this matter in a much greater context using seven facial landmark detection methods. We perform our evaluation not only on frontal faces but also on profile faces and in various regions of the face. Our results shed light on limitations of the existing methods and challenges of applying these methods in clinical settings by indicating: 1) a significant difference between the performance of state-of-the-art when tested on the profile or frontal faces of individuals with vs. without dementia; 2) insights on the existing bias for all regions of the face; and 3) the presence of this bias despite re-training/fine-tuning with various configurations of six datasets.

Azin Asgarian, Parinaz Sobhani, Ji Chao Zhang et al.

In recent years, supervised machine learning models have demonstrated tremendous success in a variety of application domains. Despite the promising results, these successful models are data hungry and their performance relies heavily on the size of training data. However, in many healthcare applications it is difficult to collect sufficiently large training datasets. Transfer learning can help overcome this issue by transferring the knowledge from readily available datasets (source) to a new dataset (target). In this work, we propose a hybrid instance-based transfer learning method that outperforms a set of baselines including state-of-the-art instance-based transfer learning approaches. Our method uses a probabilistic weighting strategy to fuse information from the source domain to the model learned in the target domain. Our method is generic, applicable to multiple source domains, and robust with respect to negative transfer. We demonstrate the effectiveness of our approach through extensive experiments for two different applications.

Ahmed Ashraf, Shehroz Khan, Nikhil Bhagwat et al.

Medical imaging machine learning algorithms are usually evaluated on a single dataset. Although training and testing are performed on different subsets of the dataset, models built on one study show limited capability to generalize to other studies. While database bias has been recognized as a serious problem in the computer vision community, it has remained largely unnoticed in medical imaging research. Transfer learning thus remains confined to the re-use of feature representations requiring re-training on the new dataset. As a result, machine learning models do not generalize even when trained on imaging datasets that were captured to study the same variable of interest. The ability to transfer knowledge gleaned from one study to another, without the need for re-training, if possible, would provide reassurance that the models are learning knowledge fundamental to the problem under study instead of latching onto the idiosyncracies of a dataset. In this paper, we situate the problem of dataset bias in the context of medical imaging studies. We show empirical evidence that such a problem exists in medical datasets. We then present a framework to unlearn study membership as a means to handle the problem of database bias. Our main idea is to take the data from the original feature space to an intermediate space where the data points are indistinguishable in terms of which study they come from, while maintaining the recognition capability with respect to the variable of interest. This will promote models which learn the more general properties of the etiology under study instead of aligning to dataset-specific peculiarities. Essentially, our proposed model learns to unlearn the dataset bias.

Azin Asgarian, Ahmed Bilal Ashraf, David Fleet et al.

Active appearance models (AAMs) are a class of generative models that have seen tremendous success in face analysis. However, model learning depends on the availability of detailed annotation of canonical landmark points. As a result, when accurate AAM fitting is required on a different set of variations (expression, pose, identity), a new dataset is collected and annotated. To overcome the need for time consuming data collection and annotation, transfer learning approaches have received recent attention. The goal is to transfer knowledge from previously available datasets (source) to a new dataset (target). We propose a subspace transfer learning method, in which we select a subspace from the source that best describes the target space. We propose a metric to compute the directional similarity between the source eigenvectors and the target subspace. We show an equivalence between this metric and the variance of target data when projected onto source eigenvectors. Using this equivalence, we select a subset of source principal directions that capture the variance in target data. To define our model, we augment the selected source subspace with the target subspace learned from a handful of target examples. In experiments done on six publicly available datasets, we show that our approach outperforms the state of the art in terms of the RMS fitting error as well as the percentage of test examples for which AAM fitting converges to the ground truth.

Babak Taati, Pranay Lohia, Avril Mansfield et al.

Because falls are funny, YouTube and other video sharing sites contain a large repository of real-life falls. We propose extracting gait and balance information from these videos to help us better understand some of the factors that contribute to falls. Proof-of-concept is explored in a single video containing multiple (n=14) falls/non-falls in the presence of an unexpected obstacle. The analysis explores: computing spatiotemporal parameters of gait in a video captured from an arbitrary viewpoint; the relationship between parameters of gait from the last few steps before the obstacle and falling vs. not falling; and the predictive capacity of a multivariate model in predicting a fall in the presence of an unexpected obstacle. Homography transformations correct the perspective projection distortion and allow for the consistent tracking of gait parameters as an individual walks in an arbitrary direction in the scene. A synthetic top view allows for computing the average stride length and a synthetic side view allows for measuring up and down motions of the head. In leave-one-out cross-validation, we were able to correctly predict whether a person would fall or not in 11 out of the 14 cases (78.6%), just by looking at the average stride length and the range of vertical head motion during the 1-4 most recent steps prior to reaching the obstacle.