SARS-COV-2 has roused the scientific community with a call to action to combat the growing pandemic. At the time of this writing, there are as yet no novel antiviral agents or approved vaccines available for deployment as a frontline defense. Understanding the pathobiology of COVID-19 could aid scientists in their discovery of potent antivirals by elucidating unexplored viral pathways. One method for accomplishing this is the leveraging of computational methods to discover new candidate drugs and vaccines in silico. In the last decade, machine learning-based models, trained on specific biomolecules, have offered inexpensive and rapid implementation methods for the discovery of effective viral therapies. Given a target biomolecule, these models are capable of predicting inhibitor candidates in a structural-based manner. If enough data are presented to a model, it can aid the search for a drug or vaccine candidate by identifying patterns within the data. In this review, we focus on the recent advances of COVID-19 drug and vaccine development using artificial intelligence and the potential of intelligent training for the discovery of COVID-19 therapeutics. To facilitate applications of deep learning for SARS-COV-2, we highlight multiple molecular targets of COVID-19, inhibition of which may increase patient survival. Moreover, we present CoronaDB-AI, a dataset of compounds, peptides, and epitopes discovered either in silico or in vitro that can be potentially used for training models in order to extract COVID-19 treatment. The information and datasets provided in this review can be used to train deep learning-based models and accelerate the discovery of effective viral therapies.

The ever-growing threat of deepfakes and large-scale societal implications has propelled the development of deepfake forensics to ascertain the trustworthiness of digital media. A common theme of existing detection methods is using Convolutional Neural Networks (CNNs) as a backbone. While CNNs have demonstrated decent performance on learning local discriminative information, they fail to learn relative spatial features and lose important information due to constrained receptive fields. Motivated by the aforementioned challenges, this work presents DFDT, an end-to-end deepfake detection framework that leverages the unique characteristics of transformer models, for learning hidden traces of perturbations from both local image features and global relationship of pixels at different forgery scales. DFDT is specifically designed for deepfake detection tasks consisting of four main components: patch extraction & embedding, multi-stream transformer block, attention-based patch selection followed by a multi-scale classifier. DFDT’s transformer layer benefits from a re-attention mechanism instead of a traditional multi-head self-attention layer. To evaluate the performance of DFDT, a comprehensive set of experiments are conducted on several deepfake forensics benchmarks. Obtained results demonstrated the surpassing detection rate of DFDT, achieving 99.41%, 99.31%, and 81.35% on FaceForensics++, Celeb-DF (V2), and WildDeepfake, respectively. Moreover, DFDT’s excellent cross-dataset & cross-manipulation generalization provides additional strong evidence on its effectiveness.

Background: Deep learning’s automatic feature extraction has proven to give superior performance in many sequence classification tasks. However, deep learning models generally require a massive amount of data to train, which in the case of Hemolytic Activity Prediction of Antimicrobial Peptides creates a challenge due to the small amount of available data. Results: Three different datasets for hemolysis activity prediction of therapeutic and antimicrobial peptides are gathered and the AMPDeep pipeline is implemented for each. The result demonstrate that AMPDeep outperforms the previous works on all three datasets, including works that use physicochemical features to represent the peptides or those who solely rely on the sequence and use deep learning to learn representation for the peptides. Moreover, a combined dataset is introduced for hemolytic activity prediction to address the problem of sequence similarity in this domain. AMPDeep fine-tunes a large transformer based model on a small amount of peptides and successfully leverages the patterns learned from other protein and peptide databases to assist hemolysis activity prediction modeling. Conclusions: In this work transfer learning is leveraged to overcome the challenge of small data and a deep learning based model is successfully adopted for hemolysis activity classification of antimicrobial peptides. This model is first initialized as a protein language model which is pre-trained on masked amino acid prediction on many unlabeled protein sequences in a self-supervised manner. Having done so, the model is fine-tuned on an aggregated dataset of labeled peptides in a supervised manner to predict secretion. Through transfer learning, hyper-parameter optimization and selective fine-tuning, AMPDeep is able to achieve state-of-the-art performance on three hemolysis datasets using only the sequence of the peptides. This work assists the adoption of large sequence-based models for peptide classification and modeling tasks in a practical manner.

Antimalarial drugs are becoming less effective due to the emergence of drug resistance. Resistance has been reported for all available malaria drugs, including artemisinin, thus creating a perpetual need for alternative drug candidates. The traditional drug discovery approach of high throughput screening (HTS) of large compound libraries for identification of new drug leads is time-consuming and resource intensive. While virtual in silico screening is a solution to this problem, however, the generalization of the models is not ideal. Artificial intelligence (AI), utilizing either structure-based or ligand-based approaches, has demonstrated highly accurate performances in the field of chemical property prediction. Leveraging the existing data, AI would be a suitable alternative to blind-search HTS or fingerprint-based virtual screening. The AI model would learn patterns within the data and help to search for hit compounds efficiently. In this work, we introduce DeepMalaria, a deep-learning based process capable of predicting the anti-Plasmodium falciparum inhibitory properties of compounds using their SMILES. A graph-based model is trained on 13,446 publicly available antiplasmodial hit compounds from GlaxoSmithKline (GSK) dataset that are currently being used to find novel drug candidates for malaria. We validated this model by predicting hit compounds from a macrocyclic compound library and already approved drugs that are used for repurposing. We have chosen macrocyclic compounds as these ligand-binding structures are underexplored in malaria drug discovery. The in silico pipeline for this process also consists of additional validation of an in-house independent dataset consisting mostly of natural product compounds. Transfer learning from a large dataset was leveraged to improve the performance of the deep learning model. To validate the DeepMalaria generated hits, we used a commonly used SYBR Green I fluorescence assay based phenotypic screening. DeepMalaria was able to detect all the compounds with nanomolar activity and 87.5% of the compounds with greater than 50% inhibition. Further experiments to reveal the compounds’ mechanism of action have shown that not only does one of the hit compounds, DC-9237, inhibits all asexual stages of Plasmodium falciparum, but is a fast-acting compound which makes it a strong candidate for further optimization.

Biometric verification systems have become prevalent in the modern world with the wide usage of smartphones. These systems heavily rely on storing the sensitive biometric data on the cloud. Due to the fact that biometric data like fingerprint and iris cannot be changed, storing them on the cloud creates vulnerability and can potentially have catastrophic consequences if these data are leaked. In the recent years, in order to preserve the privacy of the users, homomorphic encryption has been used to enable computation on the encrypted data and to eliminate the need for decryption. This work presents DeepZeroID: a privacy-preserving cloud-based and multiple-party biometric verification system that uses homomorphic encryption. Via transfer learning, training on sensitive biometric data is eliminated and one pre-trained deep neural network is used as feature extractor. By developing an exhaustive search algorithm, this feature extractor is applied on the tasks of biometric verification and liveness detection. By eliminating the need for training on and decrypting the sensitive biometric data, this system preserves privacy, requires zero knowledge of the sensitive data distribution, and is highly scalable. Our experimental results show that DeepZeroID can deliver 95.47% F1 score in the verification of combined iris and fingerprint feature vectors with zero true positives and with a 100% accuracy in liveness detection.

Recent advancements of Generative Adversarial Networks (GANs) pose emerging yet serious privacy risks threatening digital media’s integrity and trustworthiness, specifically digital video, through synthesizing hyper-realistic images and videos, i.e., DeepFakes. The need for ascertaining the trustworthiness of digital media calls for automatic yet accurate DeepFake detection algorithms. This paper presents an attention-based DeepFake detection (ADD) method that exploits the fine-grained and spatial locality attributes of artificially synthesized videos for enhanced detection. ADD framework is composed of two main components including face close-up and face shut-off data augmentation methods and is applicable to any classifier based on convolutional neural network architecture. ADD first locates potentially manipulated areas of the input image to extract representative features. Second, the detection model is forced to pay more attention to these forgery regions in the decision-making process through a particular focus on interpreting the sample in the learning phase. ADD’s performance is evaluated against two challenging datasets of DeepFake forensics, i.e., Celeb-DF (V2) and WildDeepFake. We demonstrated the generalization of ADD by evaluating four popular classifiers, namely VGGNet, ResNet, Xception, and MobileNet. The obtained results demonstrate that ADD can boost the detection performance of all four baseline classifiers significantly on both benchmark datasets. Particularly, ADD with ResNet backbone detects DeepFakes with more than 98.3% on Celeb-DF (V2), outperforming state-of-the-art DeepFake detection methods.