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In this paper, we present a new approach to time series forecasting. Time series data are prevalent in many scientific and engineering disciplines. Time series forecasting is a crucial task in modeling time series data, and is an important…

Influenza A is responsible for 290,000 to 650,000 respiratory deaths a year, though this estimate is an improvement from years past due to improvements in sanitation, healthcare practices, and vaccination programs. In this study, we perform…

The Influenza type A virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Haemagglutinin (HA) gene of the virus has the potential to be a target for…

A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to…

Influenza viruses mutate rapidly and can pose a threat to public health, especially to those in vulnerable groups. Throughout history, influenza A viruses have caused pandemics between different species. It is important to identify the…

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact,…

Influenza poses a significant threat to public health, particularly among the elderly, young children, and people with underlying dis-eases. The manifestation of severe conditions, such as pneumonia, highlights the importance of preventing…

The Influenza virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Hemagglutinin (HA) gene of the virus can be a target for antiviral drug development…

Influenza occurs every season and occasionally causes pandemics. Despite its low mortality rate, influenza is a major public health concern, as it can be complicated by severe diseases like pneumonia. A fast, accurate and low-cost method to…

High order structures (cavities and cliques) of the gene network of influenza A virus reveal tight associations among viruses during evolution and are key signals that indicate viral cross-species infection and cause pandemics. As…

Seasonal influenza kills hundreds of thousands every year, with multiple constantly-changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system,…

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between…

Influenza A viruses (IAVs) evolve antigenically at a pace that requires frequent vaccine updates, yet the haemagglutination inhibition (HI) assays used to quantify antigenicity are labor-intensive and unscalable. As a result, genomic data…

Avian Influenza breakouts cause millions of dollars in damage each year globally, especially in Asian countries such as China and South Korea. The impact magnitude of a breakout directly correlates to time required to fully understand the…

Infectious diseases pose significant human and economic burdens. Accurately forecasting disease incidence can enable public health agencies to respond effectively to existing or emerging diseases. Despite progress in the field, developing…

Laboratory models are often used to understand the interaction of related pathogens via host immunity. For example, recent experiments where ferrets were exposed to two influenza strains within a short period of time have shown how the…

Foundation models in healthcare have largely adopted self supervised pretraining objectives inherited from natural language processing and computer vision, emphasizing reconstruction and large scale representation learning prior to…

Deep transfer learning recently has acquired significant research interest. It makes use of pre-trained models that are learned from a source domain, and utilizes these models for the tasks in a target domain. Model-based deep transfer…

Epidemics of infectious diseases are an important threat to public health and global economies. Yet, the development of prevention strategies remains a challenging process, as epidemics are non-linear and complex processes. For this reason,…

This research presents the development of an Artificial Intelligence (AI) - driven crop disease detection system designed to assist farmers in rural areas with limited resources. We aim to compare different deep learning models for a…