Collaborating Authors

epitope taps AI to predict COVID-19 vaccine success


A team of researchers hailing from Harvard and Université de Montréal today launched, It's built atop an algorithm -- CAMAP -- that generates predictions for potential vaccine targets, enabling researchers to identify which parts of the virus are more likely to be exposed at the surface (epitopes) of infected cells. Project lead Dr. Tariq Daouda, who worked alongside doctorates in machine learning, immunobiologists, and bioinformaticians to build, Fewer than 12% of all drugs entering clinical trials end up in pharmacies, and it takes at least 10 years for medicines to complete the journey from discovery to the marketplace. Clinical trials alone take six to seven years, on average, putting the cost of R&D at roughly $2.6 billion, according to the Pharmaceutical Research and Manufacturers of America.

Using ``epitomes'' to model genetic diversity: Rational design of HIV vaccine cocktails

Neural Information Processing Systems

We introduce a new model of genetic diversity which summarizes a large input dataset into an epitome, a short sequence or a small set of short sequences of probability distributions capturing many overlapping subsequences fromthe dataset. The epitome as a representation has already been used in modeling real-valued signals, such as images and audio. The discrete sequence model we introduce in this paper targets applications in genetics, from multiple alignment to recombination and mutation inference. Inour experiments, we concentrate on modeling the diversity of HIV where the epitome emerges as a natural model for producing relatively smallvaccines covering a large number of immune system targets known as epitopes. Our experiments show that the epitome includes more epitopes than other vaccine designs of similar length, including cocktails of consensus strains, phylogenetic tree centers, and observed strains. We also discuss epitome designs that take into account uncertainty about T-cell cross reactivity and epitope presentation. In our experiments, we find that vaccine optimization is fairly robust to these uncertainties.