Infections and Infectious Diseases
The Morning After: Google DeepMind's Genie 2 can generate interactive 3D worlds
Google DeepMind has just revealed Genie 2, a world-modelling AI capable of creating 3D worlds and sustaining those environments for significantly longer. It's a diffusion model that generates images as the player (either a human being or another AI agent) moves through the world the software is simulating. All it needs to start is a single image prompt either generated by AI or from a real-world photo. There are limitations: DeepMind says the model can generate "consistent" worlds for up to 60 seconds, with the majority of the examples the company shared on Wednesday running for significantly less time -- most videos are between 10 to 20 seconds long. Image quality also softens and comes undone the longer Genie 2 needs to maintain the illusion of a consistent world.
What Africa needs to do to become a major AI player
Okinga-Koumu pulled a phone from the pocket of her blue jeans and opened a prototype web app she's built. Using VR and AI features, the app allows students to simulate using the necessary lab equipment--exploring 3D models of the tools in a real-world setting, like a classroom or lab. "Students could have detailed VR of lab equipment, making their hands-on experience more effective," she said. Established in 2017, the Deep Learning Indaba now has chapters in 47 of the 55 African nations and aims to boost AI development across the continent by providing training and resources to African AI researchers like Okinga-Koumu. Africa is still early in the process of adopting AI technologies, but organizers say the continent is uniquely hospitable to it for several reasons, including a relatively young and increasingly well-educated population, a rapidly growing ecosystem of AI startups, and lots of potential consumers.
The Download: AI for debates, and what to know about the Oropouche virus
Reaching a consensus in a democracy is difficult because people hold such different ideological, political, and social views. Perhaps an AI tool could help. Researchers from Google DeepMind trained a system of large language models to operate as a "caucus mediator," generating summaries that outline a group's areas of agreement on complex but important social or political issues. The researchers say their work highlights the potential of AI to help groups of people find common ground when discussing contentious subjects. But it's not going to replace human mediators anytime soon.
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
Antibodies are immune system proteins that protect the host by binding to specific antigens such as viruses and bacteria. The binding between antibodies and antigens is mainly determined by the complementarity-determining regions (CDR) of the antibodies. In this work, we develop a deep generative model that jointly models sequences and structures of CDRs based on diffusion probabilistic models and equivariant neural networks. Our method is the first deep learning-based method that generates antibodies explicitly targeting specific antigen structures and is one of the earliest diffusion probabilistic models for protein structures. The model is a "Swiss Army Knife" capable of sequence-structure co-design, sequence design for given backbone structures, and antibody optimization.
When and How to Lift the Lockdown? Global COVID-19 Scenario Analysis and Policy Assessment using Compartmental Gaussian Processes
The coronavirus disease 2019 (COVID-19) global pandemic has led many countries to impose unprecedented lockdown measures in order to slow down the outbreak. Questions on whether governments have acted promptly enough, and whether lockdown measures can be lifted soon have since been central in public discourse. Data-driven models that predict COVID-19 fatalities under different lockdown policy scenarios are essential for addressing these questions, and for informing governments on future policy directions. To this end, this paper develops a Bayesian model for predicting the effects of COVID-19 containment policies in a global context -- we treat each country as a distinct data point, and exploit variations of policies across countries to learn country-specific policy effects. Our model utilizes a two-layer Gaussian process (GP) prior -- the lower layer uses a compartmental SEIR (Susceptible, Exposed, Infected, Recovered) model as a prior mean function with "country-and-policy-specific" parameters that capture fatality curves under different "counterfactual" policies within each country, whereas the upper layer is shared across all countries, and learns lower-layer SEIR parameters as a function of country features and policy indicators.
Conformal Frequency Estimation with Sketched Data
A flexible conformal inference method is developed to construct confidence intervals for the frequencies of queried objects in very large data sets, based on a much smaller sketch of those data. The approach is data-adaptive and requires no knowledge of the data distribution or of the details of the sketching algorithm; instead, it constructs provably valid frequentist confidence intervals under the sole assumption of data exchangeability. Although our solution is broadly applicable, this paper focuses on applications involving the count-min sketch algorithm and a non-linear variation thereof. The performance is compared to that of frequentist and Bayesian alternatives through simulations and experiments with data sets of SARS-CoV-2 DNA sequences and classic English literature.
Learning Mutational Semantics
In many natural domains, changing a small part of an entity can transform its semantics; for example, a single word change can alter the meaning of a sentence, or a single amino acid change can mutate a viral protein to escape antiviral treatment or immunity. Although identifying such mutations can be desirable (for example, therapeutic design that anticipates avenues of viral escape), the rules governing semantic change are often hard to quantify. Here, we introduce the problem of identifying mutations with a large effect on semantics, but where valid mutations are under complex constraints (for example, English grammar or biological viability), which we refer to as constrained semantic change search (CSCS). We propose an unsupervised solution based on language models that simultaneously learn continuous latent representations. We report good empirical performance on CSCS of single-word mutations to news headlines, map a continuous semantic space of viral variation, and, notably, show unprecedented zero-shot prediction of single-residue escape mutations to key influenza and HIV proteins, suggesting a productive link between modeling natural language and pathogenic evolution.
The Devil is in the Detail: A Framework for Macroscopic Prediction via Microscopic Models
Macroscopic data aggregated from microscopic events are pervasive in machine learning, such as country-level COVID-19 infection statistics based on city-level data. In this paper, we propose a principled optimization framework for macroscopic prediction by fitting microscopic models based on conditional stochastic optimization. The framework leverages both macroscopic and microscopic information, and adapts to individual microscopic models involved in the aggregation. In addition, we propose efficient learning algorithms with convergence guarantees. In our experiments, we show that the proposed learning framework clearly outperforms other plug-in supervised learning approaches in real-world applications, including the prediction of daily infections of COVID-19 and medicare claims.
Online Reinforcement Learning for Mixed Policy Scopes
Combination therapy refers to the use of multiple treatments -- such as surgery, medication, and behavioral therapy - to cure a single disease, and has become a cornerstone for treating various conditions including cancer, HIV, and depression. All possible combinations of treatments lead to a collection of treatment regimens (i.e., policies) with mixed scopes, or what physicians could observe and which actions they should take depending on the context. In this paper, we investigate the online reinforcement learning setting for optimizing the policy space with mixed scopes. In particular, we develop novel online algorithms that achieve sublinear regret compared to an optimal agent deployed in the environment. The regret bound has a dependency on the maximal cardinality of the induced state-action space associated with mixed scopes.
Hierarchical Quantized Autoencoders
Despite progress in training neural networks for lossy image compression, current approaches fail to maintain both perceptual quality and abstract features at very low bitrates. Encouraged by recent success in learning discrete representations with Vector Quantized Variational Autoencoders (VQ-VAEs), we motivate the use of a hierarchy of VQ-VAEs to attain high factors of compression. We show that the combination of stochastic quantization and hierarchical latent structure aids likelihood-based image compression. This leads us to introduce a novel objective for training hierarchical VQ-VAEs. Our resulting scheme produces a Markovian series of latent variables that reconstruct images of high-perceptual quality which retain semantically meaningful features.