Discriminative neural networks offer little or no performance guarantees when deployed on data not generated by the same process as the training distribution. On such out-of-distribution (OOD) inputs, the prediction may not only be erroneous, but confidently so, limiting the safe deployment of classifiers in real-world applications. One such challenging application is bacteria identification based on genomic sequences, which holds the promise of early detection of diseases, but requires a model that can output low confidence predictions on OOD genomic sequences from new bacteria that were not present in the training data. We introduce a genomics dataset for OOD detection that allows other researchers to benchmark progress on this important problem. We investigate deep generative model based approaches for OOD detection and observe that the likelihood score is heavily affected by population level background statistics.

We study the problem of inverting a deep generative model with ReLU activations. Inversion corresponds to finding a latent code vector that explains observed measurements as much as possible. In most prior works this is performed by attempting to solve a non-convex optimization problem involving the generator. In this paper we obtain several novel theoretical results for the inversion problem. We show that for the realizable case, single layer inversion can be performed exactly in polynomial time, by solving a linear program.

We introduce the thermodynamic variational objective (TVO) for learning in both continuous and discrete deep generative models. The TVO arises from a key connection between variational inference and thermodynamic integration that results in a tighter lower bound to the log marginal likelihood than the standard variational evidence lower bound (ELBO) while remaining as broadly applicable. We provide a computationally efficient gradient estimator for the TVO that applies to continuous, discrete, and non-reparameterizable distributions and show that the objective functions used in variational inference, variational autoencoders, wake sleep, and inference compilation are all special cases of the TVO. We use the TVO to learn both discrete and continuous deep generative models and empirically demonstrate state of the art model and inference network learning. Papers published at the Neural Information Processing Systems Conference.

Missing value imputation is a fundamental problem in spatiotemporal modeling, from motion tracking to the dynamics of physical systems. Deep autoregressive models suffer from error propagation which becomes catastrophic for imputing long-range sequences. In this paper, we take a non-autoregressive approach and propose a novel deep generative model: Non-AutOregressive Multiresolution Imputation (NAOMI) to impute long-range sequences given arbitrary missing patterns. NAOMI exploits the multiresolution structure of spatiotemporal data and decodes recursively from coarse to fine-grained resolutions using a divide-and-conquer strategy. We further enhance our model with adversarial training.

A learned generative model often produces biased statistics relative to the underlying data distribution. A standard technique to correct this bias is importance sampling, where samples from the model are weighted by the likelihood ratio under model and true distributions. When the likelihood ratio is unknown, it can be estimated by training a probabilistic classifier to distinguish samples from the two distributions. We employ this likelihood-free importance weighting method to correct for the bias in generative models. We find that this technique consistently improves standard goodness-of-fit metrics for evaluating the sample quality of state-of-the-art deep generative models, suggesting reduced bias.

The usage of deep generative models for image compression has led to impressive performance gains over classical codecs while neural video compression is still in its infancy. Here, we propose an end-to-end, deep generative modeling approach to compress temporal sequences with a focus on video. Our approach builds upon variational autoencoder (VAE) models for sequential data and combines them with recent work on neural image compression. The approach jointly learns to transform the original sequence into a lower-dimensional representation as well as to discretize and entropy code this representation according to predictions of the sequential VAE. Rate-distortion evaluations on small videos from public data sets with varying complexity and diversity show that our model yields competitive results when trained on generic video content.

The best way to calculate statistics from medical data is to use the data of individual patients. In some settings, this data is difficult to obtain due to privacy restrictions. In Germany, for example, it is not possible to pool routine data from different hospitals for research purposes without the consent of the patients. The DataSHIELD software provides an infrastructure and a set of statistical methods for joint analyses of distributed data. The contained algorithms are reformulated to work with aggregated data from the participating sites instead of the individual data. If a desired algorithm is not implemented in DataSHIELD or cannot be reformulated in such a way, using artificial data is an alternative. We present a methodology together with a software implementation that builds on DataSHIELD to create artificial data that preserve complex patterns from distributed individual patient data. Such data sets of artificial patients, which are not linked to real patients, can then be used for joint analyses. We use deep Boltzmann machines (DBMs) as generative models for capturing the distribution of data. For the implementation, we employ the package "BoltzmannMachines" from the Julia programming language and wrap it for use with DataSHIELD, which is based on R. As an exemplary application, we conduct a distributed analysis with DBMs on a synthetic data set, which simulates genetic variant data. Patterns from the original data can be recovered in the artificial data using hierarchical clustering of the virtual patients, demonstrating the feasibility of the approach. Our implementation adds to DataSHIELD the ability to generate artificial data that can be used for various analyses, e. g. for pattern recognition with deep learning. This also demonstrates more generally how DataSHIELD can be flexibly extended with advanced algorithms from languages other than R.

If you go back a few hundred years, what we take for granted today would seem like magic – being able to talk to people over long distances, to transmit images, flying, accessing vast amounts of data like an oracle. These are all things that would have been considered magic a few hundred years ago.

Follow the latest updates of the outbreak on our timeline. Artificial intelligence (AI) technology provider Iktos and research centre SRI International have partnered to discover and develop drugs to treat various viruses, including the novel coronavirus that causes Covid-19 and influenza. Iktos will combine its generative modelling technology with SRI's fully automated synthetic chemistry platform called SynFini to design compounds and speed-up the identification of drug candidates. The Iktos AI technology leverages deep generative models for the accelerated drug discovery process, made possible via the automatic design of virtual molecules with the required characteristics of a new drug candidate. Iktos co-founder and CEO Yann Gaston-Mathé said: "Iktos generative AI technology has proven its value and potential to accelerate drug discovery programs in multiple collaborations with renowned pharmaceutical companies.

Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular graphs as strings of text, and learns their corresponding character-based language model. Another, more expressive, approach operates directly on the molecular graph. In this work, we address two limitations of the former: generation of invalid and duplicate molecules. To improve validity rates, we develop a language model for small molecular substructures called fragments, loosely inspired by the well-known paradigm of Fragment-Based Drug Design. In other words, we generate molecules fragment by fragment, instead of atom by atom. To improve uniqueness rates, we present a frequency-based masking strategy that helps generate molecules with infrequent fragments. We show experimentally that our model largely outperforms other language model-based competitors, reaching state-of-the-art performances typical of graph-based approaches. Moreover, generated molecules display molecular properties similar to those in the training sample, even in absence of explicit task-specific supervision.