The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise interactions, these approaches do not provide a tractable path towards modeling higher-order dependencies. Here, we show how latent variable models with nonlinear dependencies can be applied to capture beyond-pairwise constraints in biomolecules. We present a new probabilistic model for sequence families, DeepSequence, that can predict the effects of mutations across a variety of deep mutational scanning experiments significantly better than site independent or pairwise models that are based on the same evolutionary data. The model, learned in an unsupervised manner solely from sequence information, is grounded with biologically motivated priors, reveals latent organization of sequence families, and can be used to extrapolate to new parts of sequence space.

We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of the activation maximization ("deep dream") design method; and a joint procedure which combines these two approaches together. We show that these tools capture important structures of the data and, when applied to designing probes for protein binding microarrays, allow us to generate new sequences whose properties are estimated to be superior to those found in the training data. We believe that these results open the door for applying deep generative models to advance genomics research.

Deep generative models are reported to be useful in broad applications including image generation. Repeated inference between data space and latent space in these models can denoise cluttered images and improve the quality of inferred results. However, previous studies only qualitatively evaluated image outputs in data space, and the mechanism behind the inference has not been investigated. The purpose of the current study is to numerically analyze changes in activity patterns of neurons in the latent space of a deep generative model called a "variational auto-encoder" (VAE). What kinds of inference dynamics the VAE demonstrates when noise is added to the input data are identified. The VAE embeds a dataset with clear cluster structures in the latent space and the center of each cluster of multiple correlated data points (memories) is referred as the concept. Our study demonstrated that transient dynamics of inference first approaches a concept, and then moves close to a memory. Moreover, the VAE revealed that the inference dynamics approaches a more abstract concept to the extent that the uncertainty of input data increases due to noise. It was demonstrated that by increasing the number of the latent variables, the trend of the inference dynamics to approach a concept can be enhanced, and the generalization ability of the VAE can be improved.

Researchers at OpenAI have launched a library of tools that can help researchers build faster, more efficient neural networks that take up less memory on GPUs. Neural networks are made up of layers of connected nodes. The architecture for these networks are highly variable depending on the data and application, but all models are limited by the way they run on GPUs. One way to train larger models for less computation is to introduce sparse matrices. A matrix is considered sparse if it is filled with mostly zeroes.

Elon Musk believes it's highly likely that artificial intelligence (AI) will be a threat to people. The Tesla founder is concerned that a handful of major companies will end up in control of AI systems with "extreme" levels of power. In Mr Musk's opinion, there's a very small chance that humans will be safe from such systems. "Maybe there's a five to 10 percent chance of success [of making AI safe]," he told Neuralink staff after showing them a documentary on AI, reports Rolling Stone. He also told them that he invested in DeepMind in order to keep an eye on Google's development of AI.

Human-like artificial intelligence is still a long way off, but Greg Brockman believes the time to start thinking about its safety is now. That's why, after helping to build the online-payments firm Stripe, he cofounded OpenAI along with Elon Musk and others. The nonprofit research group focuses on making sure AI continues to benefit humanity even as it increases in sophistication. Brockman plays many roles at the firm, from recruiting to helping researchers test new learning algorithms. In the long term, he says, a general AI system will need something akin to a sense of shame to prevent it from misbehaving.

Deep generative models learn a mapping from a low dimensional latent space to a high-dimensional data space. Under certain regularity conditions, these models parameterize nonlinear manifolds in the data space. In this paper, we investigate the Riemannian geometry of these generated manifolds. First, we develop efficient algorithms for computing geodesic curves, which provide an intrinsic notion of distance between points on the manifold. Second, we develop an algorithm for parallel translation of a tangent vector along a path on the manifold. We show how parallel translation can be used to generate analogies, i.e., to transport a change in one data point into a semantically similar change of another data point. Our experiments on real image data show that the manifolds learned by deep generative models, while nonlinear, are surprisingly close to zero curvature. The practical implication is that linear paths in the latent space closely approximate geodesics on the generated manifold. However, further investigation into this phenomenon is warranted, to identify if there are other architectures or datasets where curvature plays a more prominent role. We believe that exploring the Riemannian geometry of deep generative models, using the tools developed in this paper, will be an important step in understanding the high-dimensional, nonlinear spaces these models learn.

Currently I'm searching for a Reinforcement Learning toolkit for autonomous driving to test the influence of several safety aspects during learning as a reward function. So far I have tested OpenAI Gym with the "Neon racer" environment, which does not provide those information. Are there any other toolkits you would suggest me for this purpose?

Variational autoencoders (VAEs) learn representations of data by jointly training a probabilistic encoder and decoder network. Typically these models encode all features of the data into a single variable. Here we are interested in learning disentangled representations that encode distinct aspects of the data into separate variables. We propose to learn such representations using model architectures that generalise from standard VAEs, employing a general graphical model structure in the encoder and decoder. This allows us to train partially-specified models that make relatively strong assumptions about a subset of interpretable variables and rely on the flexibility of neural networks to learn representations for the remaining variables. We further define a general objective for semi-supervised learning in this model class, which can be approximated using an importance sampling procedure. We evaluate our framework's ability to learn disentangled representations, both by qualitative exploration of its generative capacity, and quantitative evaluation of its discriminative ability on a variety of models and datasets.

Not content to simply transform the worlds of energy, transportation, and space exploration, in 2015, Elon Musk founded OpenAI, a San Fransisco-based artificial intelligence (AI) research company. The non-profits' goal is to further the technology in ways that will benefit humanity as a whole, and over the past two years, they've pushed AI into new territory. Recently, several researchers from OpenAI stepped away from the company to found Embodied Intelligence, a robotics start-up with a more singular focus: propel robotic automation to a higher level. Through their previous work, the founding members of Embodied Intelligence -- former OpenAI researchers Peter Abbeel, Peter Chen, and Rocky Duan and former Microsoft researcher Tianhao Zhang -- explored the potential of robots to mimic complex human action. Now, they are now confident they can use their past experience to improve the type of robots that are currently used in industry and even in the home.