The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond-several orders of magnitude beyond the duration of the longest current MD simulations. We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized highspeed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.
There has been much interest in unsupervised learning of hierarchical generative models such as deep belief networks (DBNs); however, scaling such models to full-sized, high-dimensional images remains a difficult problem. To address this problem, we present the convolutional deep belief network , a hierarchical generative model that scales to realistic image sizes. This model is translation-invariant and supports efficient bottom-up and top-down probabilistic inference. Key to our approach is probabilistic max-pooling , a novel technique that shrinks the representations of higher layers in a probabilistically sound way. Our experiments show that the algorithm learns useful high-level visual features, such as object parts, from unlabeled images of objects and natural scenes. We demonstrate excellent performance on several visual recognition tasks and show that our model can perform hierarchical (bottom-up and top-down) inference over full-sized images.
Suppose that one observes an incomplete subset of entries selected from a low-rank matrix. When is it possible to complete the matrix and recover the entries that have not been seen? We demonstrate that in very general settings, one can perfectly recover all of the missing entries from most sufficiently large subsets by solving a convex programming problem that finds the matrix with the minimum nuclear norm agreeing with the observed entries. The techniques used in this analysis draw upon parallels in the field of compressed sensing, demonstrating that objects other than signals and images can be perfectly reconstructed from very limited information.
This paper reports on the development and formal verification (proof of semantic preservation) of CompCert, a compiler from Clight (a large subset of the C programming language) to PowerPC assembly code, using the Coq proof assistant both for programming the compiler and for proving its correctness. Such a verified compiler is useful in the context of critical software and its formal verification: the verification of the compiler guarantees that the safety properties proved on the source code hold for the executable compiled code as well.
How things work visualizations use a variety of visual techniques to depict the operation of complex mechanical assemblies. We present an automated approach for generating such visualizations. Starting with a 3D CAD model of an assembly, we first infer the motions of individual parts and the interactions between parts based on their geometry and a few user specified constraints. We then use this information to generate visualizations that incorporate motion arrows, frame sequences and animation to convey the causal chain of motions and mechanical interactions between parts. We present results for a wide variety of assemblies.
Suppose that you want to delegate the ability to process your data, without giving away access to it. We show that this separation is possible: we describe a "fully homomorphic" encryption scheme that keeps data private, but that allows a worker that does not have the secret decryption key to compute any (still encrypted) result of the data, even when the function of the data is very complex. In short, a third party can perform complicated processing of data without being able to see it. Among other things, this helps make cloud computing compatible with privacy.
The services sector has grown over the last 50 years to dominate economic activity in most advanced industrial economies, yet scientific understanding of modern services is rudimentary. Here, we argue for a services science discipline to integrate across academic silos and advance service innovation more rapidly.