Molecular robotics is challenging, so it seems best to keep it simple. We consider an abstract molecular robotics model based on simple folding instructions that execute asynchronously. Turning Machines are a simple 1D to 2D folding model, also easily generalisable to 2D to 3D folding. A Turning Machine starts out as a line of connected monomers in the discrete plane, each with an associated turning number. A monomer turns relative to its neighbours, executing a unit-distance translation that drags other monomers along with it, and through collective motion the initial set of monomers eventually folds into a programmed shape. We provide a suite of tools for reasoning about Turning Machines by fully characterising their ability to execute line rotations: executing an almost-full line rotation of $5\pi/3$ radians is possible, yet a full $2\pi$ rotation is impossible. Furthermore, line rotations up to $5\pi/3$ are executed efficiently, in $O(\log n)$ expected time in our continuous time Markov chain time model. We then show that such line-rotations represent a fundamental primitive in the model, by using them to efficiently and asynchronously fold shapes. In particular, arbitrarily large zig-zag-rastered squares and zig-zag paths are foldable, as are $y$-monotone shapes albeit with error (bounded by perimeter length). Finally, we give shapes that despite having paths that traverse all their points, are in fact impossible to fold, as well as techniques for folding certain classes of (scaled) shapes without error. Our approach relies on careful geometric-based analyses of the feats possible and impossible by a very simple robotic system, and pushes conceptional hardness towards mathematical analysis and away from molecular implementation.
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Specifications of complex, large scale, computer software and hardware systems can be radically simplified by using simple maps from input sequences to output values. These "state machine maps" provide an alternative representation of classical Moore type state machines. Composition of state machine maps corresponds to state machine products and can be used to specify essentially any type of interconnection as well as parallel and distributed computation. State machine maps can also specify abstract properties of systems and are significantly more concise and scalable than traditional representations of automata. Examples included here include specifications of producer/consumer software, network distributed consensus, real-time digital circuits, and operating system scheduling. The motivation for this work comes from experience designing and developing operating systems and real-time software where weak methods for understanding and exploring designs is a well known handicap. The methods introduced here are based on ordinary discrete mathematics, primitive recursive functions and deterministic state machines and are intended, initially, to aid the intuition and understanding of the system developers. Staying strictly within the boundaries of classical deterministic state machines anchors the methods to the algebraic structures of automata and semigroups, obviates any need for axiomatic deduction systems, "formal methods", or extensions to the model, and makes the specifications more faithful to engineering practice. While state machine maps are obvious representations of state machines, the techniques introduced here for defining and composing them are novel.
Emerging distributed cloud architectures, e.g., fog and mobile edge computing, are playing an increasingly important role in the efficient delivery of real-time stream-processing applications such as augmented reality, multiplayer gaming, and industrial automation. While such applications require processed streams to be shared and simultaneously consumed by multiple users/devices, existing technologies lack efficient mechanisms to deal with their inherent multicast nature, leading to unnecessary traffic redundancy and network congestion. In this paper, we establish a unified framework for distributed cloud network control with generalized (mixed-cast) traffic flows that allows optimizing the distributed execution of the required packet processing, forwarding, and replication operations. We first characterize the enlarged multicast network stability region under the new control framework (with respect to its unicast counterpart). We then design a novel queuing system that allows scheduling data packets according to their current destination sets, and leverage Lyapunov drift-plus-penalty theory to develop the first fully decentralized, throughput- and cost-optimal algorithm for multicast cloud network flow control. Numerical experiments validate analytical results and demonstrate the performance gain of the proposed design over existing cloud network control techniques.
Molecular dynamics (MD) has long been the \emph{de facto} choice for modeling complex atomistic systems from first principles, and recently deep learning become a popular way to accelerate it. Notwithstanding, preceding approaches depend on intermediate variables such as the potential energy or force fields to update atomic positions, which requires additional computations to perform back-propagation. To waive this requirement, we propose a novel model called ScoreMD by directly estimating the gradient of the log density of molecular conformations. Moreover, we analyze that diffusion processes highly accord with the principle of enhanced sampling in MD simulations, and is therefore a perfect match to our sequential conformation generation task. That is, ScoreMD perturbs the molecular structure with a conditional noise depending on atomic accelerations and employs conformations at previous timeframes as the prior distribution for sampling. Another challenge of modeling such a conformation generation process is that the molecule is kinetic instead of static, which no prior studies strictly consider. To solve this challenge, we introduce a equivariant geometric Transformer as a score function in the diffusion process to calculate the corresponding gradient. It incorporates the directions and velocities of atomic motions via 3D spherical Fourier-Bessel representations. With multiple architectural improvements, we outperforms state-of-the-art baselines on MD17 and isomers of C7O2H10. This research provides new insights into the acceleration of new material and drug discovery.
We investigate optimal execution problems with instantaneous price impact and stochastic resilience. First, in the setting of linear price impact function we derive a closed-form recursion for the optimal strategy, generalizing previous results with deterministic transient price impact. Second, we develop a numerical algorithm for the case of nonlinear price impact. We utilize an actor-critic framework that constructs two neural-network surrogates for the value function and the feedback control. One advantage of such functional approximators is the ability to do parametric learning, i.e. to incorporate some of the model parameters as part of the input space. Precise calibration of price impact, resilience, etc., is known to be extremely challenging and hence it is critical to understand sensitivity of the strategy to these parameters. Our parametric neural network (NN) learner organically scales across 3-6 input dimensions and is shown to accurately approximate optimal strategy across a range of parameter configurations. We provide a fully reproducible Jupyter Notebook with our NN implementation, which is of independent pedagogical interest, demonstrating the ease of use of NN surrogates in (parametric) stochastic control problems.
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtual screening to detailed free energy calculations. Traditionally, MM potentials have relied on human-curated, inflexible, and poorly extensible discrete chemical perception rules or applying parameters to small molecules or biopolymers, making it difficult to optimize both types and parameters to fit quantum chemical or physical property data. Here, we propose an alternative approach that uses graph neural networks to perceive chemical environments, producing continuous atom embeddings from which valence and nonbonded parameters can be predicted using invariance-preserving layers. Since all stages are built from smooth neural functions, the entire process is modular and end-to-end differentiable with respect to model parameters, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules. We show that this approach is not only sufficiently expressive to reproduce legacy atom types, but that it can learn to accurately reproduce and extend existing molecular mechanics force fields. Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity than traditional atom or parameter typing schemes. When trained on the same quantum chemical small molecule dataset used to parameterize the openff-1.2.0 small molecule force field augmented with a peptide dataset, the resulting espaloma model shows superior accuracy vis-\`a-vis experiments in computing relative alchemical free energy calculations for a popular benchmark set.
This paper presents new deterministic and distributed low-diameter decomposition algorithms for weighted graphs. In particular, we show that if one can efficiently compute approximate distances in a parallel or a distributed setting, one can also efficiently compute low-diameter decompositions. This consequently implies solutions to many fundamental distance based problems using a polylogarithmic number of approximate distance computations. Our low-diameter decomposition generalizes and extends the line of work starting from [Rozho\v{n}, Ghaffari STOC 2020] to weighted graphs in a very model-independent manner. Moreover, our clustering results have additional useful properties, including strong-diameter guarantees, separation properties, restricting cluster centers to specified terminals, and more. Applications include: -- The first near-linear work and polylogarithmic depth randomized and deterministic parallel algorithm for low-stretch spanning trees (LSST) with polylogarithmic stretch. Previously, the best parallel LSST algorithm required $m \cdot n^{o(1)}$ work and $n^{o(1)}$ depth and was inherently randomized. No deterministic LSST algorithm with truly sub-quadratic work and sub-linear depth was known. -- The first near-linear work and polylogarithmic depth deterministic algorithm for computing an $\ell_1$-embedding into polylogarithmic dimensional space with polylogarithmic distortion. The best prior deterministic algorithms for $\ell_1$-embeddings either require large polynomial work or are inherently sequential. Even when we apply our techniques to the classical problem of computing a ball-carving with strong-diameter $O(\log^2 n)$ in an unweighted graph, our new clustering algorithm still leads to an improvement in round complexity from $O(\log^{10} n)$ rounds [Chang, Ghaffari PODC 21] to $O(\log^{4} n)$.
We present SymForce, a fast symbolic computation and code generation library for robotics applications like computer vision, state estimation, motion planning, and controls. SymForce combines the development speed and flexibility of symbolic mathematics with the performance of autogenerated, highly optimized code in C++ or any target runtime language. SymForce provides geometry and camera types, Lie group operations, and branchless singularity handling for creating and analyzing complex symbolic expressions in Python, built on top of SymPy. Generated functions can be integrated as factors into our tangent space nonlinear optimizer, which is highly optimized for real-time production use. We introduce novel methods to automatically compute tangent space Jacobians, eliminating the need for bug-prone handwritten derivatives. This workflow enables faster runtime code, faster development time, and fewer lines of handwritten code versus the state-of-the-art. Our experiments demonstrate that our approach can yield order of magnitude speedups on computational tasks core to robotics. Code is available at //github.com/symforce-org/symforce .
After spending 9 years in Quantum Computing and given the impending timeline of developing good quality quantum processing units, it is the moment to rethink the approach to advance quantum computing research. Rather than waiting for quantum hardware technologies to mature, we need to start assessing in tandem the impact of the occurrence of quantum computing in various scientific fields. However, for this purpose, we need to use a complementary but quite different approach than proposed by the NISQ vision, which is heavily focused on and burdened by the engineering challenges. That is why we propose and advocate the PISQ-approach: Perfect Intermediate-Scale Quantum computing based on the already known concept of perfect qubits. This will allow researchers to focus much more on the development of new applications by defining the algorithms in terms of perfect qubits and evaluating them on quantum computing simulators that are executed on supercomputers. It is not a long-term solution but it will allow universities to currently develop research on quantum logic and algorithms and companies can already start developing their internal know-how on quantum solutions.
Leveraging line features to improve localization accuracy of point-based visual-inertial SLAM (VINS) is gaining interest as they provide additional constraints on scene structure. However, real-time performance when incorporating line features in VINS has not been addressed. This paper presents PL-VINS, a real-time optimization-based monocular VINS method with point and line features, developed based on the state-of-the-art point-based VINS-Mono \cite{vins}. We observe that current works use the LSD \cite{lsd} algorithm to extract line features; however, LSD is designed for scene shape representation instead of the pose estimation problem, which becomes the bottleneck for the real-time performance due to its high computational cost. In this paper, a modified LSD algorithm is presented by studying a hidden parameter tuning and length rejection strategy. The modified LSD can run at least three times as fast as LSD. Further, by representing space lines with the Pl\"{u}cker coordinates, the residual error in line estimation is modeled in terms of the point-to-line distance, which is then minimized by iteratively updating the minimum four-parameter orthonormal representation of the Pl\"{u}cker coordinates. Experiments in a public benchmark dataset show that the localization error of our method is 12-16\% less than that of VINS-Mono at the same pose update frequency. %For the benefit of the community, The source code of our method is available at: //github.com/cnqiangfu/PL-VINS.
In recent years, mobile devices have gained increasingly development with stronger computation capability and larger storage. Some of the computation-intensive machine learning and deep learning tasks can now be run on mobile devices. To take advantage of the resources available on mobile devices and preserve users' privacy, the idea of mobile distributed machine learning is proposed. It uses local hardware resources and local data to solve machine learning sub-problems on mobile devices, and only uploads computation results instead of original data to contribute to the optimization of the global model. This architecture can not only relieve computation and storage burden on servers, but also protect the users' sensitive information. Another benefit is the bandwidth reduction, as various kinds of local data can now participate in the training process without being uploaded to the server. In this paper, we provide a comprehensive survey on recent studies of mobile distributed machine learning. We survey a number of widely-used mobile distributed machine learning methods. We also present an in-depth discussion on the challenges and future directions in this area. We believe that this survey can demonstrate a clear overview of mobile distributed machine learning and provide guidelines on applying mobile distributed machine learning to real applications.
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