47107463
Using Motion Planning to Study RNA Folding Kinetics
8798483
Planning with Reachable Distances: Fast Enforcement of Closure Constraints
Motion planning for closed-chain systems is particularly difficult due to additional closure constraints placed on the system. In fact, the probability of randomly selecting a set of joint angles that satisfy the closure constraints is zero. We propose planning with reachable distance (PRD) to overcome this challenge by first precomputing the subspace satisfying the closure constraints, then directly sampling in it. To do so, we represent the chain as a hierarchy of sub-chains. Then we calculate the "closure" sub-space as appropriate reachable distance ranges of sub-chains satisfying the closure constraints. This provides two distinct advantages over traditional approaches: (1) configurations are quickly sampled and converted to joint angles using basic trigonometry functions instead of more expensive inverse kinematics solvers, and (2) configurations are guaranteed to be closed. In this paper, we describe this hierarchical chain representation and give a sampling algorithm with complexity linear in the number of links. We provide the necessary motion planning primitives for most sampling-based motion planners. Our experimental results show our method is fast, making sampling closed configurations comparable to sampling open chain configurations that ignore closure constraints. Our method is general, easy to implement, and also extends to other distance-related constraints besides the ones demonstrated here
9601629
Tools for Simulating and Analyzing RNA Folding Kinetics
It has recently been found that some RNA functions are determined by the actual folding kinetics and not just the RNA's nucleotide sequence or its native structure. We present new computational tools for simulating and analyzing RNA folding kinetic metrics such as population kinetics, folding rates, and the folding of particular subsequences. Our method first builds an approximate representation (called a map) of the RNA's folding energy landscape, and then uses specialized analysis techniques to extract folding kinetics from the map. We provide a new sampling strategy called Probabilistic Boltzmann Sampling (PBS) that enables us to approximate the folding landscape with much smaller maps, typically by several orders of magnitude. We also describe a new analysis technique, Map-based Monte Carlo (MMC) simulation, to stochastically extract folding pathways from the map. We demonstrate that our technique can be applied to large RNA (e.g., 200+ nucleotides), where representing the full landscape is infeasible, and that our tools provide results comparable to other simulation methods that work on complete energy landscapes. We present results showing that our approach computes the same relative functional rates as seen in experiments for the relative plasmid replication rates of ColE1 RNAII and its mutants, and for the relative gene expression rates of MS2 phage RNA and its mutants.
29395992
Coordinated En-Route Web Caching
Web caching is an important technique for reducing Internet access latency, network traffic, and server load. This paper investigates cache management strategies for the en-route web caching environment, where caches are associated with routing nodes in the network. We propose a novel caching scheme that integrates both object placement and replacement policies and which makes caching decisions on all candidate sites in a coordinated fashion. In our scheme, cache status information along the routing path of a request is used in dynamically determining where to cache the requested object and what to replace if there is not enough space. The object placement problem is formulated as an optimization problem and the optimal locations to cache the object are obtained using a low-cost dynamic programming algorithm. Extensive simulation experiments have been performed to evaluate the proposed scheme in terms of a wide range of performance metrics. The results show that the proposed scheme significantly outperforms existing algorithms which consider either object placement or replacement at individual caches only.
3257079
Face sketch recognition
Automatic retrieval of face images from police mug-shot databases is critically important for law enforcement agencies. It can effectively help investigators to locate or narrow down potential suspects. However, in many cases, a photo image of a suspect is not available and the best substitute is often a sketch drawing based on the recollection of an eyewitness. We present a novel photo retrieval system using face sketches. By transforming a photo image into a sketch, we reduce the difference between photo and sketch significantly, thus allowing effective matching between the two. Experiments over a data set containing 188 people clearly demonstrate the efficacy of the algorithm.
1083190
Streaming media caching algorithms for transcoding proxies
Streaming media is expected to become one of the most popular types of Web content in the future. Due to increasing variety of client devices and the range of access speeds to the Internet, multimedia contents may be required to be transcoded to match the client's capability. With transcoding, both the network and the proxy CPU are potential bottlenecks for streaming media delivery. This paper discusses and compares various caching algorithms designed for transcoding proxies. In particular we propose a new adaptive algorithm that dynamically selects an appropriate metric for adjusting the management policy. Experimental results show that the proposed algorithm significantly outperforms those that cache only untranscoded or only transcoded objects. Moreover motivated by the characteristics of many video compression algorithms, we investigate partitioning a video object into sections based on frame type and handling them individually for proxy caching. It is found that partitioning improves performance when CPU power rather than network bandwidth is the limiting resource, particularly when the reference pattern is not highly skewed.
20193865
Adaptive hash routing for a cluster of client-side web proxies
Hash routing reduces cache misses for a cluster of web proxies by eliminating the duplication of cache contents. In this paper, we investigate the optimization of hash routing performance by dynamically adapting object and DNS allocations to the traffic pattern. An analytical model is developed for hash routing that takes into consideration the original request distribution, the object allocation strategy, the speeds of the proxies and the cache hit ratios. Based on this model, the optimal hash routing problem is studied. The analytical results are applied to the design of two adaptive hash routing schemes: ADA-OBJ optimizes object allocation under static client configuration, and ADA-OBJ/DNS optimizes both object and DNS allocations under dynamic client configuration. Trace-driven simulation experiments have been conducted to evaluate the performance of the proposed schemes. The results show that they significantly outperform the intuitive static hash routing scheme based only on the speeds of the proxies.
12151519
QoS-aware replica placement for content distribution
The rapid growth of new information services and business-oriented applications entails the consideration of quality of service (QoS) in content distribution. This paper investigates the QoS-aware replica placement problems for responsiveness QoS requirements. We consider two classes of service models: replica-aware services and replica-blind services. In replica-aware services, the servers are aware of the locations of replicas and can therefore optimize request routing to improve responsiveness. We show that the QoS-aware placement problem for replica-aware services is NP-complete. Several heuristic algorithms for fast computation of good solutions are proposed and experimentally evaluated. In replica-blind services, the servers are not aware of the locations of replicas or even their existence. As a result, each replica only serves the requests flowing through it under some given routing strategy. We show that there exist polynomial optimal solutions to the QoS-aware placement problem for replica-blind services. Efficient algorithms are proposed to compute the optimal locations of replicas under different cost models.