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Recent documents in Worksen-usSat, 25 Nov 2017 02:13:54 PST3600Melanoblast Development Coincides With The Late Emerging Cells From The Dorsal Neural Tube In Turtle Trachemys Scripta
http://works.swarthmore.edu/fac-biology/542
http://works.swarthmore.edu/fac-biology/542Tue, 21 Nov 2017 10:34:09 PST
Ectothermal reptiles have internal pigmentation, which is not seen in endothermal birds and mammals. Here we show that the development of the dorsal neural tube-derived melanoblasts in turtle Trachemys scripta is regulated by similar mechanisms as in other amniotes, but significantly later in development, during the second phase of turtle trunk neural crest emigration. The development of melanoblasts coincided with a morphological change in the dorsal neural tube between stages mature G15 and G16. The melanoblasts delaminated and gathered in the carapacial staging area above the neural tube at G16, and differentiated into pigment-forming melanocytes during in vitro culture. The Mitf-positive melanoblasts were not restricted to the dorsolateral pathway as in birds and mammals but were also present medially through the somites similarly to ectothermal anamniotes. This matched a lack of environmental barrier dorsal and lateral to neural tube and the somites that is normally formed by PNA-binding proteins that block entry to medial pathways. PNA-binding proteins may also participate in the patterning of the carapacial pigmentation as both the migratory neural crest cells and pigment localized only to PNA-free areas.
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R. Rice et al.Holobionts As Units Of Selection And A Model Of Their Population Dynamics And Evolution
http://works.swarthmore.edu/fac-biology/541
http://works.swarthmore.edu/fac-biology/541Tue, 21 Nov 2017 10:34:06 PST
Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host.
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J. Roughgarden et al.Land Use Type, Forest Cover, And Forest Edges Modulate Avian Cross-Habitat Spillover
http://works.swarthmore.edu/fac-biology/540
http://works.swarthmore.edu/fac-biology/540Fri, 17 Nov 2017 09:31:23 PST
1. Natural habitats adjacent to agricultural areas are often considered sources of species that provide beneficial regulating ecosystem services through cross-habitat spillover. Both inter-habitat matrix and landscape configuration can influence spillover by controlling organismal ability to disperse through landscapes, and affecting the provision of additional or supplementary resources that impact organism survival. 2. To understand how landscape structure in terms of matrix land use type, forest cover, and edge density might facilitate avian cross-habitat spillover, we sampled avian communities in forest patches and adjacent land use types (coffee plantations or cattle pastures) using a well-replicated study design across 92 sampling sites across a landscape-context forest cover gradient (6-60%). 3. Land use type was a key factor influencing avian cross-habitat spillover, facilitating species movement into coffee plantations and acting as a barrier to spillover into cattle pastures. We found that 24% of the forest-dependent species pool was capable of spillover into coffee plantations, while spillover was nearly non-existent in cattle pastures. 4. Forest cover was also the main driver of spillover into coffee plantations. There was a positive relationship between forest cover and spillover, potentially due to processes related with i) a higher density of organisms in-patches, ii) decreased isolation among patches facilitating species movement, and iii) higher landscape supplementation processes. 5. Finally, we found edge density had an additive effect with forest cover on spillover. Spillover was higher in high-forested landscapes with many forest-matrix edges, possibly due to increased structural connectivity for species able to move through edges, and to improved access for forest-dwelling species to different resource types (complementation processes). 6. Synthesis and applications. We demonstrate that land use type is a key factor facilitating species spillover into agricultural matrices and that the influence of land use type on spillover is further modulated by a combination of native habitat amount and edge density. These results should be considered in efforts to design or manage sustainable agricultural landscapes in order to enhance both bird persistence and the provision of bird-mediated ecosystem services.
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A. L. Boesing et al.Solomon Northup’s Singing Book
http://works.swarthmore.edu/fac-english-lit/334
http://works.swarthmore.edu/fac-english-lit/334Fri, 10 Nov 2017 13:27:18 PST
This essay examines the musical score included at the end of Solomon Northup’s Twelve Years a Slave (1853), a setting of a song called “Roaring River” that Northup earlier recounted enslaved people singing as they patted juba. I argue that “Roaring River” stages questions that the narrative itself cannot ask about how to represent the experience of slavery once one is outside of it. In particular, it asks how to love what’s made in the shadow of slavery—the intimacies forged, and especially the music borne of them.
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Lara Langer CohenNon-Adaptive Data Structure Bounds For Dynamic Predecessor Search
http://works.swarthmore.edu/fac-comp-sci/99
http://works.swarthmore.edu/fac-comp-sci/99Thu, 09 Nov 2017 10:01:59 PST
In this work, we continue the examination of the role non-adaptivity} plays in maintaining dynamic data structures, initiated by Brody and Larsen [BL15].. We consider nonadaptive data structures for predecessor search in the w-bit cell probe model. Predecessor search is one of the most well-studied data structure problems. For this problem, using non-adaptivity comes at a steep price. We provide exponential cell probe complexity separations between (i) adaptive and non-adaptive data structures and (ii) non-adaptive and memoryless data structures for predecessor search.
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Joseph W. Boninger , '16 et al.Dependent Random Graphs And Multi-Party Pointer Jumping
http://works.swarthmore.edu/fac-comp-sci/98
http://works.swarthmore.edu/fac-comp-sci/98Thu, 09 Nov 2017 10:01:55 PST
We initiate a study of a relaxed version of the standard Erdos-Renyi random graph model, where each edge may depend on a few other edges. We call such graphs "dependent random graphs". Our main result in this direction is a thorough understanding of the clique number of dependent random graphs. We also obtain bounds for the chromatic number. Surprisingly, many of the standard properties of random graphs also hold in this relaxed setting. We show that with high probability, a dependent random graph will contain a clique of size ((1-o(1))log(n))/log(1/p), and the chromatic number will be at most (nlog(1/(1-p)))/log(n). We expect these results to be of independent interest. As an application and second main result, we give a new communication protocol for the k-player Multi-Party Pointer Jumping problem (MPJk) in the number-on-the-forehead (NOF) model. Multi-Party Pointer Jumping is one of the canonical NOF communication problems, yet even for three players, its communication complexity is not well understood. Our protocol for MPJ3 costs O((n * log(log(n)))/log(n)) communication, improving on a bound from [BrodyChakrabarti08]. We extend our protocol to the non-Boolean pointer jumping problem, achieving an upper bound which is o(n) for any k >= 4 players. This is the first o(n) protocol and improves on a bound of Damm, Jukna, and Sgall, which has stood for almost twenty years.
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Joshua Brody et al.The Information Complexity Of Hamming Distance
http://works.swarthmore.edu/fac-comp-sci/97
http://works.swarthmore.edu/fac-comp-sci/97Thu, 09 Nov 2017 10:01:51 PST
The Hamming distance function Ham_{n,d} returns 1 on all pairs of inputs x and y that differ in at most d coordinates and returns 0 otherwise. We initiate the study of the information complexity of the Hamming distance function. We give a new optimal lower bound for the information complexity of the Ham_{n,d} function in the small-error regime where the protocol is required to err with probability at most epsilon < d/n. We also give a new conditional lower bound for the information complexity of Ham_{n,d} that is optimal in all regimes. These results imply the first new lower bounds on the communication complexity of the Hamming distance function for the shared randomness two-way communication model since Pang and El-Gamal (1986). These results also imply new lower bounds in the areas of property testing and parity decision tree complexity.
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E. Blais et al.Cryptogenography
http://works.swarthmore.edu/fac-comp-sci/96
http://works.swarthmore.edu/fac-comp-sci/96Thu, 09 Nov 2017 10:01:48 PST
We consider the following cryptographic secret leaking problem. A group of players communicate with the goal of learning (and perhaps revealing) a secret held initially by one of them. Their conversation is monitored by a computationally unlimited eavesdropper, who wants to learn the identity of the secret-holder. Despite the unavailability of key, some protection can be provided to the identity of the secret-holder. We call the study of such communication problems, either from the group's or the eavesdropper's point of view, cryptogenography. We introduce a basic cryptogenography problem and show that two players can force the eavesdropper to missguess the origin of a secret bit with probability 1/3; we complement this with a hardness result showing that they cannot do better than than 3/8. We prove that larger numbers of players can do better than 0.5644, but no group of any size can achieve 0.75.
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Joshua Brody et al.Beyond Set Disjointness: The Communication Complexity Of Finding The Intersection
http://works.swarthmore.edu/fac-comp-sci/95
http://works.swarthmore.edu/fac-comp-sci/95Thu, 09 Nov 2017 10:01:44 PST
We consider the following fundamental communication problem - there is data that is distributed among servers, and the servers want to compute the intersection of their data sets, e.g., the common records in a relational database. They want to do this with as little communication and as few messages (rounds) as possible. They are willing to use randomization, and fail with a tiny probability. Given a protocol for computing the intersection, it can also be used to compute the exact Jaccard similarity, the rarity, the number of distinct elements, and joins between databases. Computing the intersection is at least as hard as the set disjointness problem, which asks whether the intersection is empty. Formally, in the two-server setting, the players hold subsets S, T ⊆ [n]. In many realistic scenarios, the sizes of S and T are significantly smaller than n, so we impose the constraint that |S|, |T| ≤ k. We study the minimum number of bits the parties need to communicate in order to compute the intersection set S ∩ T, given a certain number r of messages that are allowed to be exchanged. While O(k log (n/k)) bits is achieved trivially and deterministically with a single message, we ask what is possible with more than one message and with randomization. We give a smooth communication/round tradeoff which shows that with O(log* k) rounds, O(k) bits of communication is possible, which improves upon the trivial protocol by an order of magnitude. This is in contrast to other basic problems such as computing the union or symmetric difference, for which Ω(k log(n/k)) bits of communication is required for any number of rounds. For two players, known lower bounds for the easier problem of set disjointness imply our algorithms are optimal up to constant factors in communication and number of rounds. We extend our protocols to $m$-player protocols, obtaining an optimal O(mk) bits of communication with a similarly small number of rounds.
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Joshua Brody et al.TerraStream: From Elevation Data To Watershed Hierarchies
http://works.swarthmore.edu/fac-comp-sci/94
http://works.swarthmore.edu/fac-comp-sci/94Thu, 09 Nov 2017 10:01:40 PST
We consider the problem of extracting a river network and a watershed hierarchy from a terrain given as a set of irregularly spaced points. We describe TERRASTREAM, a "pipelined" solution that consists of four main stages: construction of a digital elevation model (DEM), hydrological conditioning, extraction of river networks, and construction of a watershed hierarchy. Our approach has several advantages over existing methods. First, we design and implement the pipeline so that each stage is scalable to massive data sets; a single non-scalable stage would create a bottleneck and limit overall scalability. Second, we develop the algorithms in a general framework so that they work for both TIN and grid DEMs. Furthermore, TERRASTREAM is flexible and allows users to choose from various models and parameters, yet our pipeline is designed to reduce (or eliminate) the need for manual intervention between stages. We have implemented TERRASTREAM and we present experimental results on real elevation point sets, which show that our approach handles massive multi-gigabyte terrain data sets. For example, we can process a data set containing over 300 million points---over 20GB of raw data---in under 26 hours, where most of the time (76%) is spent in the initial CPU-intensive DEM construction stage.
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Andrew Danner et al.Bridge Detection In Grid Terrains And Improved Drainage Enforcement
http://works.swarthmore.edu/fac-comp-sci/93
http://works.swarthmore.edu/fac-comp-sci/93Thu, 09 Nov 2017 10:01:37 PST
Bare Earth gridded digital elevation models (DEMs) are often used to extract hydrologic features such as rivers and watersheds. DEMs must be conditioned by removing spurious sinks (or depressions) which impede water flow in the model, but are not true hydrologic barriers. This conditioning process is designed to enforce proper drainage and connect real hydrologic networks (rivers) that would otherwise be disconnected in the unconditioned DEM. Primary means of conditioning DEMs include filling sinks and cutting barriers. The availability of high resolution DEMs derived from lidar introduces new forms of false hydrologic barriers, primarily bridges. While attempts are made to automatically remove trees, buildings and bridges from bare Earth terrains, in practice many bridges remain in the final "cleaned" DEM. We present a supervised machine learning approach for detecting bridges and other hydrologic barriers in DEMs. Furthermore, we locally apply a simple cutting algorithm to condition DEMs in areas tagged as barriers by the machine learning step. After cutting, we use a filling technique to remove any remaining spurious depressions. Experimental results indicate that our approach accurately identifies a variety of bridge and bridge-like features. Our final conditioned DEM both modifies fewer grid cells and modifies cells to a lesser extent than other traditional conditioning approaches. The result is more realistic hydrologic models on high resolution terrains.
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Ryan A. Carlson , '11 et al.Hybrid MPI/GPU Interpolation For Grid DEM Construction
http://works.swarthmore.edu/fac-comp-sci/92
http://works.swarthmore.edu/fac-comp-sci/92Thu, 09 Nov 2017 10:01:34 PST
The proliferation of lidar technology in remote sensing has resulted in extremely large, high resolution point clouds covering a wide variety of terrain. Constructing a grid digital elevation model (DEM) from these large data sets requires extensive computational resources and ample disk space. We propose a framework for leveraging modern computing resources including multi-core distributed systems and general purpose GPU computing to reduce computational bottlenecks and accelerate DEM construction. We employ an I/O-efficient strategy using quad trees to automatically partition the lidar point clouds into a set of independent work bundles. We then distribute these work bundles to multiple GPU-equipped hosts which independently interpolate a portion of the DEM and return partial results. Finally, we gather the partial results and assemble the final DEM I/O-efficiently. Our approach balances I/O, computation, and network communication to reduce bottlenecks. Experimental results show that our approach scales linearly with the number of compute hosts, and achieves speed-ups of 25 × or greater using GPU computing. These results make it practical to use more complex interpolation methods such as regularized splines with tension, which provide geomorphological advantages over simpler interpolation methods such as linear interpolation, nearest neighbor interpolation, or natural neighbor interpolation.
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Andrew Danner et al.A Hybrid Connectionist And BDI Architecture For Modeling Embedded Rational Agents
http://works.swarthmore.edu/fac-comp-sci/91
http://works.swarthmore.edu/fac-comp-sci/91Thu, 02 Nov 2017 12:44:26 PDT
In this paper, our ongoing work on a hybrid, connectionist and belief-desire-intention (BDI) based, rational agent architecture is described. The architecture makes specific commitments in order to achieve a harmony among the tasks of reasoning and acting. The architecture uses a bottom-up learning strategy to acquire rules for reactive behavior.
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D. Kumar et al.Bridging The Gap Between Robot Simulations And Reality With Improved Models Of Sensor Noise
http://works.swarthmore.edu/fac-comp-sci/90
http://works.swarthmore.edu/fac-comp-sci/90Thu, 02 Nov 2017 12:44:21 PDT
Traditionally sensors have been assumed to behave independently of one another. In this paper evidence is presented that shows that for certain types of sensors this assumption of independence is incorrect. In fact, in some cases groups of sensors respond in a highly correlated fashion. A new model of sensor noise is introduced which combines independent noise with dependent noise to produce sensor responses with varying degrees of correlation. This new model is then compared to the standard model in a set of evolutionary computation experiments. The results reveal that by adopting the new model transfer of simulation results to reality is improved.
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Lisa A. MeedenNature Versus Nurture In Evolutionary Computation: Balancing The Roles Of The Training Environment And The Fitness Function In Producing Behavior
http://works.swarthmore.edu/fac-comp-sci/89
http://works.swarthmore.edu/fac-comp-sci/89Thu, 02 Nov 2017 12:44:17 PDTJordan J. Wales , '01 et al.Heterogeneity In The Coevolved Behaviors Of Mobile Robots: The Emergence Of Specialists
http://works.swarthmore.edu/fac-comp-sci/88
http://works.swarthmore.edu/fac-comp-sci/88Thu, 02 Nov 2017 12:44:13 PDT
Many mobile robot tasks can be most efficiently solved when a group of robots is utilized. The type of organization, and the level of coordination and communication within a team of robots affects the type of tasks that can be solved. This paper examines the tradeoff of homogeneity versus heterogeneity in the control systems by allowing a team of robots to coevolve their high-level controllers given different levels of difficulty of the task. Our hypothesis is that simply increasing the difficulty of a task is not enough to induce a team of robots to create specialists. The key factor is not difficulty per se, but the number of skill sets necessary to successfully solve the task. As the number of skills needed increases, the more beneficial and necessary heterogeneity becomes. We demonstrate this in the task domain of herding, where one or more robots must herd another robot into a confined space.
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M. A. Potter et al.An Emergent Framework For Self-Motivation In Developmental Robotics
http://works.swarthmore.edu/fac-comp-sci/87
http://works.swarthmore.edu/fac-comp-sci/87Thu, 02 Nov 2017 12:44:10 PDT
This paper explores a philosophy and connectionist algorithm for creating a long-term, self-motivated developmental robot control system. Self-motivation is viewed as an emergent property arising from two competing pressures: the need to accurately predict the environment while simultaneously wanting to seek out novelty in the environment. These competing internal pressures are designed to drive the system in a manner reminiscent of a co-evolutionary arms race.
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J. Marshall et al.Category-Based Intrinsic Motivation
http://works.swarthmore.edu/fac-comp-sci/86
http://works.swarthmore.edu/fac-comp-sci/86Thu, 02 Nov 2017 12:44:05 PDT
A goal of epigenetic robotics is to design a control architecture that implements an ongoing, autonomous developmental process which is unsupervised, unscheduled, and task-independent. The developmental process we are currently exploring contains three essential mechanisms: categorization, prediction, and intrinsic motivation. In this paper we describe a hybrid approach that uses Growing Neural Gas for categorization, neural networks for prediction, and Intelligent Adaptive Curiosity for intrinsic motivation. We apply this system to a physical robot operating in a dynamic visual environment and analyze the types of categories it forms.
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Rachel M. Lee , '10 et al.Curiosity: Emergent Behavior Through Interacting Multi-Level Predictions
http://works.swarthmore.edu/fac-comp-sci/85
http://works.swarthmore.edu/fac-comp-sci/85Thu, 02 Nov 2017 12:44:02 PDT
Over the past 15 years our research group has been exploring models of developmental robotics and curiosity. Our research is based on the premise that intelligent behavior arises through emergent interactions between opposing forces in an open-ended, task-independent environment. In an initial experiment we constructed a recurrent neural network model where self-motivation was "an emergent property generated by the competing pressures that arise in attempting to balance predictability and novelty". The system first focused on its error, then learned to successfully predict its error, and finally became habituated to what caused the error. This process of focusing, learning, and habituating can be seen as a rudimentary type of curiosity.
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Lisa A. Meeden et al.A Developmental Robotics Manifesto
http://works.swarthmore.edu/fac-comp-sci/84
http://works.swarthmore.edu/fac-comp-sci/84Thu, 02 Nov 2017 12:43:58 PDTD. Blank et al.