@STRING{aaai-94 = {Proc.\ 12th Natl. Conf.\ on Artificial Intelligence (AAAI-94)} } @STRING{icra-00 = {Proc.\ 2000 {IEEE} Intl.\ Conf.\ on Robotics and Automation} } @STRING{icra-02 = {Proc.\ 2002 {IEEE} Intl.\ Conf.\ on Robotics and Automation} } @STRING{icra-04 = {Proc.\ 2004 {IEEE} Intl.\ Conf.\ on Robotics and Automation} } @STRING{icra-05 = {Proc.\ 2005 {IEEE} Intl.\ Conf.\ on Robotics and Automation} } @STRING{ijrr = {Intl.\ J.\ of Robotics Research} } @STRING{iros-01 = {Proc.\ 2001 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems} } @STRING{iros-06 = {Proc.\ 2006 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems} } @STRING{iros-07 = {Proc.\ 2007 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems} } @STRING{mit-addr= {Cambridge, MA} } @STRING{spr = {Springer Verlag} } @STRING{tro = {{IEEE} Trans.\ on Robotics} } @Article{ moll2008labelhash:-a-toolbox-for-matching-structural, author = {Mark Moll and Drew H. Bryant and Lydia E. Kavraki}, journal = {Nucleic Acids Research}, note = {Submitted.}, title = {{LabelHash}: a toolbox for matching structural protein motifs}, year = {2008} } @InProceedings{ moll2008matching-of-structural-motifs, abstract = {There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However, experimental protein function determination is expensive and very time-consuming. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Our focus is on methods that determine binding site similarity. Although several such methods exist, it still remains a challenging problem to quickly find all functionally-related matches for structural motifs in large data sets with high specificity. In this context, a structural motif is a set of 3D points annotated with physicochemical information that characterize a molecular function. We propose a new method called LabelHash that creates hash tables of $n$-tuples of residues for a set of targets. Using these hash tables, we can quickly look up partial matches to a motif and expand those matches to complete matches. We show that by applying only very mild geometric constraints we can find statistically significant matches with extremely high specificity in very large data sets and for very general structural motifs. We demonstrate that our method requires a reasonable amount of storage when employing a simple geometric filter and further improves on the specificity of our previous work while maintaining very high sensitivity. Our algorithm is evaluated on 20 homolog classes and a non-redundant version of the Protein Data Bank as our background data set. We use cluster analysis to analyze why certain classes of homologs are more difficult to classify than others. The LabelHash algorithm is implemented on a web server at http://kavrakilab.org/labelhash/.}, author = {Mark Moll and Lydia E. Kavraki}, booktitle = {The Seventh Annual International Conference on Computational Systems Bioinformatics (CSB2008)}, note = {To appear.}, title = {Matching of Structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction}, year = {2008} } @InProceedings{ shen2007multifunctional-and-reconfigurable-superbot-modules, author = {Wei-Min Shen and Behnam Salemi and Mark Moll and Chi Ho Chiu and Jacob Everist and Feili Hou and Nadeesha Ranasinghe and Michael Rubenstein}, booktitle = iros-07, note = {(video)} , title = {Multifunctional Behaviors of Reconfigurable SuperBot Modules}, year = {2007} } @InProceedings{ shen2006modular-multifunctional-and-reconfigurable-superbot, abstract = {The traditional approach of building special robots for each of a large variety of tasks in space may become increasingly impractical because it requires many specialized robots that are expensive and difficult to deploy. This paper describes a new SuperBot robotic system that uses modularity and self-reconfiguration as an effective means to achieve low cost, multifunction, and adaptive capabilities. SuperBot consists of Lego-like but autonomous robotic modules that can reconfigure into different systems for different tasks. Examples of configurable systems include rolling tracks or wheels (for efficient travel), spiders or centipedes (for climbing), snakes (for burrowing in ground), long arms (for inspection and repair in space), and devices that can fly in micro-gravity environment. Each module is a complete robotic system and has a power supply, micro-controllers, sensors, communication, three degrees of freedom, and six connecting faces (front, back, left, right, up and down) to dynamically connect to other modules. This design allows flexible bending, docking, and continuous rotation. A single module can move forward, back, left, right, flip-over, and rotate as a wheel. Modules can communication with each other for totally distributed control and can support arbitrary module reshuffling during their operation. They have both internal and external sensors for monitoring self status and environmental parameters. They can form arbitrary configurations (graphs) and can control these configurations for different functionality such as locomotion, manipulation, and self-repair. Some application scenarios have been developed to utilize the new capability, and they include Multi-Use Lunar Explorer (MULE), a Habitat Maintenance and Operations System (HOMS), a cost-effective robotic method to detect H2O or seismic features, and a set of flying maneuvers and mini-RMS for inspection and maintenance on and near CEV or Space Station. }, address = {San Jose, CA}, author = {Wei-Min Shen and Behnam Salemi and Mark Moll}, booktitle = {Space 2006}, month = sep, title = {Modular, Multifunctional and Reconfigurable {SuperBot} for Space Applications}, year = {2006} } @Article{ fofanov2008correcting-systematic-bias-caused, abstract = {Motivation: Knowledge of the exact biological function of every protein could have a great impact on drug design and could greatly improve the general understanding of the processes governing a cell. However, experimental methods of protein function prediction can be expensive and time consuming. High-throughput computational approaches, such as Partial Structural Comparison methods, seek to guide and accelerate the process of functional annotation by searching for instances of statistically significant geometric and chemical similarity (matches) between known active sites and substructures within functionally uncharacterized proteins. One common difficulty of all geometric comparison techniques is the computational cost of obtaining a match. In an effort to maintain practical efficiency, some algorithms employ efficient geometric threshold based searches, which greatly improve performance but can introduce a systematic bias into statistical models of substructural similarity. Because statistical models are essential for filtering out true matches from spurious matches that occur by chance, this bias can cause a significant reduction in accuracy of the method. Results: We propose an approach that removes the dependence of statistical scores from the parameters used during geometric comparison, thereby correcting the systematic bias caused by geometric thresholds. Using the Match Augmentation algorithm as an example, we demonstrate the effect our approach has on improving accuracy of functionally related protein identification. We also illustrate the effect of our model on prediction accuracy and evaluate several standard techniques for reducing PDB bias, such as sequentially Non-Redundant PDB and CATH fold classification schemes. }, author = {Viacheslav Y. Fofanov and Brian Y. Chen and Drew Bryant and Mark Moll and Olivier Lichtarge and Lydia Kavraki and Marek Kimmel}, journal = {BMC Biology Direct}, note = {Submitted.}, title = {Correcting Systematic Bias Caused by Algorithmic Thresholds in Statistical Models of Protein Sub-structural Similarity}, year = {2008} } @Article{ yim2007modular-self-reconfigurable-robot-systems, abstract = {The field of modular self-reconfigurable robotic systems addresses the design, fabrication, motion planning, and control of autonomous kinematic machines with variable morphology. Beyond conventional actuation, sensing, and control typically found in fixed-morphology robots, self-reconfigurable robots are also able to deliberately change their own shape by rearranging the connectivity of their parts in order to adapt to new circumstances, perform new tasks, or recover from damage. Over the last two decades, this field has advanced from proof-of-concept systems to elaborate physical implementations and simulations. The goal of this article is to outline some of this progress and identify key challenges and opportunities that lay ahead.}, author = {Mark Yim and Wei-Min Shen and Benham Salemi and Daniela Rus and Mark Moll and Hod Lipson and Eric Klavins}, doi = {10.1109/MRA.2007.339623}, journal = {{IEEE} Robotics \& Automation Magazine}, month = mar, number = {1}, pages = {43--52}, title = {Modular Self-reconfigurable Robot Systems: Challenges and Opportunities for the Future}, volume = {14}, year = {2007} } @TechReport{ ter-doest1996language-engineering-in-dialogue-systems, abstract = {The analysis of natural language in the context of keyboard-driven dialogue systems is the central issue addressed in this paper. A module that corrects typing errors, performs domain-specific morphological analysis is developed. A parser for typed unification grammars has been designed and implemented in C++; for description of the lexicon and the grammar a suitable specification language has been developed. It is argued that typed unification grammars and especially the newly developed specification language are convenient formalisms for describing natural language use in dialogue systems. Finally we present a dialogue manager that is based on a finite state automaton; transitions in the automaton depend upon availability of information in utterances of the user. In order to keep track of the history of the dialogue, a context stack is constructed during the dialogue. The manager is implemented in Prolog. }, author = {Ter Doest, Hugo and Mark Moll and Ren{\'e} Bos and Van de Burgt, Stan and Anton Nijholt}, institution = {Department of Computer Science, University of Twente}, month = jan, number = {96-2}, title = {Language Engineering in Dialogue Systems}, type = {Memoranda Informatica}, year = {1996} } @Article{ moll2008workshop-on-self-reconfigurable-modular-robots, author = {Mark Moll and Daniela Rus}, doi = {10.1177/0278364908089348}, journal = ijrr, month = {March/April}, number = {3/4}, pages = {277-278}, title = {Special Issue on Self-Reconfiguring Modular Robots (Guest Editorial)}, volume = {27}, year = {2008} } @InProceedings{ salemi2006superbot, abstract = {Self-reconfigurable robots are modular robots that can autonomously change their shape and size to meet specific operational demands. Recently, there has been a great interest in using self-reconfigurable robots in applications such as reconnaissance, rescue missions, and space applications. Designing and controlling self-reconfigurable robots is a difficult task. Hence, the research has primarily been focused on developing systems that can function in a controlled environment. This paper presents a novel self-reconfigurable robotic system called SuperBot, which addresses the challenges of building and controlling deployable self-reconfigurable robots. Six prototype modules have been built and preliminary experimental results demonstrate that SuperBot is a flexible and powerful system that can be used in challenging real-world applications.}, address = {Beijing, China}, author = {Behnam Salemi and Mark Moll and Wei-Min Shen}, booktitle = iros-06, doi = {10.1109/IROS.2006.281719}, keywords = {prl}, month = oct, pages = {3636--3641}, title = {{SUPERBOT}: A Deployable, Multi-Functional, and Modular Self-Reconfigurable Robotic System}, year = {2006} } @InProceedings{ moll2006distributed-control-of-the-center-of-mass, abstract = {We present a distributed controller for the center of mass of a modular robot. This is useful for locomotion of a modular robot over uneven and unknown terrain. By controlling the center of mass, a robot can prevent itself from falling over. We present a distributed and decentralized algorithm that computes the mass properties of the robot. Additionally, each module also computes the mass properties of the modules that are directly or indirectly connected to each of its connectors. With this information, each module can independently steer the center of mass towards a desired position by adjusting its joint positions. We present simulation results that show the feasibility of the approach.}, address = {Beijing, China}, author = {Mark Moll and Peter Will and Maks Krivokon and Wei-Min Shen}, booktitle = iros-06, doi = {10.1109/IROS.2006.282261}, month = oct, pages = {4710--4715}, title = {Distributed Control of the Center of Mass of a Modular Robot}, year = {2006} } @InCollection{ moll2007roadmap-methods-for-protein-folding, abstract = {Protein folding refers to the process whereby a protein assumes its intricate three-dimensional shape. Different aspects of this problem have attracted much attention in the last decade. Both experimental and computational methods have been used to study protein folding and there has been considerable progress This chapter reviews a class of methods for studying protein folding called roadmap methods. These methods are relatively new and are still under active development. Roadmap methods are computational methods that have been developed to understand the process or the mechanism by which a protein folds or unfolds. It is typically assumed that the folded state is already known. Note that this is not a comprehensive survey of all existing computational protein folding methods. In particular, it does not cover Molecular Dynamics (MD) methods, Monte Carlo methods (MC), the use of coarse grain models in simulations and many others. }, author = {Mark Moll and David Schwarz and Lydia E. Kavraki}, booktitle = {Protein Structure Prediction: Methods and Protocols}, edition = {Second}, editor = {Mohammed Zaki and Chris Bystroff}, month = oct, publisher = {Humana Press}, series = {Methods In Molecular Biology}, title = {Roadmap Methods for Protein Folding}, url = {http://www.springer.com/humana+press/biochemistry/book/978-1-58829-752-5?detailsPage=toc} , year = {2007}, bdsk-url-1 = {http://www.humanapress.com/index.php?option=com_bookdetails&task=bookdetails&product_code=1-58829-752-7&category=books} } @Article{ das2006low-dimensional-free-energy-landscapes, abstract = {The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the ``simple'' case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding.}, author = {Payel Das and Mark Moll and Hernan Stamati and Lydia E. Kavraki and Cecilia Clementi}, doi = {10.1073/pnas.0603553103}, journal = {Proc.\ Natl.\ Acad.\ of Science USA}, keywords = {reaction coordinate, transition state, manifold, embedding, ISOMAP, ScIMAP}, month = jun, number = {26}, pages = {9885--9890}, title = {Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction}, volume = {103}, year = {2006}, bdsk-file-2 = {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} } @Article{ moll2006path-planning-for-deformable-linear, abstract = {We present a new approach to path planning for deformable linear (one-dimensional) objects such as flexible wires. We introduce a method for efficiently computing stable configurations of a wire subject to manipulation constraints. These configurations correspond to minimal-energy curves. By restricting the planner to minimal-energy curves, the execution of a path becomes easier. Our curve representation is adaptive in the sense that the number of parameters automatically varies with the complexity of the underlying curve. We introduce a planner that computes paths from one minimal-energy curve to another such that all intermediate curves are also minimal-energy curves. This planner can be used as a powerful local planner in a sampling-based roadmap method. This makes it possible to compute a roadmap of the entire ``shape space,'' which is not possible with previous approaches. Using a simplified model for obstacles, we can find minimal-energy curves of fixed length that pass through specified tangents at given control points. Our work has applications in cable routing, and motion planning for surgical suturing and snake-like robots.}, author = {Mark Moll and Lydia E. Kavraki}, doi = {10.1109/TRO.2006.878933}, journal = tro, month = aug, number = {4}, pages = {625--636}, title = {Path Planning for Deformable Linear Objects}, volume = {22}, year = {2006} } @InProceedings{ moll-erdmann2000:uncer-reduc-using-dynam, abstract = {For assembly tasks parts often have to be oriented before they can be put in an assembly. The results presented in this paper are a component of the automated design of parts orienting devices. The focus is on orienting parts with minimal sensing and manipulation. We present a new approach to parts orienting through the manipulation of pose distributions. Through dynamic simulation we can determine the pose distribution for an object being dropped from an arbitrary height on an arbitrary surface. By varying the drop height and the shape of the support surface we can find the initial conditions that will result in a pose distribution with minimal entropy. We are trying to uniquely orient a part with high probability just by varying the initial conditions. We will derive a condition on the pose and velocity of an object in contact with a sloped surface that will allow us to quickly determine the final resting configuration of the object. This condition can then be used to quickly compute the pose distribution. We also show simulation and experimental results that confirm that our dynamic simulator can be used to find the true pose distribution of an object.}, address = {San Francisco, California}, author = {Mark Moll and Michael A. Erdmann}, booktitle = icra-00, doi = {10.1109/ROBOT.2000.845304}, keywords = {pose distributions, parts orienting, dynamic simulation}, pages = {3673--3680}, title = {Uncertainty Reduction Using Dynamics}, year = 2000 } @InCollection{ moll-erdmann2001:manip-pose-distr, abstract = {For assembly tasks parts often have to be oriented before they can be put in an assembly. The results presented in this paper are a component of the automated design of parts orienting devices. The focus is on orienting parts with minimal sensing and manipulation. We present a new approach to parts orienting through the manipulation of pose distributions. Through dynamic simulation we can determine the pose distribution for an object being dropped from an arbitrary height on an arbitrary surface. By varying the drop height and the shape of the support surface we can find the initial conditions that will result in a pose distribution with minimal entropy. We are trying to uniquely orient a part with high probability just by varying the initial conditions. We will derive a condition on the pose and velocity of an object in contact with a sloped surface that will allow us to quickly determine the final resting configuration of the object. This condition can then be used to quickly compute the pose distribution. We also present simulation and experimental results that show how dynamic simulation can be used to find optimal shapes and drop heights for a given part.}, author = {Mark Moll and Michael A. Erdmann}, booktitle = {Algorithmic and Computational Robotics: New Directions}, editor = {Bruce R. Donald and Kevin M. Lynch and Daniela Rus}, keywords = {pose distributions, parts orienting, dynamic simulation}, pages = {127--141}, publisher = {A. K. Peters}, title = {Manipulation of Pose Distributions}, url = {http://www.akpeters.com/book.asp?bID=139}, year = 2001, bdsk-url-1 = {http://www.akpeters.com/book.asp?bID=139} } @InProceedings{ moll-erdmann2001:recon-shape-motion-using, abstract = {We present a new method to reconstruct the shape of an unknown object using tactile sensors without requiring object immobilization. Instead, the robot manipulates the object without prehension. The robot infers the shape, motion and center of mass of the object based on the motion of the contact points as measured by tactile sensors. Our analysis is supported by simulation and experimental results.}, address = {Maui, HI}, author = {Mark Moll and Michael A. Erdmann}, booktitle = iros-01, doi = {10.1109/IROS.2001.976250}, keywords = {tactile sensing, shape reconstruction, contact kinematics}, month = {October/November}, pages = {691--700}, title = {Reconstructing Shape from Motion Using Tactile Sensors}, year = 2001 } @TechReport{ moll-erdmann2001:shape-recon-planar-dynam, abstract = {We present a a new method to reconstruct the shape of an unknown object using tactile sensors, without requiring object immobilization. Instead, sensing and nonprehensile manipulation occur simultaneously. The robot infers the shape, motion and center of mass of the object based on the motion of the contact points as measured by the tactile sensors. We present analytic results and simulation results assuming quasistatic dynamics. We prove that the shape and motion are observable in both the quasistatic and the fully dynamic case.}, author = {Mark Moll and Michael A. Erdmann}, institution = {Dept. of Computer Science, Carnegie Mellon University}, keywords = {tactile reconstruction, contact kinematics, nonlinear observer theory, tactile sensing}, number = {CMU-CS-01-107}, title = {Shape Reconstruction in a Planar Dynamic Environment}, year = 2001 } @InProceedings{ moll-erdmann2002:dynam-shape-recon-using, abstract = {We present new results on reconstruction of the shape and motion of an unknown object using tactile sensors without requiring object immobilization. A robot manipulates the object with two flat palms covered with tactile sensors. We model the full dynamics and prove local observability of the shape, motion and center of mass of the object based on the motion of the contact points as measured by the tactile sensors.}, author = {Mark Moll and Michael A. Erdmann}, booktitle = icra-02, doi = {10.1109/ROBOT.2002.1014777}, keywords = {shape reconstruction, tactile sensing, observability}, pages = {1636--1641}, title = {Dynamic Shape Reconstruction Using Tactile Sensors}, year = 2002 } @Article{ moll-erdmann2002:manip-pose-distr, abstract = {For assembly tasks parts often have to be oriented before they can be put in an assembly. The results presented in this paper are a component of the automated design of parts orienting devices. The focus is on orienting parts with minimal sensing and manipulation. We present a new approach to parts orienting through the manipulation of pose distributions. Through dynamic simulation we can determine the pose distribution for an object being dropped from an arbitrary height on an arbitrary surface. By varying the drop height and the shape of the support surface we can find the initial conditions that will result in a pose distribution with minimal entropy. We are trying to uniquely orient a part with high probability just by varying the initial conditions. We will derive a condition on the pose and velocity of a simple planar object in contact with a sloped surface that will allow us to quickly determine the final resting configuration of the object. This condition can then be used to quickly compute the pose distribution. We also present simulation and experimental results that show how dynamic simulation can be used to find optimal shapes and drop heights for a given part.}, author = {Mark Moll and Michael A. Erdmann}, doi = {10.1177/027836402320556449}, journal = ijrr, keywords = {pose distributions, parts orienting, dynamic simulation}, month = mar, number = 3, pages = {277--292}, title = {Manipulation of Pose Distributions}, volume = 21, year = 2002 } @InCollection{ moll-erdmann2003:recon-shape-motion-unknow, abstract = {We present a method to simultaneously reconstruct the shape and motion of an unknown smooth convex object. The object is manipulated by planar palms covered with tactile elements. The shape and dynamics of the object can be expressed as a function of the sensor values and the motion of the palms. We present a brief review of previous results for the planar case. In this paper we show that the 3D case is fundamentally different from the planar case, due to increased tangent dimensionality. The main contribution of this paper is a shape-dynamics analysis in 3D, and the synthesis of shape approximation methods via reconstructed contact point curves.}, author = {Mark Moll and Michael A. Erdmann}, booktitle = {Algorithmic Foundations of Robotics V}, doi = {10.1007/b80173}, editor = {Jean-Daniel Boissonnat and Joel Burdick and Ken Goldberg and Seth Hutchinson}, keywords = {tactile sensing, shape reconstruction, nonprehensile manipulation, contact kinematics}, pages = {293--310}, publisher = spr, title = {Reconstructing the Shape and Motion of Unknown Objects with Active Tactile Sensors}, year = 2003 } @InProceedings{ moll-kavraki2004:path-plann-minim-energ, abstract = {In this paper we present a new path planning technique for a flexible wire. We first introduce a new parametrization designed to represent low-energy configurations. Based on this parametrization we can find curves that satisfy endpoint constraints. Next, we present three different techniques for minimizing energy within the self-motion manifold of the curve. We introduce a local planner to find smooth minimal energy deformations for these curves that can be used by a general path planning algorithm. Using a simplified model for obstacles, we can find minimal energy curves of fixed length that pass through specified tangents at given control points. Finally, we show that the parametrization introduced in this paper is a good approximation of true minimal energy curves. Our work has applications in surgical suturing and snake-like robots.}, author = {Mark Moll and Lydia E. Kavraki}, booktitle = icra-04, doi = {10.1109/ROBOT.2004.1307489}, keywords = {path planning, curve parametrization, minimal energy curves}, pages = {2826--2831}, title = {Path Planning for Minimal Energy Curves of Constant Length}, year = 2004 } @InProceedings{ moll-kavraki2005:path-plann-variab-resol, abstract = {We present a new approach to path planning for flexible wires. We introduce a method for computing stable configurations of a wire subject to manipulation constraints. These configurations correspond to minimal-energy curves. The representation is adaptive in the sense that the number of parameters automatically varies with the complexity of the underlying curve. We introduce a planner that computes paths from one minimal-energy curve to another such that all intermediate curves are also minimal-energy curves. Using a simplified model for obstacles, we can find minimal-energy curves of fixed length that pass through specified tangents at given control points. Our work has applications in motion planning for surgical suturing and snake-like robots.}, author = {Mark Moll and Lydia E. Kavraki}, booktitle = icra-05, keywords = {path planning, minimal-energy curves, subdivision}, pages = {2142--2147}, title = {Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1570428} , year = 2005, bdsk-url-1 = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1570428} } @Article{ moll-miikkulainen1997:conver-zone-episod-memor, abstract = {Human episodic memory provides a seemingly unlimited storage for everyday experiences, and a retrieval system that allows us to access the experiences with partial activation of their components. The system is believed to consist of a fast, temporary storage in the hippocampus, and a slow, long-term storage within the neocortex. This paper presents a neural network model of the hippocampal episodic memory inspired by Damasio's idea of Convergence Zones. The model consists of a layer of perceptual feature maps and a binding layer. A perceptual feature pattern is coarse coded in the binding layer, and stored on the weights between layers. A partial activation of the stored features activates the binding pattern, which in turn reactivates the entire stored pattern. For many configurations of the model, a theoretical lower bound for the memory capacity can be derived, and it can be an order of magnitude or higher than the number of all units in the model, and several orders of magnitude higher than the number of binding-layer units. Computational simulations further indicate that the average capacity is an order of magnitude larger than the theoretical lower bound, and making the connectivity between layers sparser causes an even further increase in capacity. Simulations also show that if more descriptive binding patterns are used, the errors tend to be more plausible (patterns are confused with other similar patterns), with a slight cost in capacity. The convergence-zone episodic memory therefore accounts for the immediate storage and associative retrieval capability and large capacity of the hippocampal memory, and shows why the memory encoding areas can be much smaller than the perceptual maps, consist of rather coarse computational units, and be only sparsely connected to the perceptual maps.}, author = {Mark Moll and Risto Miikkulainen}, doi = {10.1016/S0893-6080(97)00016-6}, journal = {Neural Networks}, number = 6, pages = {1017--1036}, title = {Convergence-Zone Episodic Memory: Analysis and Simulations}, volume = 10, year = 1997 } @InProceedings{ moll+1994:capac-conver-zone-episod, abstract = {Human episodic memory provides a seemingly unlimited storage for everyday experiences, and a retrieval system that allows us to access the experiences with partial activation of their components. This paper presents a neural network model of episodic memory inspired by Damasio's idea of Convergence Zones. The model consists of a layer of perceptual feature maps and a binding layer. A perceptual feature pattern is coarse coded in the binding layer, and stored on the weights between layers. A partial activation of the stored features activates the binding pattern which in turn reactivates the entire stored pattern. A worst-case analysis shows that with realistic-size layers, the memory capacity of the model is several times larger than the number of units in the model, and could account for the large capacity of human episodic memory.}, address = mit-addr, author = {Mark Moll and Risto Miikkulainen and Jonathan Abbey}, booktitle = aaai-94, doi = {10.1109/ICNN.1994.375017}, pages = {68--73}, publisher = {MIT Press}, title = {The Capacity of Convergence-Zone Episodic Memory}, year = 1994 } @Article{ moll+2002:align-parts-micro-assem, abstract = {Orienting parts that measure only a few micrometers in diameter introduces several challenges that need not be considered at the macro-scale. First, there are several kinds of sticking effects due to Van der Waals forces and static electricity which complicate hand-off motions and release of a part. Second, the degrees of freedom of micro-manipulators are limited. This paper proposes a pair of manipulation primitives and a complete algorithm that addresses these challenges. We will show that a sequence of these two manipulation primitives can uniquely orient any asymmetric part while maintaining contact without sensing. This allows us to apply the same plan to many (identical) parts simultaneously. For asymmetric parts we can find a plan of length O(n) in O(n) time that orients the part, where n is the number of vertices.}, author = {Mark Moll and Ken Goldberg and Michael A. Erdmann and Ron Fearing}, doi = {10.1108/01445150210416673}, journal = {Assembly Automation}, keywords = {micromanipulation, parts orienting, parts feeding, rolling}, month = feb, number = 1, pages = {46--54}, title = {Aligning Parts for Micro Assemblies}, volume = 22, year = 2002 } @InProceedings{ moll+2002:orien-micro-scale-parts, abstract = {Orienting parts that measure only a few micrometers in diameter introduces several challenges that need not be considered at the macro-scale. First, there are several kinds of sticking effects due to Van der Waals forces and static electricity which complicate hand-off motions and release of a part. Second, the degrees of freedom of micro-manipulators are limited. This paper proposes a pair of manipulation primitives and a complete algorithm that addresses these challenges. We will show that a sequence of these two manipulation primitives can uniquely orient any asymmetric part while maintaining contact without sensing. This allows us to apply the same plan to many (identical) parts simultaneously. For asymmetric parts we can find a plan of length O(n) in O(n) time that orients the part, where n is the number of vertices.}, author = {Mark Moll and Ken Goldberg and Michael A. Erdmann and Ron Fearing}, booktitle = icra-02, doi = {10.1109/ROBOT.2002.1014823}, keywords = {micromanipulation, parts orienting, rolling}, pages = {1931--1936}, title = {Orienting Micro-Scale Parts with Squeeze and Roll Primitives}, year = 2002 } @TechReport{ moll+2004:dockin-flexib-ligan, abstract = {The activity of most drugs is regulated by the binding of one molecule (the ligand) to a pocket of another, usually larger, molecule, which is commonly a protein. This report describes a new approach to creating low-energy structures of flexible proteins to which ligands can be docked. The flexibility of molecules is encoded with thousands of parameters making the search for valid complexes a formidable problem. Our method takes into account the flexibility of the protein as this can be encoded by its major modes of motion. The output of the program consists of low-energy protein conformations that can then be docked with a ligand using a traditional docking program. We employ a robotics-based approach for exploring the conformational space of the protein. Our long term goal is to develop an efficient, accurate, and automated algorithm that will be used to screen large databases of molecules for novel therapeutics.}, address = {Houston, TX}, author = {Mark Moll and David Schwarz and Allison Heath and Lydia E. Kavraki}, institution = {Rice University}, number = {04-443}, title = {On Flexible Docking Using Expansive Search}, year = 2004 } @MastersThesis{ moll1995:head-parsin-typed-featur, abstract = {In this report a description will be given of how typed feature structures can be specified. A specification language will be presented for the specification of types, words and grammar rules. An unification algorithm for typed feature structures as well as an algorithm to compute the least upper bound relation for a type lattice will be given. Finally, a head-corner parsing schema for typed feature structures will be presented.}, author = {Mark Moll}, school = {Department of Computer Science, University of Twente}, title = {Head-corner Parsing Using Typed Feature Structures}, year = 1995 } @TechReport{ moll1996:mappin-scien, address = {Leiden, the Netherlands}, author = {Mark Moll}, institution = {Centre for Science and Technology Studies (CWTS)}, month = {August}, note = {Research report to the Netherlands Organization for Scientific Research (NWO), Foundation for Economic and Socio-Cultural Sciences (ESR)}, number = {96-06}, title = {Mapping Science: Methods and Tools for the Automatic Creation of Semantic Maps of Large Corpora}, type = {Report CWTS}, year = 1996 } @PhDThesis{ moll2002:shape-recon-using-activ, abstract = {We present a new method to reconstruct the shape of an unknown object using tactile sensors, without requiring object immobilization. Instead, sensing and nonprehensile manipulation occur simultaneously. The robot infers the shape, motion and center of mass of the object based on the motion of the contact points as measured by the tactile sensors. This allows for a natural, continuous interaction between manipulation and sensing. We analyze the planar case first by assuming quasistatic dynamics, and present simulation results and experimental results obtained using this analysis. We extend this analysis to the full dynamics and prove observability of the nonlinear system describing the shape and motion of the object being manipulated. In our simulations, a simple observer based on Newton's method for root finding performs really well. Using the same framework we can also describe the shape and dynamics of three-dimensional objects. However, there are some fundamental differences between the planar and three-dimensional case, due to increased tangent dimensionality. Also, perfect global shape reconstruction is impossible in the 3D case, but it is almost trivial to obtain upper and lower bounds on the shape. The 3D shape reconstruction method has also been implemented and we present some simulation results.}, address = {Pittsburgh, PA}, author = {Mark Moll}, keywords = {tactile sensing, shape reconstruction, nonprehensile manipulation}, month = jul, school = {Computer Science Department, Carnegie Mellon University}, title = {Shape Reconstruction Using Active Tactile Sensors}, year = 2002 } @InProceedings{ op+1995:parsin-dialog-system-typed, abstract = {The analysis of natural language in the context of keyboard-driven dialogue systems is the central issue addressed in this paper. A module that corrects typing errors, performs domain-specific morphological analysis is developed. A parser for typed unification grammars is designed and implemented in C++; for description of the lexicon and the grammer a specialised specification language is developed. It is argued that typed unification grammars and especially the newly developed specification language are convenient formalisms for describing natural language use in dialogue systems. Research on these issues is carried out in the context of the Schisma project, a research project in linguistic engineering; participants in Schisma are KPN Research and the University of Twente.}, address = {Prague/Karlovy Vary, Czech Republic}, author = {Op den Akker, Rieks and Ter Doest, Hugo and Mark Moll and Anton Nijholt}, booktitle = {Proceedings of the International Workshop on Parsing Technologies}, title = {Parsing in Dialogue Systems using Typed Feature Structures}, year = 1995 } @TechReport{ op+1995:parsin-dialog-system-typed-tr, abstract = {The analysis of natural language in the context of keyboard-driven dialogue systems is the central issue addressed in this paper. A module that corrects typing errors and performs domain-specific morphological analysis has been developed. A parser for typed unification grammars is designed and implemented in C++; for description of the lexicon and the grammer a specialised specification language has been developed. It is argued that typed unification grammars and especially the newly developed specification language are convenient formalisms for describing natural language use in dialogue systems. Research on these issues is carried out in the context of the Schisma project, a research project of the Parlevink group in linguistic engineering; participants in Schisma are KPN Research and the University of Twente. The aims of the Schisma project are twofold: both the accumulation of knowledge in the field of computational linguistics and the development of a natural language interfaced theatre information and booking system is envisaged. The Schisma project serves as a testbed for the development of the various language analysis modules necessary for dialogue systems.}, author = {Op den Akker, Rieks and Ter Doest, Hugo and Mark Moll and Anton Nijholt}, institution = {Department of Computer Science, University of Twente}, number = {95-25}, title = {Parsing in Dialogue Systems using Typed Feature Structures}, type = {Memoranda Informatica}, year = 1995 } @InProceedings{ ter+1996:languag-engin-dialog-system, abstract = {The analysis of natural language in the context of keyboard-driven dialogue systems is the central issue addressed in this paper. A module that corrects typing errors, performs domain-specific morphological analysis is developed. A parser for typed unification grammars has been designed and implemented in C++; for description of the lexicon and the grammar a suitable specification language has been developed. It is argued that typed unification grammars and especially the newly developed specification language are convenient formalisms for describing natural language use in dialogue systems. Finally we present a dialogue manager that is based on a finite state automaton; transitions in the automaton depend upon availability of information in utterances of the user. In order to keep track of the history of the dialogue, a context stack is constructed during the dialogue. The manager is implemented in Prolog. }, address = {Houston, TX}, author = {Ter Doest, Hugo and Mark Moll and Ren{\'e} Bos and Van de Burgt, Stan and Anton Nijholt}, booktitle = {Computers in Engineering Symposium}, pages = {68--79}, title = {Language Engineering in Dialogue Systems}, year = 1996 }