@Article{ moll2011the-labelhash-server-and-tools-for-substructure-based,
abstract = {Summary: The LabelHash server and tools are designed for large- scale substructure
comparison. The main use is to predict the function of unknown proteins. Given a
set of (putative) functional residues, LabelHash finds all occurrences of matching
substructures in the entire Protein Data Bank, along with a statistical
significance estimate and known functional annotations for each match. The results
can be downloaded for further analysis in any molecular viewer. For Chimera there
is a plugin to facilitate this process.
Availability: The website is free and open to all users with no login requirements
at http://labelhash.kavrakilab.org.
Contact: mmoll@rice.edu},
author = {Mark Moll and Drew H. Bryant and Lydia E. Kavraki},
doi = {10.1093/bioinformatics/btr343},
journal = {Bioinformatics},
month = jun,
number = {15},
pages = {2161--2162},
title = {The {LabelHash} Server and Tools for Substructure-Based Functional Annotation},
volume = {27},
year = {2011}
}
@Article{ bryant2010analysis-of-substructural-variation-in-families,
abstract = {Background Structural variations caused by a wide range of physicochemical and
biological sources directly influence the function of a protein. For enzymatic
proteins, the structure and chemistry of the catalytic binding site residues can be
loosely defined as a substructure of the protein. Comparative analysis of
drug-receptor substructures across and within species has been used for lead
evaluation. Substructure-level similarity between the binding sites of functionally
similar proteins has also been used to identify instances of convergent evolution
among proteins. In functionally homologous protein families, shared chemistry and
geometry at catalytic sites provide a common, local point of comparison among
proteins that may differ significantly at the sequence, fold, or domain topology
levels.
Results This paper describes two key results that can be used separately or in
combination for protein function analysis. The Family-wise Analysis of
SubStructural Templates (FASST) method uses all-against-all substructure comparison
to determine Substructural Clusters (SCs). SCs characterize the binding site
substructural variation within a protein family. In this paper we focus on examples
of automatically determined SCs that can be linked to phylogenetic distance between
family members, segregation by conformation, and organization by homology among
convergent protein lineages. The Motif Ensemble Statistical Hypothesis (MESH)
framework constructs a representative motif for each protein cluster among the SCs
determined by FASST to build motif ensembles that are shown through a series of
function prediction experiments to improve the function prediction power of
existing motifs.
Conclusions FASST contributes a critical feedback and assessment step to existing
binding site substructure identification methods and can be used for the thorough
investigation of structure-function relationships. The application of MESH allows
for an automated, statistically rigorous procedure for incorporating structural
variation data into protein function prediction pipelines. Our work provides an
unbiased, automated assessment of the structural variability of identified binding
site substructures among protein structure families and a technique for exploring
the relation of substructural variation to protein function. As available proteomic
data continues to expand, the techniques proposed will be indispensable for the
large-scale analysis and interpretation of structural data.
},
author = {Drew H. Bryant and Mark Moll and Brian Y. Chen and Viacheslav Y. Fofanov and Lydia
E. Kavraki},
doi = {10.1186/1471-2105-11-242},
journal = {BMC Bioinformatics},
month = may,
number = {242},
pmcid = {PMC2885373},
pmid = {20459833},
title = {Analysis of substructural variation in families of enzymatic proteins with
applications to protein function prediction},
volume = {11},
year = {2010}
}
@Article{ haspel2010tracing-conformational-changes-in-proteins,
abstract = {Background Many proteins undergo extensive conformational changes as part of their
functionality. Tracing these changes is important for understanding the way these
proteins function. Traditional biophysics-based conformational search methods
require a large number of calculations and are hard to apply to large-scale
conformational motions.
Results In this work we investigate the application of a robotics-inspired method,
using backbone and limited side chain representation and a coarse grained energy
function to trace large-scale conformational motions. We tested the algorithm on
four well known medium to large proteins and we show that even with relatively
little information we are able to trace low-energy conformational pathways
efficiently. The conformational pathways produced by our methods can be further
filtered and refined to produce more useful information on the way proteins
function under physiological conditions.
Conclusions The proposed method effectively captures large-scale conformational
changes and produces pathways that are consistent with experimental data and other
computational studies. The method represents an important first step towards a
larger scale modeling of more complex biological systems.},
author = {Nurit Haspel and Mark Moll and Matthew L. Baker and Wah Chiu and Lydia E.
Kavraki},
doi = {10.1186/1472-6807-10-S1-S1},
journal = {BMC Structural Biology},
number = {Suppl. 1},
pages = {S1},
pmcid = {PMC2873824},
pmid = {20487508},
title = {Tracing Conformational Changes in Proteins},
volume = {10},
year = {2010}
}
@Article{ moll2010the-labelhash-algorithm-for-substructure-matching,
abstract = {Background 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.
Results We present LabelHash, a novel algorithm for matching substructural motifs
to large collections of protein structures. The algorithm consists of two phases.
In the first phase the proteins are preprocessed in a fashion that allows for
instant lookup of partial matches to any motif. In the second phase, partial
matches for a given motif are expanded to complete matches. The general
applicability of the algorithm is demonstrated with three different case studies.
First, we show that we can accurately identify members of the enolase superfamily
with a single motif. Next, we demonstrate how LabelHash can complement SOIPPA, an
algorithm for motif identification and pairwise substructure alignment. Finally, a
large collection of Catalytic Site Atlas motifs is used to benchmark the
performance of the algorithm. LabelHash runs very efficiently in parallel; matching
a motif against all proteins in the 95% sequence identity filtered non-redundant
Protein Data Bank typically takes no more than a few minutes. The LabelHash
algorithm is available through a web server and as a suite of standalone programs
at http://labelhash.kavrakilab.org. The output of the LabelHash algorithm can be
further analyzed with Chimera through a plugin that we developed for this purpose.
Conclusions LabelHash is an efficient, versatile algorithm for large-scale
substructure matching. When LabelHash is running in parallel, motifs can typically
be matched against the entire PDB on the order of minutes. The algorithm is able to
identify functional homologs beyond the twilight zone of sequence identity and even
beyond fold similarity. The three case studies presented in this paper illustrate
the versatility of the algorithm.},
author = {Mark Moll and Drew H. Bryant and Lydia E. Kavraki},
doi = {10.1186/1471-2105-11-555},
journal = {BMC Bioinformatics},
month = nov,
number = {555},
pmcid = {PMC2996407},
pmid = {21070651},
title = {The {LabelHash} Algorithm for Substructure Matching},
volume = {11},
year = {2010}
}
@InProceedings{haspel2009tracing-conformational-changes-in-proteins,
abstract = {Many proteins undergo extensive conformational changes as part of their
functionality. Tracing these changes is important for understanding the way these
proteins function. Traditional biophysics-based conformational search methods
require a large number of calculations and are hard to apply to large-scale
conformational motions. In this work we investigate the application of a
robotics-inspired method, using backbone and limited side chain representation and
a coarse grained energy function to trace large-scale conformational motions. We
tested the algorithm on three well known medium to large proteins and we show that
even with relatively little information we are able to trace low-energy
conformational pathways efficiently. The conformational pathways produced by our
methods can be further filtered and refined to produce more useful information on
the way proteins function under physiological conditions.},
address = {Washington, DC},
author = {Nurit Haspel and Mark Moll and Matthew L. Baker and Wah Chiu and Lydia E.
Kavraki},
booktitle = {{IEEE} Intl.\ Conf.\ on Bioinformatics and Biomedicine Workshops (BIBMW)},
doi = {10.1109/BIBMW.2009.5332115},
month = nov,
pages = {120--127},
title = {Tracing Conformational Changes in Proteins},
year = {2009}
}
@InProceedings{fofanov2008a-statistical-model-to-correct-systematic,
abstract = {The identification of protein function is crucial to understanding cellular
processes and selecting novel proteins as drug targets. However, experimental
methods for determining protein function can be expensive and time-consuming.
Protein partial structure comparison methods seek to guide and accelerate the
process of function determination by matching characterized functional site
representations, motifs, to substructures within uncharacterized proteins, matches.
One common difficulty of all protein structural 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 to
eliminate biologically irrelevant matches. Thresholds refine and accelerate the
method by limiting the number of potential matches that need to be considered.
However, because statistical models rely on the output of the geometric matching
method to accurately measure statistical significance, geometric thresholds can
also artificially distort the basis of statistical models, making statistical
scores dependant on geometric thresholds and potentially causing significant
reductions in accuracy of the functional annotation method. This paper proposes a
point-weight based correction approach to quantify and model the dependence of
statistical scores to account for the systematic bias introduced by heuristics.
Using a benchmark dataset of 20 structural motifs, we show that the point-weight
correction procedure accurately models the information lost during the geometric
comparison phase, removing systematic bias and greatly reducing misclassification
rates of functionally related proteins, while maintaining specificity. },
author = {Viacheslav Y. Fofanov and Brian Y. Chen and Drew H. Bryant and Mark Moll and
Olivier Lichtarge and Lydia E. Kavraki and Marek Kimmel},
booktitle = {{IEEE} Intl.\ Conf.\ on Bioinformatics and Biomedicine Workshops (BIBMW)},
doi = {10.1109/BIBMW.2008.4686202},
pages = {1--8},
title = {A statistical model to correct systematic bias introduced by algorithmic
thresholds in protein structural comparison algorithms},
year = {2008}
}
@InProceedings{moll2008labelhash-a-flexible-and-extensible-method,
address = {Toronto, Canada},
author = {Mark Moll and Lydia E. Kavraki},
booktitle = {Automated Function Prediction / BioSapiens Meeting (AFP-BioSapiens)},
doi = {10.1038/npre.2008.2199.1},
note = {Available from Nature Precedings},
title = {{LabelHash}: A Flexible and Extensible Method for Matching Structural 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)},
doi = {10.1142/9781848162648_0014},
pages = {157-168},
pmid = {19642277},
title = {Matching of Structural Motifs Using Hashing on Residue Labels and Geometric
Filtering for Protein Function Prediction},
url = {http://csb2008.org/csb2008papers/077Moll.pdf},
year = {2008}
}
@InProceedings{chen2007representations-of-structural-motifs-for-protein,
address = {Vienna, Austria},
author = {Brian Y. Chen and Drew H. Bryant and Joseph H. Bylund and Amanda E. Cruess and
David M. Kristensen and Viacheslav Y. Fofanov and Mark Moll and Marek Kimmel and
Olivier Lichtarge and Lydia E. Kavraki},
booktitle = {15th Annual Intl.\ Conf.\ on Intelligent Systems for Molecular Biology (ISMB) \&
6th European Conf.\ on Comp.\ Bio.\ (ECCB)},
title = {Representations of Structural Motifs for Protein Function Prediction},
url = {http://www.iscb.org/uploaded/css/E108Moll.pdf},
year = {2007}
}
@InProceedings{chen2007geometry-inspired-optimization-methods-for-structural,
address = {Vienna, Austria},
author = {Brian Y. Chen and Drew H. Bryant and Viacheslav Y. Fofanov and David M. Kristensen
and Mark Moll and Marek Kimmel and Olivier Lichtarge and Lydia E. Kavraki},
booktitle = {Automated Function Prediction Meeting (AFP)},
title = {Geometry-inspired Optimization Methods for Structural Motifs for Protein Function
Prediction},
url = {http://biofunctionprediction.org/files/afp-biosap-2007-full-program.pdf},
year = {2007}
}
@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},
doi = {10.1007/978-1-59745-574-9},
edition = {Second},
editor = {Mohammed Zaki and Chris Bystroff},
month = oct,
pmid = {18075168},
publisher = {Humana Press},
series = {Methods In Molecular Biology},
title = {Roadmap Methods for Protein Folding},
year = {2007}
}
@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},
pmcid = {PMC1502548},
pmid = {16785435},
title = {Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear
dimensionality reduction},
volume = {103},
year = {2006}
}
@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}
}
@Article{ bekris2011safe-distributed-motion-coordination,
abstract = {When multiple robots operate in the same environment, it is critical to coordinate
their motion in a distributed fashion so that they reach their goals safely. If the
robots have to respect second-order dynamics, this becomes a challenging problem,
even for known static environments. This work presents a replanning framework where
each robot computes partial plans independently during a planning cycle, while
executing a previously computed trajectory. Each robot communicates with its
neighbors to select a trajectory that is safe over an infinite time horizon. The
proposed approach does not require synchronization and allows the robots to
dynamically change their planning cycles over time. This paper proves that the
proposed motion coordination algorithm guarantees safety under this general
setting. An important advantage is that this framework is not specific to the
underlying robot dynamics nor to the planning or control algorithm used to generate
the robot trajectories. The performance of the approach is evaluated using a
distributed multi-robot simulator on a computing cluster, where the simulated
robots are forced to communicate by exchanging messages. The simulation results
confirm the safety of the algorithm in various environments with up to 32 robots
governed by second-order dynamics.},
author = {Kostas E. Bekris and Devin K. Grady and Mark Moll and Lydia E. Kavraki},
doi = {10.1177/0278364911430420},
journal = {Intl.\ J.\ of Robotics Research},
month = feb,
number = {2},
pages = {129--149},
title = {Safe Distributed Motion Coordination for Second-Order Systems with Different
Planning Cycles},
volume = {31},
year = {2012}
}
@InProceedings{grady2011look-before-you-leap,
abstract = {This paper describes a novel method for identifying multiple targets with multiple
robots in a partially known environment. Two main issues are addressed. The first
relates to the use of motion planning algorithms to determine whether robots can
reach ``good'' positions that offer the most informative measurements. The second
concerns the use of predictive sensing to decide where sensor measurements should
be taken. The problem is formulated similar to a next-best-view problem with
differential constraints on the robots' motion, with additional layers of
complexity due to visual occlusions as well as navigational obstacles. We propose a
new distributed sensing strategy that exploits the structure of image manifolds to
predict the utility of the measurements at a given position. This information is
encoded in a cost map that guides a motion planning algorithm. Coordination among
robots is achieved by incorporating additional information in each robot's cost
map. A range of simulations indicates that our approach outperforms current
approaches and demonstrates the advantages of predictive sensing and accounting for
reachability constraints.},
author = {Devin K. Grady and Mark Moll and Chinmay Hegde and Aswin C. Sankaranarayanan and
Richard G. Baraniuk and Lydia E. Kavraki},
booktitle = {Workshop on Progress and Open Problems in Motion Planning at the {IEEE}/{RSJ}
Conf.\ on Intelligent Robots and Systems},
title = {Look Before You Leap: Predictive Sensing and Opportunistic Navigation},
year = {2011}
}
@InProceedings{moll2011teaching-motion-planning-concepts,
abstract = {Motion planning is a central problem in robotics. Although it is an engaging topic
for undergraduate students, it is difficult to teach, and as a result, the material
is often only covered at an abstract level. Deep learning could be achieved by
having students implement and test different algorithms. However, there is usually
no time within a single class to have students completely implement several motion
planning algorithms as they require the development of many lower-level data
structures. We present an ongoing project to develop a teaching module for robotic
motion planning centered around an integrated software environment. The module can
be taught early in the undergraduate curriculum, after students have taken an
introductory programming class.},
author = {Mark Moll and Ioan A. \c{S}ucan and Janice Bordeaux and Lydia E. Kavraki},
booktitle = {IEEE Workshop on Advanced Robotics and its Social Impacts (ARSO)},
title = {Teaching Motion Planning Concepts to Undergraduate Students},
year = {2011}
}
@Article{ moll2010teaching-robot-motion-planning,
abstract = {Robot motion planning is a fairly intuitive and engaging topic, yet it is
difficult to teach. The material is taught in undergraduate and graduate robotics
classes in computer science, electrical engineering, mechanical engineering and
aeronautical engineering, but at an abstract level. Deep learning could be achieved
by having students implement and test different motion planning strategies.
However, it is practically impossible in the context of a single class to have
undergraduates implement motion planning algorithms that are powerful and fun to
use, even when the students have proficient programming skills. Due to lack of
supporting educational material, students are often asked to implement simple (and
uninteresting) motion planning algorithms from scratch, or access thousands of
lines of code and just figure out how things work. We present an ongoing project to
develop microworld software and a modeling curriculum that supports undergraduate
acquisition of motion planning knowledge and tool use by computer science and
engineering students. The goal is to open the field of motion planning and robotics
to young and enthusiastic talent.},
author = {Mark Moll and Janice Bordeaux and Lydia E. Kavraki},
journal = {Computers in Education (Special Issue on Novel Approaches to Robotics Education)},
number = {3},
pages = {50--59},
title = {Teaching Robot Motion Planning},
volume = {20},
year = {2010}
}
@Article{ moll2008workshop-on-self-reconfigurable-modular-robots,
author = {Mark Moll and Daniela Rus},
doi = {10.1177/0278364908089348},
journal = {Intl.\ J.\ of Robotics Research},
month = {March/April},
number = {3/4},
pages = {277-278},
title = {Special Issue on Self-Reconfiguring Modular Robots (Guest Editorial)},
volume = {27},
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 = {Proc.\ 2007 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems},
note = {\href{http://www.isi.edu/robots/superbot/movies/SuperBot.mov}{Video}},
title = {Multifunctional Behaviors of Reconfigurable {SuperBot} Modules},
year = {2007}
}
@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}
}
@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 = {Proc.\ 2006 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems},
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}
}
@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 = {{IEEE} Trans.\ on Robotics},
month = aug,
number = {4},
pages = {625--636},
title = {Path Planning for Deformable Linear Objects},
volume = {22},
year = {2006}
}
@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 = {Proc.\ 2006 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems},
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{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 = {Proc.\ 2005 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
doi = {10.1109/ROBOT.2005.1570428},
keywords = {path planning, minimal-energy curves, subdivision},
pages = {2142--2147},
title = {Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length},
year = {2005}
}
@InCollection{moll2004reconstructing-the-shape-and-motion-of-unknown,
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 = {Springer Verlag},
series = {Springer Tracts in Advanced Robotics},
title = {Reconstructing the Shape and Motion of Unknown Objects with Active Tactile
Sensors},
year = {2004}
}
@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 = {Proc.\ 2004 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
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-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 = {Proc.\ 2002 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
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 = {Intl.\ J.\ of Robotics Research},
keywords = {pose distributions, parts orienting, dynamic simulation},
month = mar,
number = {3},
pages = {277--292},
title = {Manipulation of Pose Distributions},
volume = {21},
year = {2002}
}
@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 = {Proc.\ 2002 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
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}
}
@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}
}
@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.crcpress.com/product/isbn/9781568811253},
year = {2001}
}
@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 = {Proc.\ 2001 {IEEE/RSJ} Intl.\ Conf.\ on Intelligent Robots and Systems},
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-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 = {Proc.\ 2000 {IEEE} Intl.\ Conf.\ on Robotics and Automation},
doi = {10.1109/ROBOT.2000.845304},
keywords = {pose distributions, parts orienting, dynamic simulation},
pages = {3673--3680},
title = {Uncertainty Reduction Using Dynamics},
year = {2000}
}
@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 = {Cambridge, MA},
author = {Mark Moll and Risto Miikkulainen and Jonathan Abbey},
booktitle = {Proc.\ 12th Natl. Conf.\ on Artificial Intelligence (AAAI-94)},
pages = {68--73},
publisher = {MIT Press},
title = {The Capacity of Convergence-Zone Episodic Memory},
year = {1994}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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},
url = {http://eprints.eemcs.utwente.nl/9891/},
year = {1995}
}