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Mark Moll

dblp:43/4154 · DBLP profile ↗
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37ranked-venue papers
15as first author
1since 2021 · last 2021
0000-0002-0451-2797ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 28 · 11 first-author · 1 since 2021Systems, architecture and hardware · 21 · 8 first-author · 1 since 2021Applied, interdisciplinary, general and emerging computing · 9 · 4 first-authorGraphics, computer vision, multimedia, augmented reality and games · 2 · 1 first-author

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
18 papers
Motion planning and robot control · 76% Planning, search and constraint satisfaction · 8% Multi-agent systems · 6%
Theoretical computer science
3 papers
Graph algorithms and graph theory · 49% Automated reasoning and model checking · 42% Information theory · 9%

Topics — the 29 heaviest of 34, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Robotics › Motion planning and robot control
motion planning
2.292020
Informing Multi-Modal Planning with Synergistic Discrete Leads · ICRA 2020
Online Multilayered Motion Planning with Dynamic Constraints for Autonomous Underwater Vehicles · ICRA 2019
Lazy Evaluation of Goal Specifications Guided by Motion Planning · ICRA 2019
Robotics › Motion planning and robot control › motion planning
sampling-based motion planning
0.952015
Experience-based planning with sparse roadmap spanners · ICRA 2015
Fast stochastic motion planning with optimality guarantees using local policy reconfiguration · ICRA 2014
Optimal and Efficient Stochastic Motion Planning in Partially-Known Environments · AAAI 2014
Robotics › Motion planning and robot control › motion planning
manipulation planning
0.412020
Informing Multi-Modal Planning with Synergistic Discrete Leads · ICRA 2020
Knowledge, reasoning and agents › Multi-agent systems › multimodal agent
multimodal planning
0.412020
Informing Multi-Modal Planning with Synergistic Discrete Leads · ICRA 2020
Robotics › Motion planning and robot control › motion planning › real-time motion planning
online trajectory planning
0.412019
Online Multilayered Motion Planning with Dynamic Constraints for Autonomous Underwater Vehicles · ICRA 2019
Robotics › Motion planning and robot control
trajectory optimization
0.412019
Online Multilayered Motion Planning with Dynamic Constraints for Autonomous Underwater Vehicles · ICRA 2019
Robotics › Motion planning and robot control
path planning
0.332015
A heuristic approach to finding diverse short paths · ICRA 2015
Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length · ICRA 2005
Path Planning for Minimal Energy Curves of Constant Length · ICRA 2004
Knowledge, reasoning and agents › Planning, search and constraint satisfaction
planning under uncertainty
0.222014
Automated model approximation for robotic navigation with POMDPs · ICRA 2013
Optimal and Efficient Stochastic Motion Planning in Partially-Known Environments · AAAI 2014
Robotics › Motion planning and robot control › motion planning › learning-based motion planning
experience-based motion planning
0.212015
Experience-based planning with sparse roadmap spanners · ICRA 2015
Knowledge, reasoning and agents › Planning, search and constraint satisfaction › planning under uncertainty
partially observable markov decision process
0.212015
Extending the Applicability of POMDP Solutions to Robotic Tasks · IEEE Trans. Robotics 2015
Machine learning › Reinforcement learning
markov decision process
0.212014
Optimal and Efficient Stochastic Motion Planning in Partially-Known Environments · AAAI 2014
Robotics › Motion planning and robot control
task and motion planning
0.212014
SMT-based synthesis of integrated task and motion plans from plan outlines · ICRA 2014
Robotics › Robot navigation and mapping › mobile robot navigation
navigation under uncertainty
0.212013
Automated model approximation for robotic navigation with POMDPs · ICRA 2013
Knowledge, reasoning and agents › Planning, search and constraint satisfaction › planning under uncertainty
POMDP planning
0.212013
Automated model approximation for robotic navigation with POMDPs · ICRA 2013
Robotics › Robot manipulation › grasping
pick-and-place
0.112020
Informing Multi-Modal Planning with Synergistic Discrete Leads · ICRA 2020
Bioinformatics and computational biology
protein function prediction
0.112011
The LabelHash Server and Tools for substructure-based functional annotation · Bioinform. 2011
Human-robot interaction › human-robot collaboration
collaborative robot
0.112019
Lazy Evaluation of Goal Specifications Guided by Motion Planning · ICRA 2019
Robotics › Motion planning and robot control › motion planning
configuration space
0.112015
Experience-based planning with sparse roadmap spanners · ICRA 2015
Graph algorithms and graph theory
shortest path
0.112015
A heuristic approach to finding diverse short paths · ICRA 2015
Robotics › Motion planning and robot control › motion planning › manipulation planning
deformable object motion planning
0.112006
Path planning for deformable linear objects · IEEE Trans. Robotics 2006
Robotics › Motion planning and robot control
robot control
0.112014
Fast stochastic motion planning with optimality guarantees using local policy reconfiguration · ICRA 2014
Robotics › Motion planning and robot control
stochastic optimal control
0.112014
Fast stochastic motion planning with optimality guarantees using local policy reconfiguration · ICRA 2014
Automated reasoning and model checking
satisfiability modulo theories
0.112014
SMT-based synthesis of integrated task and motion plans from plan outlines · ICRA 2014
Robotics › Motion planning and robot control › motion planning › optimal motion planning
asymptotically optimal motion planning
0.012013
Anytime solution optimization for sampling-based motion planning · ICRA 2013
Robotics › Robot manipulation
manipulation primitives
0.012002
Orienting Micro-Scale Parts with Squeeze and Roll Primitives · ICRA 2002
Robotics › Robot manipulation › tactile sensing › tactile surface perception
tactile shape reconstruction
0.012002
Dynamic Shape Reconstruction using Tactile Sensors · ICRA 2002
Robotics › Robot manipulation › assembly › assembly task
parts orienting
0.012000
Uncertainty Reduction Using Dynamics · ICRA 2000
Robotics › Robot manipulation › medical robotics
surgical suturing
0.012006
Path planning for deformable linear objects · IEEE Trans. Robotics 2006
Emerging computing paradigms
neuromorphic computing
0.011994
The Capacity of Convergence-Zone Episodic Memory · AAAI 1994

Methods — techniques the papers use, named apart from their topics

variable grounding · 0.8motion planning · 0.6layered planning · 0.4discrete lead biasing · 0.4sampling-based planning · 0.4reward/penalty strategy · 0.4reward-penalty strategy · 0.4inevitable collision state · 0.4finite horizon planning · 0.4bounded-parameter markov decision process · 0.4probabilistic sampling · 0.2heuristic search · 0.2satisfiability modulo theories · 0.2substructure matching · 0.1statistical significance estimation · 0.1convergence-zone network analysis · 0.0
YearPublicationVenuePosition
2021 HyperPlan: A Framework for Motion Planning Algorithm Selection and Parameter Optimization
abstract
Over the years, many motion planning algorithms have been proposed. It is often unclear which algorithm might be best suited for a particular class of problems. The problem is compounded by the fact that algorithm performance can be highly dependent on parameter settings. This paper shows that hyperparameter optimization is an effective tool in both algorithm selection and parameter tuning over a given set of motion planning problems. We present different loss functions for optimization that capture different notions of optimality. The approach is evaluated on a broad range of scenes using two different manipulators, a Fetch and a Baxter. We show that optimized planning algorithm performance significantly improves upon baseline performance and generalizes broadly in the sense that performance improvements carry over to problems that are very different from the ones considered during optimization.
Mark Moll, Constantinos Chamzas, Zachary Kingston, Lydia E. Kavraki
IROS1
2020 Informing Multi-Modal Planning with Synergistic Discrete Leads
abstract
Robotic manipulation problems are inherently continuous, but typically have underlying discrete structure, e.g., whether or not an object is grasped. This means many problems are multi-modal and in particular have a continuous infinity of modes. For example, in a pick-and-place manipulation domain, every grasp and placement of an object is a mode. Usually manipulation problems require the robot to transition into different modes, e.g., going from a mode with an object placed to another mode with the object grasped. To successfully find a manipulation plan, a planner must find a sequence of valid single-mode motions as well as valid transitions between these modes. Many manipulation planners have been proposed to solve tasks with multi-modal structure. However, these methods require mode-specific planners and fail to scale to very cluttered environments or to tasks that require long sequences of transitions. This paper presents a general layered planning approach to multi-modal planning that uses a discrete "lead" to bias search towards useful mode transitions. The difficulty of achieving specific mode transitions is captured online and used to bias search towards more promising sequences of modes. We demonstrate our planner on complex scenes and show that significant performance improvements are tied to both our discrete "lead" and our continuous representation.
Zachary Kingston, Andrew M. Wells, Mark Moll, Lydia E. Kavraki
ICRA3
2020 Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
abstract
BACKGROUND: The rapid growth of available knowledge on metabolic processes across thousands of species continues to expand the possibilities of producing chemicals by combining pathways found in different species. Several computational search algorithms have been developed for automating the identification of possible heterologous pathways; however, these searches may return thousands of pathway results. Although the large number of results are in part due to the large number of possible compounds and reactions, a subset of core reaction modules is repeatedly observed in pathway results across multiple searches, suggesting that some subpaths between common compounds were more consistently explored than others.To reduce the resources spent on searching the same metabolic space, a new meta-algorithm for metabolic pathfinding, Hub Pathway search with Atom Tracking (HPAT), was developed to take advantage of a precomputed network of subpath modules. To investigate the efficacy of this method, we created a table describing a network of common hub metabolites and how they are biochemically connected and only offloaded searches to and from this hub network onto an interactive webserver capable of visualizing the resulting pathways. RESULTS: A test set of nineteen known pathways taken from literature and metabolic databases were used to evaluate if HPAT was capable of identifying known pathways. HPAT found the exact pathway for eleven of the nineteen test cases using a diverse set of precomputed subpaths, whereas a comparable pathfinding search algorithm that does not use precomputed subpaths found only seven of the nineteen test cases. The capability of HPAT to find novel pathways was demonstrated by its ability to identify novel 3-hydroxypropanoate (3-HP) synthesis pathways. As for pathway visualization, the new interactive pathway filters enable a reduction of the number of displayed pathways from hundreds down to less than ten pathways in several test cases, illustrating their utility in reducing the amount of presented information while retaining pathways of interest. CONCLUSIONS: This work presents the first step in incorporating a precomputed subpath network into metabolic pathfinding and demonstrates how this leads to a concise, interactive visualization of pathway results. The modular nature of metabolic pathways is exploited to facilitate efficient discovery of alternate pathways.
Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett, Lydia E. Kavraki
BMC Bioinform.3
2019 Lazy Evaluation of Goal Specifications Guided by Motion Planning
abstract
Nowadays robotic systems are expected to share workspaces and collaborate with humans. In such collaborative environments, an important challenge is to ground or establish the correct semantic interpretation of a human request. Once such an interpretation is available, the request must be translated into robot motion commands in order to complete the desired task. It is not unusual that a human request cannot be grounded to a unique interpretation, thus leading to an ambiguous request. A simple example is to ask a robot to “put a cup on the table,” when there are multiple cups available. In order to deal with this kind of ambiguous request, we propose a delayed or lazy variable grounding. The focus of this paper is a motion planning algorithm that, given goal regions that represent different valid groundings, lazily finds a feasible path to any one valid grounding. This algorithm includes a reward-penalty strategy, which attempts to prioritize those goal regions that seem more promising to provide a solution. We validate our approach by solving requests with multiple valid alternatives in both simulation and real-world experiments.
Juan David Hernández, Mark Moll, Lydia E. Kavraki
ICRA2
2019 Online Multilayered Motion Planning with Dynamic Constraints for Autonomous Underwater Vehicles
abstract
Underwater robots are subject to complex hydro-dynamic forces. These forces define how the vehicle moves, so it is important to consider them when planning trajectories. However, performing motion planning considering the dynamics on the robot's onboard computer is challenging due to the limited computational resources available. In this paper an efficient motion planning framework for autonomous underwater vehicles (AUVs) is presented. By introducing a loosely coupled multilayered planning design, our framework is able to generate dynamically feasible trajectories while keeping the planning time low enough for online planning. First, a fast path planner operating in a lower-dimensional projected space computes a lead path from the start to the goal configuration. Then, the lead path is used to bias the sampling of a second motion planner, which takes into account all the dynamic constraints. Furthermore, we propose a strategy for online planning that saves computational resources by generating the final trajectory only up to a finite horizon. By using the finite horizon strategy together with the multilayered approach, the sampling of the second planner focuses on regions where good quality solutions are more likely to be found, significantly reducing the planning time. To provide strong safety guarantees our framework also incorporates the conservative approximations of inevitable collision states (icss). finally, we present simulations and experiments using a real underwater robot to demonstrate the capabilities of our framework.
Eduard Vidal, Mark Moll, Narcís Palomeras, Juan David Hernández, Marc Carreras, Lydia E. Kavraki
ICRA2
2017 Decoupling Constraints from Sampling-Based Planners
Zachary Kingston, Mark Moll, Lydia E. Kavraki
ISRR2
2016 Planning feasible and safe paths online for autonomous underwater vehicles in unknown environments
abstract
We present a framework for planning collision-free and safe paths online for autonomous underwater vehicles (AUVs) in unknown environments. We build up on our previous work and propose an improved approach. While preserving its main modules (mapping, planning and mission handler), the framework now considers motion constraints to plan feasible paths, i.e., those that meet vehicle's motion capabilities. The new framework also incorporates a risk function to avoid navigating close to nearby obstacles, and reuses the last best known solution to eliminate time-consuming pruning routines. To evaluate this approach, we use the Sparus II AUV, a torpedo-shaped vehicle performing autonomous missions in a 2-dimensional workspace. We validate the framework's new features by solving tasks in both simulation and real-world in-water trials and comparing results with our previous approach.
Juan David Hernández, Mark Moll, Eduard Vidal, Marc Carreras, Lydia E. Kavraki
IROS2
2016 A General Algorithm for Time-Optimal Trajectory Generation Subject to Minimum and Maximum Constraints
Stephen D. Butler, Mark Moll, Lydia E. Kavraki
WAFR2
2015 Structure-guided selection of Specificity Determining Positions in the human kinome
abstract
It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. This is also the case for inhibitors of many other protein families. A better understanding of binding selectivity would enhance the design of drugs that target only a subfamily, thereby minimizing possible side-effects. The increased availability of protein 3D structures has made it possible to study the structural variation within a given protein family. However, not every structural variation is related to binding specificity. We propose a greedy algorithm that computes a subset of residue positions in a multiple sequence alignment such that structural and chemical variation in those positions helps explain known binding affinities. By providing this information, the main purpose of the algorithm is to provide experimentalists with possible insights into how the selectivity profile of certain inhibitors is achieved, which is useful for lead optimization. In addition, the algorithm can also be used to predict binding affinities for structures whose affinity for a given inhibitor is unknown. The algorithm's performance is demonstrated using an extensive dataset for the human kinome, which includes a large and important set of drug targets. We show that the binding affinity of 38 different kinase inhibitors can be explained with consistently high precision and accuracy using the variation of at most six residue positions in the kinome binding site.
Mark Moll, Paul W. Finn, Lydia E. Kavraki
BIBM1
2015 Improving protein conformational sampling by using guiding projections
abstract
Sampling-based motion planning algorithms from the field of robotics have been very successful in exploring the conformational space of proteins. However, studying the flexibility of large proteins with hundreds or thousands of Degrees of Freedom (DoFs) remains a big challenge. Large proteins are also highly-constrained systems, which makes them more challenging for standard robotic approaches. So-called "expansive" motion planning algorithms were specifically developed to address highly-dimensional and highly-constrained problems. Many such planners employ a low-dimensional projection to estimate exploration coverage and direct their search based on this information. We believe that such a projection plays an essential role in the success of these planners. This paper shows how the low-dimensional projection used by expansive planners can be tailored with respect to a given molecular system to enhance the process of conformational sampling. We introduce a methodology to generate an expert projection using any available information about a given protein. We evaluate this methodology on several conformational search problems involving proteins with hundreds of DoFs. Our experiments demonstrate that incorporating expert knowledge into the projection can significantly benefit the exploration process.
Anastasia Novinskaya, Didier Devaurs, Mark Moll, Lydia E. Kavraki
BIBM3
2015 Experience-based planning with sparse roadmap spanners
abstract
We present an experience-based planning framework called Thunder that learns to reduce computation time required to solve high-dimensional planning problems in varying environments. The approach is especially suited for large configuration spaces that include many invariant constraints, such as those found with whole body humanoid motion planning. Experiences are generated using probabilistic sampling and stored in a sparse roadmap spanner (SPARS), which provides asymptotically near-optimal coverage of the configuration space, making storing, retrieving, and repairing past experiences very efficient with respect to memory and time. The Thunder framework improves upon past experience-based planners by storing experiences in a graph rather than in individual paths, eliminating redundant information, providing more opportunities for path reuse, and providing a theoretical limit to the size of the experience graph. These properties also lead to improved handling of dynamically changing environments, reasoning about optimal paths, and reducing query resolution time. The approach is demonstrated on a 30 degrees of freedom humanoid robot and compared with the Lightning framework, an experience-based planner that uses individual paths to store past experiences. In environments with variable obstacles and stability constraints, experiments show that Thunder is on average an order of magnitude faster than Lightning and planning from scratch. Thunder also uses 98.8% less memory to store its experiences after 10,000 trials when compared to Lightning. Our framework is implemented and freely available in the Open Motion Planning Library.
Dave Coleman, Ioan Alexandru Sucan, Mark Moll, Kei Okada, Nikolaus Correll
ICRA3
2015 A heuristic approach to finding diverse short paths
abstract
We present an algorithm that seeks to find a set of diverse, short paths through a roadmap graph. The usefulness of a such a set is illustrated in robotic motion planning and routing applications wherein a precomputed roadmap of the environment is partially invalidated by some change, for example, relocation of obstacles or reconfiguration of the robot. Our algorithm employs the heuristic that nearby configurations are likely to be invalidated by the same change. To find diverse short paths, the algorithm finds the shortest detour avoiding a collection of balls imposed on the graph as simulated obstacles. Different collections yield different short paths. Paths may then be checked for validity as a cheap alternative to checking or reconstructing the entire roadmap. We describe a formal definition of path set diversity and several measures on which to evaluate our algorithm. We compare the speed and quality of our heuristic algorithm's results against an exact algorithm that computes the optimally shortest set of paths on the roadmap having a minimum diversity. We show that, with tolerable loss in shortness, we produce equally diverse path sets orders of magnitude more quickly.
Mark Moll, Lydia E. Kavraki
ICRA2
2015 Extending the Applicability of POMDP Solutions to Robotic Tasks
abstract
Partially observable Markov decision processes (POMDPs) are used in many robotic task classes from soccer to household chores. Determining an approximately optimal action policy for POMDPs is PSPACE-complete, and the exponential growth of computation time prohibits solving large tasks. This paper describes two techniques to extend the range of robotic tasks that can be solved using a POMDP. Our first technique reduces the motion constraints of a robot and, then, uses state-of-the-art robotic motion planning techniques to respect the true motion constraints at runtime. We then propose a novel task decomposition that can be applied to some indoor robotic tasks. This decomposition transforms a long time horizon task into a set of shorter tasks. We empirically demonstrate the performance gain provided by these two techniques through simulated execution in a variety of environments. Comparing a direct formulation of a POMDP to solving our proposed reductions, we conclude that the techniques proposed in this paper can provide significant enhancement to current POMDP solution techniques, extending the POMDP instances that can be solved to include large continuous-state robotic tasks.
Devin K. Grady, Mark Moll, Lydia E. Kavraki
IEEE Trans. Robotics2
2014 Optimal and Efficient Stochastic Motion Planning in Partially-Known Environments
abstract
A framework capable of computing optimal control policies for a continuous system in the presence of both action and environment uncertainty is presented in this work. The framework decomposes the planning problem into two stages: an offline phase that reasons only over action uncertainty and an online phase that quickly reacts to the uncertain environment. Offline, a bounded-parameter Markov decision process (BMDP) is employed to model the evolution of the stochastic system over a discretization of the environment. Online, an optimal control policy over the BMDP is computed. Upon the discovery of an unknown environment feature during policy execution, the BMDP is updated and the optimal control policy is efficiently recomputed. Depending on the desired quality of the control policy, a suite of methods is presented to incorporate new information into the BMDP with varying degrees of detail online. Experiments confirm that the framework recomputes high-quality policies in seconds and is orders of magnitude faster than existing methods.
Ryan Luna, Morteza Lahijanian, Mark Moll, Lydia E. Kavraki
AAAI3
2014 Fast stochastic motion planning with optimality guarantees using local policy reconfiguration
abstract
This work presents a framework for fast reconfiguration of local control policies for a stochastic system to satisfy a high-level task specification. The motion of the system is abstracted to a class of uncertain Markov models known as bounded-parameter Markov decision processes (BMDPs). During the abstraction, an efficient sampling-based method for stochastic optimal control is used to construct several policies within a discrete region of the state space in order for the system to transit between neighboring regions. A BMDP is then used to find an optimal strategy over the local policies by maximizing a continuous reward function; a new policy can be computed quickly if the reward function changes. The efficacy of the framework is demonstrated using a sequence of online tasks, showing that highly desirable policies can be obtained by reconfiguring existing local policies in just a few seconds.
Ryan Luna, Morteza Lahijanian, Mark Moll, Lydia E. Kavraki
ICRA3
2014 SMT-based synthesis of integrated task and motion plans from plan outlines
abstract
We present a new approach to integrated task and motion planning (ITMP) for robots performing mobile manipulation. In our approach, the user writes a high-level specification that captures partial knowledge about a mobile manipulation setting. In particular, this specification includes a plan outline that syntactically defines a space of plausible integrated plans, a set of logical requirements that the generated plan must satisfy, and a description of the physical space that the robot manipulates. A synthesis algorithm is now used to search for an integrated plan that falls within the space defined by the plan outline, and also satisfies all requirements. Our synthesis algorithm complements continuous motion planning algorithms with calls to a Satisfiability Modulo Theories (SMT) solver. From the scene description, a motion planning algorithm is used to construct a placement graph, an abstraction of a manipulation graph whose paths represent feasible, low-level motion plans. An SMT-solver is now used to symbolically explore the space of all integrated plans that correspond to paths in the placement graph, and also satisfy the constraints demanded by the plan outline and the requirements. Our approach is implemented in a system called Ro-bosynth. We have evaluated Robosynth on a generalization of an ITMP problem investigated in prior work. The experiments demonstrate that our method is capable of generating integrated plans for a number of interesting variations on the problem.
Srinivas Nedunuri, Sailesh Prabhu, Mark Moll, Swarat Chaudhuri, Lydia E. Kavraki
ICRA3
2014 Asymptotically Optimal Stochastic Motion Planning with Temporal Goals
Ryan Luna, Morteza Lahijanian, Mark Moll, Lydia E. Kavraki
WAFR3
2013 Resolution Independent Density Estimation for motion planning in high-dimensional spaces
abstract
This paper presents a new motion planner, Search Tree with Resolution Independent Density Estimation (STRIDE), designed for rapid exploration and path planning in high-dimensional systems (greater than 10). A Geometric Near-neighbor Access Tree (GNAT) is maintained to estimate the sampling density of the configuration space, allowing an implicit, resolution-independent, Voronoi partitioning to provide sampling density estimates, naturally guiding the planner towards unexplored regions of the configuration space. This planner is capable of rapid exploration in the full dimension of the configuration space and, given that a GNAT requires only a valid distance metric, STRIDE is largely parameter-free. Extensive experimental results demonstrate significant dimension-dependent performance improvements over alternative state-of-the-art planners. In particular, high-dimensional systems where the free space is mostly defined by narrow passages were found to yield the greatest performance improvements. Experimental results are shown for both a classical 6-dimensional problem and those for which the dimension incrementally varies from 3 to 27.
Bryant Gipson, Mark Moll, Lydia E. Kavraki
ICRA2
2013 Automated model approximation for robotic navigation with POMDPs
abstract
Partially-Observable Markov Decision Processes (POMDPs) are a problem class with significant applicability to robotics when considering the uncertainty present in the real world, however, they quickly become intractable for large state and action spaces. A method to create a less complex but accurate action model approximation is proposed and evaluated using a state-of-the-art POMDP solver. We apply this general and powerful formulation to a robotic navigation task under state and sensing uncertainty. Results show that this method can provide a useful action model that yields a policy with similar overall expected reward compared to the true action model, often with significant computational savings. In some cases, our reduced complexity model can solve problems where the true model is too complex to find a policy that accomplishes the task. We conclude that this technique of building problem-dependent approximations can provide significant computational advantages and can help expand the complexity of problems that can be considered using current POMDP techniques.
Devin K. Grady, Mark Moll, Lydia E. Kavraki
ICRA2
2013 Anytime solution optimization for sampling-based motion planning
abstract
Recent work in sampling-based motion planning has yielded several different approaches for computing good quality paths in high degree of freedom systems: path shortcutting methods that attempt to shorten a single solution path by connecting non-consecutive configurations, a path hybridization technique that combines portions of two or more solutions to form a shorter path, and asymptotically optimal algorithms that converge to the shortest path over time. This paper presents an extensible meta-algorithm that incorporates a traditional sampling-based planning algorithm with offline path shortening techniques to form an anytime algorithm which exhibits competitive solution lengths to the best known methods and optimizers. A series of experiments involving rigid motion and complex manipulation are performed as well as a comparison with asymptotically optimal methods which show the efficacy of the proposed scheme, particularly in high-dimensional spaces.
Ryan Luna, Ioan Alexandru Sucan, Mark Moll, Lydia E. Kavraki
ICRA3
2013 Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome
abstract
The protein kinases are a large family of enzymes that play fundamental roles in propagating signals within the cell. Because of the high degree of binding site similarity shared among protein kinases, designing drug compounds with high specificity among the kinases has proven difficult. However, computational approaches to comparing the 3-dimensional geometry and physicochemical properties of key binding site residue positions have been shown to be informative of inhibitor selectivity. The Combinatorial Clustering Of Residue Position Subsets (ccorps) method, introduced here, provides a semi-supervised learning approach for identifying structural features that are correlated with a given set of annotation labels. Here, ccorps is applied to the problem of identifying structural features of the kinase atp binding site that are informative of inhibitor binding. ccorps is demonstrated to make perfect or near-perfect predictions for the binding affinity profile of 8 of the 38 kinase inhibitors studied, while only having overall poor predictive ability for 1 of the 38 compounds. Additionally, ccorps is shown to identify shared structural features across phylogenetically diverse groups of kinases that are correlated with binding affinity for particular inhibitors; such instances of structural similarity among phylogenetically diverse kinases are also shown to not be rare among kinases. Finally, these function-specific structural features may serve as potential starting points for the development of highly specific kinase inhibitors.
Drew H. Bryant, Mark Moll, Paul W. Finn, Lydia E. Kavraki
PLoS Comput. Biol.2
2011 The LabelHash Server and Tools for substructure-based functional annotation
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 web site is free and open to all users with no login requirements at http://labelhash.kavrakilab.org
Mark Moll, Drew H. Bryant, Lydia E. Kavraki
Bioinform.1
2010 Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
abstract
BACKGROUND: Structural variations caused by a wide range of physico-chemical 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.
Drew H. Bryant, Mark Moll, Brian Y. Chen, Viacheslav Fofanov, Lydia E. Kavraki
BMC Bioinform.2
2010 The 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.
Mark Moll, Drew H. Bryant, Lydia E. Kavraki
BMC Bioinform.1
2007 Multifunctional behaviors of reconfigurable superbot robots
abstract
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), and climbers (for inspection and repair in space). This video shows several configurations and behaviors that are new for modular and reconfigurable robots. Each SuperBot 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. The modules 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. This video shows the latest status the SuperBot modules and all these behaviors were made in just one week. The fact that SuperBot can achieve so much in so short a time demonstrates the unique value of modular, multifunctional and self-reconfigurable robots.
Wei-Min Shen, Behnam Salemi, Mark Moll, Michael Rubenstein, Harris Chi Ho Chiu, Jacob Everist, Feili Hou, Nadeesha Ranasinghe
IROS3
2006 Distributed Control of the Center of Mass of a Modular Robot
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
Mark Moll, Peter M. Will, Maks Krivokon, Wei-Min Shen
IROS1
2006 SUPERBOT: A Deployable, Multi-Functional, and Modular Self-Reconfigurable Robotic System
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
Behnam Salemi, Mark Moll, Wei-Min Shen
IROS2
2006 Path planning for deformable linear objects
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
Mark Moll, Lydia E. Kavraki
IEEE Trans. Robotics1
2005 Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length
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.
Mark Moll, Lydia E. Kavraki
ICRA1
2004 Path Planning for Minimal Energy Curves of Constant Length
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.
Mark Moll, Lydia E. Kavraki
ICRA1
2002 Dynamic Shape Reconstruction using Tactile Sensors
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.
Mark Moll, Michael A. Erdmann
ICRA1
2002 Orienting Micro-Scale Parts with Squeeze and Roll Primitives
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 micromanipulators are limited. The paper proposes a pair of manipulation primitives and a complete algorithm that addresses these challenges. We 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.
Mark Moll, Kenneth Y. Goldberg, Michael A. Erdmann, Ronald S. Fearing
ICRA1
2002 Reconstructing the Shape and Motion of Unknown Objects with Active Tactile Sensors
Mark Moll, Michael A. Erdmann
WAFR1
2001 Reconstructing shape from motion using tactile sensors
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 the 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.
Mark Moll, Michael A. Erdmann
IROS1
2000 Uncertainty Reduction Using Dynamics
abstract
For assembly tasks parts often have to be oriented before they can be put in an assembly. 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 attempt to uniquely orient a part with high probability just by varying the initial conditions. We 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 which confirm that our dynamic simulator can be used to find the true pose distribution of an object.
Mark Moll, Michael A. Erdmann
ICRA1
1997 Convergence-Zone Episodic Memory: Analysis and Simulations
Mark Moll, Risto Miikkulainen
Neural Networks1
1994 The Capacity of Convergence-Zone Episodic Memory
Mark Moll, Risto Miikkulainen, Jonathan Abbey
AAAI1