Matching Items (14)

129289-Thumbnail Image.png

Directional Sensor Control: Heuristic Approaches

Description

We study the problem of controlling multiple 2-D directional sensors while maximizing an objective function based on the information gain corresponding to multiple target locations. We assume a joint prior Gaussian distribution for the target locations. A sensor generates a

We study the problem of controlling multiple 2-D directional sensors while maximizing an objective function based on the information gain corresponding to multiple target locations. We assume a joint prior Gaussian distribution for the target locations. A sensor generates a (noisy) measurement of a target only if the target lies within the field-of-view of the sensor, where the statistical properties of the measurement error depend on the location of the target with respect to the sensor and direction of the sensor. The measurements from the sensors are fused to form global estimates of target locations. This problem is combinatorial in nature-the computation time increases exponentially with the number of sensors. We develop heuristic methods to solve the problem approximately, and provide analytical results on performance guarantees. We then improve the performance of our heuristic approaches by applying an approximate dynamic programming approach called rollout. In addition, we address a variant of the above problem, where the goal is to map the sensors to the targets while maximizing the abovementioned objective function. This mapping problem also turns out to be combinatorial in nature, so we extend one of the above heuristics to solve this mapping problem approximately. We compare the performance of these heuristic approaches analytically and empirically.

Contributors

Created

Date Created
2015-01-01

128997-Thumbnail Image.png

MultiRTA: A Simple Yet Reliable Method for Predicting Peptide Binding Affinities for Multiple Class II MHC Allotypes

Description

Background: The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune

Background: The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune diseases and allergies. However, comprehensive experimental determination of peptide-MHC binding affinities is infeasible due to MHC diversity and the large number of possible peptide sequences. Computational methods trained on the limited experimental binding data can address this challenge. We present the MultiRTA method, an extension of our previous single-type RTA prediction method, which allows the prediction of peptide binding affinities for multiple MHC allotypes not used to train the model. Thus predictions can be made for many MHC allotypes for which experimental binding data is unavailable.

Results: We fit MultiRTA models for both HLA-DR and HLA-DP using large experimental binding data sets. The performance in predicting binding affinities for novel MHC allotypes, not in the training set, was tested in two different ways. First, we performed leave-one-allele-out cross-validation, in which predictions are made for one allotype using a model fit to binding data for the remaining MHC allotypes. Comparison of the HLA-DR results with those of two other prediction methods applied to the same data sets showed that MultiRTA achieved performance comparable to NetMHCIIpan and better than the earlier TEPITOPE method. We also directly tested model transferability by making leave-one-allele-out predictions for additional experimentally characterized sets of overlapping peptide epitopes binding to multiple MHC allotypes. In addition, we determined the applicability of prediction methods like MultiRTA to other MHC allotypes by examining the degree of MHC variation accounted for in the training set. An examination of predictions for the promiscuous binding CLIP peptide revealed variations in binding affinity among alleles as well as potentially distinct binding registers for HLA-DR and HLA-DP. Finally, we analyzed the optimal MultiRTA parameters to discover the most important peptide residues for promiscuous and allele-specific binding to HLA-DR and HLA-DP allotypes.

Conclusions: The MultiRTA method yields competitive performance but with a significantly simpler and physically interpretable model compared with previous prediction methods. A MultiRTA prediction webserver is available at http://bordnerlab.org/MultiRTA.

Contributors

Created

Date Created
2010-09-24

129549-Thumbnail Image.png

A Fast Algorithm for Constructing Efficient Event-Related Functional Magnetic Resonance Imaging Designs

Description

We propose a novel, efficient approach for obtaining high-quality experimental designs for event-related functional magnetic resonance imaging (ER-fMRI), a popular brain mapping technique. Our proposed approach combines a greedy hill-climbing algorithm and a cyclic permutation method. When searching for optimal

We propose a novel, efficient approach for obtaining high-quality experimental designs for event-related functional magnetic resonance imaging (ER-fMRI), a popular brain mapping technique. Our proposed approach combines a greedy hill-climbing algorithm and a cyclic permutation method. When searching for optimal ER-fMRI designs, the proposed approach focuses only on a promising restricted class of designs with equal frequency of occurrence across stimulus types. The computational time is significantly reduced. We demonstrate that our proposed approach is very efficient compared with a recently proposed genetic algorithm approach. We also apply our approach in obtaining designs that are robust against misspecification of error correlations.

Contributors

Created

Date Created
2013-11-30

128974-Thumbnail Image.png

Prediction of the Binding Affinities of Peptides to Class II MHC Using a Regularized Thermodynamic Model

Description

Background: The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous number of possible peptide epitopes prevents

Background: The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous number of possible peptide epitopes prevents their complete experimental characterization. Computational methods can utilize the limited experimental data to predict the binding affinities of peptides to class II MHC.

Results: We have developed the Regularized Thermodynamic Average, or RTA, method for predicting the affinities of peptides binding to class II MHC. RTA accounts for all possible peptide binding conformations using a thermodynamic average and includes a parameter constraint for regularization to improve accuracy on novel data. RTA was shown to achieve higher accuracy, as measured by AUC, than SMM-align on the same data for all 17 MHC allotypes examined. RTA also gave the highest accuracy on all but three allotypes when compared with results from 9 different prediction methods applied to the same data. In addition, the method correctly predicted the peptide binding register of 17 out of 18 peptide-MHC complexes. Finally, we found that suboptimal peptide binding registers, which are often ignored in other prediction methods, made significant contributions of at least 50% of the total binding energy for approximately 20% of the peptides.

Conclusions: The RTA method accurately predicts peptide binding affinities to class II MHC and accounts for multiple peptide binding registers while reducing overfitting through regularization. The method has potential applications in vaccine design and in understanding autoimmune disorders. A web server implementing the RTA prediction method is available at http://bordnerlab.org/RTA/.

Contributors

Created

Date Created
2010-01-20

151716-Thumbnail Image.png

Batch mode active learning for multimedia pattern recognition

Description

The rapid escalation of technology and the widespread emergence of modern technological equipments have resulted in the generation of humongous amounts of digital data (in the form of images, videos and text). This has expanded the possibility of solving real

The rapid escalation of technology and the widespread emergence of modern technological equipments have resulted in the generation of humongous amounts of digital data (in the form of images, videos and text). This has expanded the possibility of solving real world problems using computational learning frameworks. However, while gathering a large amount of data is cheap and easy, annotating them with class labels is an expensive process in terms of time, labor and human expertise. This has paved the way for research in the field of active learning. Such algorithms automatically select the salient and exemplar instances from large quantities of unlabeled data and are effective in reducing human labeling effort in inducing classification models. To utilize the possible presence of multiple labeling agents, there have been attempts towards a batch mode form of active learning, where a batch of data instances is selected simultaneously for manual annotation. This dissertation is aimed at the development of novel batch mode active learning algorithms to reduce manual effort in training classification models in real world multimedia pattern recognition applications. Four major contributions are proposed in this work: $(i)$ a framework for dynamic batch mode active learning, where the batch size and the specific data instances to be queried are selected adaptively through a single formulation, based on the complexity of the data stream in question, $(ii)$ a batch mode active learning strategy for fuzzy label classification problems, where there is an inherent imprecision and vagueness in the class label definitions, $(iii)$ batch mode active learning algorithms based on convex relaxations of an NP-hard integer quadratic programming (IQP) problem, with guaranteed bounds on the solution quality and $(iv)$ an active matrix completion algorithm and its application to solve several variants of the active learning problem (transductive active learning, multi-label active learning, active feature acquisition and active learning for regression). These contributions are validated on the face recognition and facial expression recognition problems (which are commonly encountered in real world applications like robotics, security and assistive technology for the blind and the visually impaired) and also on collaborative filtering applications like movie recommendation.

Contributors

Agent

Created

Date Created
2013

152149-Thumbnail Image.png

Modeling and control for microgrids

Description

Traditional approaches to modeling microgrids include the behavior of each inverter operating in a particular network configuration and at a particular operating point. Such models quickly become computationally intensive for large systems. Similarly, traditional approaches to control do not use

Traditional approaches to modeling microgrids include the behavior of each inverter operating in a particular network configuration and at a particular operating point. Such models quickly become computationally intensive for large systems. Similarly, traditional approaches to control do not use advanced methodologies and suffer from poor performance and limited operating range. In this document a linear model is derived for an inverter connected to the Thevenin equivalent of a microgrid. This model is then compared to a nonlinear simulation model and analyzed using the open and closed loop systems in both the time and frequency domains. The modeling error is quantified with emphasis on its use for controller design purposes. Control design examples are given using a Glover McFarlane controller, gain sched- uled Glover McFarlane controller, and bumpless transfer controller which are compared to the standard droop control approach. These examples serve as a guide to illustrate the use of multi-variable modeling techniques in the context of robust controller design and show that gain scheduled MIMO control techniques can extend the operating range of a microgrid. A hardware implementation is used to compare constant gain droop controllers with Glover McFarlane controllers and shows a clear advantage of the Glover McFarlane approach.

Contributors

Agent

Created

Date Created
2013

150153-Thumbnail Image.png

Adaptive mesh generation for solution of incompressible fluid flows using high order gradients

Description

A new method of adaptive mesh generation for the computation of fluid flows is investigated. The method utilizes gradients of the flow solution to adapt the size and stretching of elements or volumes in the computational mesh as is

A new method of adaptive mesh generation for the computation of fluid flows is investigated. The method utilizes gradients of the flow solution to adapt the size and stretching of elements or volumes in the computational mesh as is commonly done in the conventional Hessian approach. However, in the new method, higher-order gradients are used in place of the Hessian. The method is applied to the finite element solution of the incompressible Navier-Stokes equations on model problems. Results indicate that a significant efficiency benefit is realized.

Contributors

Agent

Created

Date Created
2011

152833-Thumbnail Image.png

Multi-task learning and its applications to biomedical informatics

Description

In many fields one needs to build predictive models for a set of related machine learning tasks, such as information retrieval, computer vision and biomedical informatics. Traditionally these tasks are treated independently and the inference is done separately for each

In many fields one needs to build predictive models for a set of related machine learning tasks, such as information retrieval, computer vision and biomedical informatics. Traditionally these tasks are treated independently and the inference is done separately for each task, which ignores important connections among the tasks. Multi-task learning aims at simultaneously building models for all tasks in order to improve the generalization performance, leveraging inherent relatedness of these tasks. In this thesis, I firstly propose a clustered multi-task learning (CMTL) formulation, which simultaneously learns task models and performs task clustering. I provide theoretical analysis to establish the equivalence between the CMTL formulation and the alternating structure optimization, which learns a shared low-dimensional hypothesis space for different tasks. Then I present two real-world biomedical informatics applications which can benefit from multi-task learning. In the first application, I study the disease progression problem and present multi-task learning formulations for disease progression. In the formulations, the prediction at each point is a regression task and multiple tasks at different time points are learned simultaneously, leveraging the temporal smoothness among the tasks. The proposed formulations have been tested extensively on predicting the progression of the Alzheimer's disease, and experimental results demonstrate the effectiveness of the proposed models. In the second application, I present a novel data-driven framework for densifying the electronic medical records (EMR) to overcome the sparsity problem in predictive modeling using EMR. The densification of each patient is a learning task, and the proposed algorithm simultaneously densify all patients. As such, the densification of one patient leverages useful information from other patients.

Contributors

Agent

Created

Date Created
2014

153597-Thumbnail Image.png

Test-based falsification and conformance testing for cyber-physical systems

Description

In this dissertation, two problems are addressed in the verification and control of Cyber-Physical Systems (CPS):

1) Falsification: given a CPS, and a property of interest that the CPS must satisfy under all allowed operating conditions, does the CPS violate, i.e.

In this dissertation, two problems are addressed in the verification and control of Cyber-Physical Systems (CPS):

1) Falsification: given a CPS, and a property of interest that the CPS must satisfy under all allowed operating conditions, does the CPS violate, i.e. falsify, the property?

2) Conformance testing: given a model of a CPS, and an implementation of that CPS on an embedded platform, how can we characterize the properties satisfied by the implementation, given the properties satisfied by the model?

Both problems arise in the context of Model-Based Design (MBD) of CPS: in MBD, the designers start from a set of formal requirements that the system-to-be-designed must satisfy.

A first model of the system is created.

Because it may not be possible to formally verify the CPS model against the requirements, falsification tries to verify whether the model satisfies the requirements by searching for behavior that violates them.

In the first part of this dissertation, I present improved methods for finding falsifying behaviors of CPS when properties are expressed in Metric Temporal Logic (MTL).

These methods leverage the notion of robust semantics of MTL formulae: if a falsifier exists, it is in the neighborhood of local minimizers of the robustness function.

The proposed algorithms compute descent directions of the robustness function in the space of initial conditions and input signals, and provably converge to local minima of the robustness function.

The initial model of the CPS is then iteratively refined by modeling previously ignored phenomena, adding more functionality, etc., with each refinement resulting in a new model.

Many of the refinements in the MBD process described above do not provide an a priori guaranteed relation between the successive models.

Thus, the second problem above arises: how to quantify the distance between two successive models M_n and M_{n+1}?

If M_n has been verified to satisfy the specification, can it be guaranteed that M_{n+1} also satisfies the same, or some closely related, specification?

This dissertation answers both questions for a general class of CPS, and properties expressed in MTL.

Contributors

Agent

Created

Date Created
2015

153297-Thumbnail Image.png

A variational approach to planning, allocation and mapping in robot swarms using infinite dimensional models

Description

This thesis considers two problems in the control of robotic swarms. Firstly, it addresses a trajectory planning and task allocation problem for a swarm of resource-constrained robots that cannot localize or communicate with each other and that exhibit stochasticity in

This thesis considers two problems in the control of robotic swarms. Firstly, it addresses a trajectory planning and task allocation problem for a swarm of resource-constrained robots that cannot localize or communicate with each other and that exhibit stochasticity in their motion and task switching policies. We model the population dynamics of the robotic swarm as a set of advection-diffusion- reaction (ADR) partial differential equations (PDEs).

Specifically, we consider a linear parabolic PDE model that is bilinear in the robots' velocity and task-switching rates. These parameters constitute a set of time-dependent control variables that can be optimized and transmitted to the robots prior to their deployment or broadcasted in real time. The planning and allocation problem can then be formulated as a PDE-constrained optimization problem, which we solve using techniques from optimal control. Simulations of a commercial pollination scenario validate the ability of our control approach to drive a robotic swarm to achieve predefined spatial distributions of activity over a closed domain, which may contain obstacles. Secondly, we consider a mapping problem wherein a robotic swarm is deployed over a closed domain and it is necessary to reconstruct the unknown spatial distribution of a feature of interest. The ADR-based primitives result in a coefficient identification problem for the corresponding system of PDEs. To deal with the inherent ill-posedness of the problem, we frame it as an optimization problem. We validate our approach through simulations and show that reconstruction of the spatially-dependent coefficient can be achieved with considerable accuracy using temporal information alone.

Contributors

Agent

Created

Date Created
2014