Finding All Global Minimum Cuts in Practice

We present a practically efficient algorithm that finds all global minimum cuts in huge undirected graphs. Our algorithm uses a multitude of kernelization rules to reduce the graph to a small equivalent instance and then finds all minimum cuts using an optimized version of the algorithm of Nagamochi, Nakao and Ibaraki. In shared memory we are able to find all minimum cuts of graphs with up to billions of edges and millions of minimum cuts in a few minutes. We also give a new linear time algorithm to find the most balanced minimum cuts given as input the representation of all minimum cuts

Single-cell RNA sequencing for subtype discovery in Plasmodium falciparum and mammalian cells

Since the dawn of massively parallel sequencing technologies in mid-2000s their utility in profiling the expression of genes in a genome-wide fashion has matured and progressed from cell populations to individual cells. In particular, single-cell RNA sequencing (scRNA-seq) has impacted numerous domains in life sciences and hold immense promise in biology and medicine. Indeed, it has become realistic to chart the complete set of cell types and states in multicellular organisms, and projects have started to map out cell types in humans (i.e. the Human Cell Atlas project) and model organsims. In this thesis, I present the application of scRNA-seq to infectious disease and cancer as well as a computational assessment of the general possibilities and limitations of scRNA-seq for enumerating cell types and states de novo. In Paper I, we describe the ability of scRNA-seq to profile transcriptomes from individual malaria-causing P. falciparum parasites. We reveal heterogeneity even among synchronized cultures of parasites during their red blood cell life cycle. Moreover, we identify a subset of sexually differentiated P. falciparum with a distinct gene signature, likely important for parasite transmission that may be exploited for the design of transmission- blocking drugs and/or vaccines. In Paper II, I present a computational strategy to identify the magnitude of biological gene expression differences needed for accurate inference of cell identities using scRNA-seq. Interestingly, rather large differences are needed for proper cell state discrimination, irrespective of scRNA-seq protocol, implying that large number of cell states may escape detection. In Paper III, we used scRNA-seq and bulk RNA-seq to characterize the molecular programs during the later stages of lung metastasis. We demonstrate that a transition from epithelial to mesenchymal cell characteristics occurs in cancer cells during metastasis, and that the mesenchymal properties are maintained during metastasis growth extending over a week. In Paper IV we performed transcriptome analyses on stem and progenitor populations in myelodysplastic syndrome (MDS) patients. We provide evidence that the MDS stem cells and the progenitors have distinct transcriptome. Altogether, this thesis expands the applications of scRNA-seq towards parasite biology and cancer metastasis and we provide valuable insights into the abilities of current scRNA-seq technologies in mapping cell states in an unbiased fashion

Modeling and Optimizing Space Networks for Improved Communication Capacity.

There are a growing number of individual and constellation small-satellite missions seeking to download large quantities of science, observation, and surveillance data. The existing ground station infrastructure to support these missions constrains the potential data throughput because the stations are low-cost, are not always available because they are independently owned and operated, and their ability to collect data is often inefficient. The constraints of the small satellite form factor (e.g. mass, size, power) coupled with the ground network limitations lead to significant operational and communication scheduling challenges. Faced with these challenges, our goal is to maximize capacity, defined as the amount of data that is successfully downloaded from space to ground communication nodes. In this thesis, we develop models, tools, and optimization algorithms for spacecraft and ground network operations. First, we develop an analytical modeling framework and a high-fidelity simulation environment that capture the interaction of on-board satellite energy and data dynamics, ground stations, and the external space environment. Second, we perform capacity-based assessments to identify excess and deficient resources for comparison to mission-specific requirements. Third, we formulate and solve communication scheduling problems that maximize communication capacity for a satellite downloading to a network of globally and functionally heterogeneous ground stations. Numeric examples demonstrate the applicability of the models and tools to assess and optimize real-world existing and upcoming small satellite mission scenarios that communicate to global ground station networks as well as generic communication scheduling problem instances. We study properties of optimal satellite communication schedules and sensitivity of communication capacity to various deterministic and stochastic satellite vehicle and network parameters. The models, tools, and optimization techniques we develop lay the ground work for our larger goals: optimal satellite vehicle design and autonomous real-time operational scheduling of heterogeneous satellite missions and ground station networks.PhDAerospace EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/97912/1/saracs_1.pd

The 1982 NASA/ASEE Summer Faculty Fellowship Program

A NASA/ASEE Summer Faculty Fellowship Research Program was conducted to further the professional knowledge of qualified engineering and science faculty members, to stimulate an exchange of ideas between participants and NASA, to enrich and refresh the research and teaching activities of participants' institutions, and to contribute to the research objectives of the NASA Centers

Publications of the Jet Propulsion Laboratory, July 1969 - June 1970

JPL bibliography of technical reports released from July 1969 through June 197

Algorithms incorporating concurrency and caching

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 189-203).This thesis describes provably good algorithms for modern large-scale computer systems, including today's multicores. Designing efficient algorithms for these systems involves overcoming many challenges, including concurrency (dealing with parallel accesses to the same data) and caching (achieving good memory performance.) This thesis includes two parallel algorithms that focus on testing for atomicity violations in a parallel fork-join program. These algorithms augment a parallel program with a data structure that answers queries about the program's structure, on the fly. Specifically, one data structure, called SP-ordered-bags, maintains the series-parallel relationships among threads, which is vital for uncovering race conditions (bugs) in the program. Another data structure, called XConflict, aids in detecting conflicts in a transactional-memory system with nested parallel transactions. For a program with work T and span To, maintaining either data structure adds an overhead of PT, to the running time of the parallel program when executed on P processors using an efficient scheduler, yielding a total runtime of O(T1/P + PTo). For each of these data structures, queries can be answered in 0(1) time. This thesis also introduces the compressed sparse rows (CSB) storage format for sparse matrices, which allows both Ax and ATx to be computed efficiently in parallel, where A is an n x n sparse matrix with nnz > n nonzeros and x is a dense n-vector. The parallel multiplication algorithm uses e(nnz) work and ... span, yielding a parallelism of ... , which is amply high for virtually any large matrix.(cont.) Also addressing concurrency, this thesis considers two scheduling problems. The first scheduling problem, motivated by transactional memory, considers randomized backoff when jobs have different lengths. I give an analysis showing that binary exponential backoff achieves makespan V2e(6v 1- i ) with high probability, where V is the total length of all n contending jobs. This bound is significantly larger than when jobs are all the same size. A variant of exponential backoff, however, achieves makespan of ... with high probability. I also present the size-hashed backoff protocol, specifically designed for jobs having different lengths, that achieves makespan ... with high probability. The second scheduling problem considers scheduling n unit-length jobs on m unrelated machines, where each job may fail probabilistically. Specifically, an input consists of a set of n jobs, a directed acyclic graph G describing the precedence constraints among jobs, and a failure probability qij for each job j and machine i. The goal is to find a schedule that minimizes the expected makespan. I give an O(log log(min {m, n}))-approximation for the case of independent jobs (when there are no precedence constraints) and an O(log(n + m) log log(min {m, n}))-approximation algorithm when precedence constraints form disjoint chains. This chain algorithm can be extended into one that supports precedence constraints that are trees, which worsens the approximation by another log(n) factor. To address caching, this thesis includes several new variants of cache-oblivious dynamic dictionaries.(cont.) A cache-oblivious dictionary fills the same niche as a classic B-tree, but it does so without tuning for particular memory parameters. Thus, cache-oblivious dictionaries optimize for all levels of a multilevel hierarchy and are more portable than traditional B-trees. I describe how to add concurrency to several previously existing cache-oblivious dictionaries. I also describe two new data structures that achieve significantly cheaper insertions with a small overhead on searches. The cache-oblivious lookahead array (COLA) supports insertions/deletions and searches in O((1/B) log N) and O(log N) memory transfers, respectively, where B is the block size, M is the memory size, and N is the number of elements in the data structure. The xDict supports these operations in O((1/1B E1-) logB(N/M)) and O((1/)0logB(N/M)) memory transfers, respectively, where 0 < E < 1 is a tunable parameter. Also on caching, this thesis answers the question: what is the worst possible page-replacement strategy? The goal of this whimsical chapter is to devise an online strategy that achieves the highest possible fraction of page faults / cache misses as compared to the worst offline strategy. I show that there is no deterministic strategy that is competitive with the worst offline. I also give a randomized strategy based on the most recently used heuristic and show that it is the worst possible pagereplacement policy. On a more serious note, I also show that direct mapping is, in some sense, a worst possible page-replacement policy. Finally, this thesis includes a new algorithm, following a new approach, for the problem of maintaining a topological ordering of a dag as edges are dynamically inserted.(cont.) The main result included here is an O(n2 log n) algorithm for maintaining a topological ordering in the presence of up to m < n(n - 1)/2 edge insertions. In contrast, the previously best algorithm has a total running time of O(min { m3/ 2, n5/2 }). Although these algorithms are not parallel and do not exhibit particularly good locality, some of the data structural techniques employed in my solution are similar to others in this thesis.by Jeremy T. Fineman.Ph.D

A critical investigation of deaf comprehension of signed tv news interpretation

This study investigates factors hampering comprehension of sign language interpretations rendered on South African TV news bulletins in terms of Deaf viewers’ expectancy norms and corpus analysis of authentic interpretations. The research fills a gap in the emerging discipline of Sign Language Interpreting Studies, specifically with reference to corpus studies. The study presents a new model for translation/interpretation evaluation based on the introduction of Grounded Theory (GT) into a reception-oriented model. The research question is addressed holistically in terms of target audience competencies and expectations, aspects of the physical setting, interpreters’ use of language and interpreting choices. The South African Deaf community are incorporated as experts into the assessment process, thereby empirically grounding the research within the socio-dynamic context of the target audience. Triangulation in data collection and analysis was provided by applying multiple mixed data collection methods, namely questionnaires, interviews, eye-tracking and corpus tools. The primary variables identified by the study are the small picture size and use of dialect. Secondary variables identified include inconsistent or inadequate use of non-manual features, incoherent or non-simultaneous mouthing, careless or incorrect sign execution, too fast signing, loss of visibility against skin or clothing, omission of vital elements of sentence structure, adherence to source language structures, meaningless additions, incorrect referencing, oversimplification and violations of Deaf norms of restructuring, information transfer, gatekeeping and third person interpreting. The identification of these factors allows the construction of a series of testable hypotheses, thereby providing a broad platform for further research. Apart from pioneering corpus-driven sign language interpreting research, the study makes significant contributions to present knowledge of evaluative models, interpreting strategies and norms and systems of transcription and annotation.Linguistics and Modern LanguagesThesis (D. Litt.et Phil.) (Linguistics

Research reports: The 1980 NASA/ASEE Summer Faculty Fellowship Program

The Summer Faculty Fellowship Research Program objectives are: to further the professional knowledge of qualified engineering and science faculty members; to stimulate an exchange of ideas between participants and NASA; to enrich and refresh the research and teaching activities of participants and institutions; and to contribute to the research objectives at the NASA centers. The Faculty Fellows engaged in research projects commensurate with their interests and background and worked in collaboration with a NASA/MSFC colleague