Learning condition-specific networks

Condition-specific cellular networks are networks of genes and proteins that describe functional interactions among genes occurring under different environmental conditions. These networks provide a systems-level view of how the parts-list (genes and proteins) interact within the cell as it functions under changing environmental conditions and can provide insight into mechanisms of stress response, cellular differentiation and disease susceptibility. The principle challenge, however, is that cellular networks remain unknown for most conditions and must be inferred from activity levels of genes (mRNA levels) under different conditions. This dissertation aims to develop computational approaches for inferring, analyzing and validating cellular networks of genes from expression data. This dissertation first describes an unsupervised machine learning framework for inferring cellular networks using expression data from a single condition. Here cellular networks are represented as undirected probabilistic graphical models and are learned using a novel, data-driven algorithm. Then several approaches are described that can learn networks using data from multiple conditions. These approaches apply to cases where the condition may or may not be known and, therefore, must be inferred as part of the learning problem. For the latter, the condition variable is allowed to influence expression of genes at different levels of granularity: condition variable per gene to a single condition variable for all genes. Results on simulated data suggest that the algorithm performance depends greatly on the size and number of connected components of the union network of all conditions. These algorithms are also applied to microarray data from two yeast populations, quiescent and non-quiescent, isolated from glucose starved cultures. Our results suggest that by sharing information across multiple conditions, better networks can be learned for both conditions, with many more biologically meaningful dependencies, than if networks were learned for these conditions independently. In particular, processes that were shared among both cell populations were involved in response to glucose starvation, whereas the processes specific to individual populations captured characteristics unique to each population. These algorithms were also applied for learning networks across multiple species: yeast (S. cerevisiae) and fly (D. melanogaster). Preliminary analysis suggests that sharing patterns across species is much more complex than across different populations of the same species and basic metabolic processes are shared across the two species. Finally, this dissertation focuses on validation of cellular networks. This validation framework describes scores for measuring how well network learning algorithms capture higher-order dependencies. This framework also introduces a measure for evaluating the entire inferred network structure based on the extent to which similarly functioning genes are close together on the network

Stable Matching Games: Manipulation via Subgraph Isomorphism

In this paper we consider a problem that arises from a strategic issue in the stable matching model (with complete preference lists) from the viewpoint of exact-exponential time algorithms. Specifically, we study the Stable Extension of Partial Matching (SEOPM) problem, where the input consists of the complete preference lists of men, and a partial matching. The objective is to find (if one exists) a set of preference lists of women, such that the men-optimal Gale Shapley algorithm outputs a perfect matching that contains the given partial matching. Kobayashi and Matsui [Algorithmica, 2010] proved this problem is NP-complete. In this article, we give an exact-exponential algorithm for SEOPM running in time 2^{O(n)}, where n denotes the number of men/women. We complement our algorithmic finding by showing that unless Exponential Time Hypothesis (ETH) fails, our algorithm is asymptotically optimal. That is, unless ETH fails, there is no algorithm for SEOPM running in time 2^{o(n)}. Our algorithm is a non-trivial combination of a parameterized algorithm for Subgraph Isomorphism, a relationship between stable matching and finding an out-branching in an appropriate graph and enumerating non-isomorphic out-branchings

Organocatalytic Transformation of Carbon Dioxide

Catalytic transformation of CO2 into the value-added organic compounds is a very important and hot research topic in organic synthetic chemistry and green chemistry from the viewpoint of developing CO2 as C resource. Organocatalytic reactions employing metal-free organic molecules as catalysts have received unprecedented attention in recent years, with the significant advantages of the catalysts being usually inexpensive and stable, and the reactions can be performed under air. This chapter summarizes and gives an overview of the recent advances in the organocatalytic transformation of CO2 into cyclic carbonates, 2-oxazolidinones, carboxylic derivatives, as well as the synthesis of CO2-adducts and their application as CO2 carriers

Browning's Poems of Faith and Doubt

The subject of my thesis being 'Browning's Poems of Faith and Doubt' I have limited my study to those poems that deal directly with the theme of religious doubt and uncertainty. I have divided the study into six chapters. The first chapter deals with the Victorian Age and the multiple forces within it that gave rise to the sense of religious doubt. The remaining chapters are devoted to the poems dealing with matters of faith and unbelief, commencing with Christmas-Eve and Easter-Pay (1850) and concluding with Asolando: Fancies and Facts (1889). My endeavour has been to trace the theme of faith in the poems and to relate it to the development of the poet's personal belief. Chapter I deals with the conflicting forces acting on the different spheres of life-moral, political and social, and the effect of these forces upon the minds of Victorian poets. Chapter II takes up the problem concerning faith in some detail, the poem under discussion being Christmas-Eve and Easter-Day. Chapter III traces the line of development of Browning's faith by examining the monologues from Men and Women (1855) and Dramatis Personae (1864). In Chapter IV, The Ring and the Book (1868-9), my approach has been an examination of truth, partial truth and deviation from truth in the separate monologues, and to relate the entire poem to Browning's religious convictions. Chapter V deals with the poems written after 1870. Red Cotton Night-Cap Country, La Saisiaz, Ferishtah's Fancies and Parleyings with Certain People of Importance in Their Bay have consequently been discussed under the heading 'Browning's Later Poetry'. Chapter V concludes with Parleyings with Certain People of Importance in Their Day. Chapter VI deals with Asolando; Fancies and Facts (1889). In this chapter I have traced the final thoughts of Browning regarding (a) the nature of truth, (b) the nature of the next world and of the consequences that follow when a certainty of eternal life is provided to man. The poems on which attention has been centred are the Prologue, Dubiety, Rephan, Development, Reverie and the Epilogue. Dubiety deals with the necessity of doubt, Rephan and Reverie concern the problem of whether there is, or is not, an existence after death, Development deals with Browning's personal experience. The title 'Reverie' and stanza seven of the poem in particular suggest that Browning is recording his own thoughts in this poem. Consequently, I have traced a parallel between the ideas presented in the poem and the poet's personal hopes and speculations. Once more, the emphasis has fallen on the most human of all virtues---love. In the Asolando volume, Browning continues his quest, trusting to his personal convictions which in turn are based upon his capacity to love. My aim has been to show that, to Browning, life is a process of continuous growth and, consequently, the efficacy of an eternal life would remain incomplete unless the strivings were continued in the life to come. Seen thus, the Epilogue does not proclaim a final solution, but offers a set of hopeful assumptions founded on Browning's personal experiences. No simple answer has been found and the question of 'Doubt and Faith' remains open

Contextual experiences of overseas trained teachers before and after obtaining a teaching position in a public secondary school of Western Australia and South Australia in reference to their cultural perspectives

The focus of this research was an exploration of the experiences of overseas trained teachers in the public secondary schools of Western Australia and South Australia, in reference to their cultural perspectives. Due to ongoing teacher shortage in the Australian public secondary schools (Weldon, 2015) many overseas trained teachers opt to migrate to Australia in the hope of establishing a new teaching career in the country. In the process, overseas trained teachers often undergo a range of contextual experiences, some that are challenging and some rewarding. It becomes meaningful, therefore, to explore the contextual experiences of overseas trained teachers and also examine how their adaptation process to Australian public secondary schools might be affected by their cultural perspectives. The review of literature highlighted four themes which formed the conceptual framework in this research. These four themes were: contextual experiences of overseas trained teachers prior to obtaining a teaching position in a public secondary school; contextual experiences of overseas trained teachers after obtaining a teaching position in a public secondary school; effects of culture on the adaptation process of overseas trained teachers to the public secondary schools of Australia; and the contribution of overseas trained teachers to the public school sector. The epistemological approach of this research was that of constructivism. Specifically, an interpretive paradigm with a filter of symbolic interactionism was used to explore the experiences of overseas trained teachers in reference to their cultural perspectives. The chosen methodology for the study was an instrumental case study design. Methods of data collection included in-depth, semi-structured interviews of twelve overseas trained teachers from different backgrounds and researcher generated field notes. Miles and Huberman\u27s (1994) interactive model of data management was used for data display, management and analysis. Results from this inquiry indicated that overseas trained teachers face multiple contextual challenges, both before and after obtaining a teaching position in a public secondary school. Some of the major challenges faced by overseas trained teachers before obtaining a teaching position in a public secondary school are: lack of in-depth information on post immigration life in Australia; registration delays; and apparent lack of consistency in the teacher orientation process. Some of the challenges faced by overseas trained teachers after obtaining a teaching position in a public secondary school are: apparent lack of effective in-school induction and mentoring; student behaviour management issues: pedagogical and cultural dissonance; and perceived workplace harassment and discrimination. In spite of those challenges, a majority of the overseas trained teachers in the study were grateful for their multiple positive and rewarding experiences in Australia. The data highlighted that the cultural attributes of overseas trained teachers play a significant role on their adaptation process to the Australian public secondary schools. In addition, the data indicated that the challenges experienced by overseas trained teachers are influenced by the level of their familiarity with the Australian culture. Furthermore, the data also indicated that the adaptation process for overseas trained teachers from native English speaking background (NEST) was far less complicated than their counterparts from culturally and linguistically diverse and non-English speaking background (CALD/NESB). Most importantly, the research illustrated that irrespective of circumstances, personal attitude and outlook can play an important role in shaping the professional experiences of overseas trained teachers in the public secondary schools of Western Australia and South Australia

Resolute control: Forbidding candidates from winning an election is hard

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On the (Parameterized) Complexity of Almost Stable Marriage

In the Stable Marriage problem, when the preference lists are complete, all agents of the smaller side can be matched. However, this need not be true when preference lists are incomplete. In most real-life situations, where agents participate in the matching market voluntarily and submit their preferences, it is natural to assume that each agent wants to be matched to someone in his/her preference list as opposed to being unmatched. In light of the Rural Hospital Theorem, we have to relax the "no blocking pair" condition for stable matchings in order to match more agents. In this paper, we study the question of matching more agents with fewest possible blocking edges. In particular, the goal is to find a matching whose size exceeds that of a stable matching in the graph by at least t and has at most k blocking edges. We study this question in the realm of parameterized complexity with respect to several natural parameters, k,t,d, where d is the maximum length of a preference list. Unfortunately, the problem remains intractable even for the combined parameter k+t+d. Thus, we extend our study to the local search variant of this problem, in which we search for a matching that not only fulfills each of the above conditions but is "closest", in terms of its symmetric difference to the given stable matching, and obtain an FPT algorithm