761 research outputs found

    2023-2024 Graduate School Catalog

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    You and your peers represent more than 67 countries and your shared scholarship spans 140 programs - from business administration and biomedical engineering to history, horticulture, musical performance, marine science, and more. Your ideas and interests will inform public health, create opportunities for art and innovation, contribute to the greater good, and positively impact economic development in Maine and beyond

    Beyond Quantity: Research with Subsymbolic AI

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    How do artificial neural networks and other forms of artificial intelligence interfere with methods and practices in the sciences? Which interdisciplinary epistemological challenges arise when we think about the use of AI beyond its dependency on big data? Not only the natural sciences, but also the social sciences and the humanities seem to be increasingly affected by current approaches of subsymbolic AI, which master problems of quality (fuzziness, uncertainty) in a hitherto unknown way. But what are the conditions, implications, and effects of these (potential) epistemic transformations and how must research on AI be configured to address them adequately

    Silence that matters: HIV Nondisclosure and the limits of Consent

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    This dissertation explores the legal and sociocultural linguistic implications of the Supreme Court of Canada’s decision in R. v. Cuerrier (1998) where it was ruled that the nondisclosure of HIV-positive status could vitiate otherwise freely given consent, resulting in the sexual act being deemed aggravated assault or aggravated sexual assault. Specifically, I am interested in how the logic of HIV nondisclosure law is deeply interwoven with heteronormative assumptions about sexuality and how consent is negotiated in practice. To interrogate the often-unstated assumptions underlying the Court’s decision, I examine how the legal imperative to speak about one’s HIV status is resolved within gay sexual spaces (where consent is customarily negotiated wordlessly). My goal, in doing this, is to identify how these competing imperatives (i.e., the legal obligation to speak and a custom of staying silent) are resolved within cultural and linguistic practice. In this study, I use autoethnography, semi-structured interviews, and legal analysis to examine the legal and political implications of the criminalization of HIV nondisclosure. My findings suggest that existing approaches to HIV nondisclosure in criminal law are insufficiently attentive to how regulatory apparatuses, including social norms, shape the interpretation of sexual practices. This often results in courts confounding sexual diversity with sexual violence, which continues a long-held tradition of criminalizing sexual minorities. Guided by these insights, my legal analysis challenges the logic of HIV nondisclosure law more directly. Specifically, I argue that privileging putatively “rational” faculties, like autonomy, in the regulation of sexualities fails to adequately capture the complexities embodied in sex and negotiations of sexual consent. As an alternative, I offer a new model—what I call bodily subjectivity—to more fully capture the visceral harm enacted by acts of sexual assault

    Theme Aspect Argumentation Model for Handling Fallacies

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    From daily discussions to marketing ads to political statements, information manipulation is rife. It is increasingly more important that we have the right set of tools to defend ourselves from manipulative rhetoric, or fallacies. Suitable techniques to automatically identify fallacies are being investigated in natural language processing research. However, a fallacy in one context may not be a fallacy in another context, so there is also a need to explain how and why it has come to be judged a fallacy. For the explainable fallacy identification, we present a novel approach to characterising fallacies through formal constraints, as a viable alternative to more traditional fallacy classifications by informal criteria. To achieve this objective, we introduce a novel context-aware argumentation model, the theme aspect argumentation model, which can do both: the modelling of a given argumentation as it is expressed (rhetorical modelling); and a deeper semantic analysis of the rhetorical argumentation model. By identifying fallacies with formal constraints, it becomes possible to tell whether a fallacy lurks in the modelled rhetoric with a formal rigour. We present core formal constraints for the theme aspect argumentation model and then more formal constraints that improve its fallacy identification capability. We show and prove the consequences of these formal constraints. We then analyse the computational complexities of deciding the satisfiability of the constraints

    Is the metric signature really electromagnetic in origin?

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    The program of “pre-metric electromagnetism,” developed by Hehl and collaborators, seeks to derive certain aspects of the spacetime geometry of the world (in particular, metrical signature) from elementary, empirically informed axioms regarding electromagnetic fields. The program should, therefore, be of profound interest to both empiricist and relationalist philosophers. Up to this point, however, pre-metric electromagnetism has received very little attention within the philosophy of physics; this paper seeks to rectify the situation, by engaging in a detailed foundational study of the program. In particular, in this article, we (a) present a streamlined version of the program, identifying key input assumptions, (b) consider the connections between this program and other notable projects in the foundations of spacetime theories, for example, (i) the dynamical approach to spacetime and (ii) constructive axiomatics, and (c) consider in detail the extent to which this program can be generalized beyond electromagnetism. In achieving these tasks, we hope to open up to philosophers an extraordinarily fecund—but lamentably little-known!—project within the foundations of physics

    Higher-order interactions in single-cell gene expression: towards a cybergenetic semantics of cell state

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    Finding and understanding patterns in gene expression guides our understanding of living organisms, their development, and diseases, but is a challenging and high-dimensional problem as there are many molecules involved. One way to learn about the structure of a gene regulatory network is by studying the interdependencies among its constituents in transcriptomic data sets. These interdependencies could be arbitrarily complex, but almost all current models of gene regulation contain pairwise interactions only, despite experimental evidence existing for higher-order regulation that cannot be decomposed into pairwise mechanisms. I set out to capture these higher-order dependencies in single-cell RNA-seq data using two different approaches. First, I fitted maximum entropy (or Ising) models to expression data by training restricted Boltzmann machines (RBMs). On simulated data, RBMs faithfully reproduced both pairwise and third-order interactions. I then trained RBMs on 37 genes from a scRNA-seq data set of 70k astrocytes from an embryonic mouse. While pairwise and third-order interactions were revealed, the estimates contained a strong omitted variable bias, and there was no statistically sound and tractable way to quantify the uncertainty in the estimates. As a result I next adopted a model-free approach. Estimating model-free interactions (MFIs) in single-cell gene expression data required a quasi-causal graph of conditional dependencies among the genes, which I inferred with an MCMC graph-optimisation algorithm on an initial estimate found by the Peter-Clark algorithm. As the estimates are model-free, MFIs can be interpreted either as mechanistic relationships between the genes, or as substructures in the cell population. On simulated data, MFIs revealed synergy and higher-order mechanisms in various logical and causal dynamics more accurately than any correlation- or information-based quantities. I then estimated MFIs among 1,000 genes, at up to seventh-order, in 20k neurons and 20k astrocytes from two different mouse brain scRNA-seq data sets: one developmental, and one adolescent. I found strong evidence for up to fifth-order interactions, and the MFIs mostly disambiguated direct from indirect regulation by preferentially coupling causally connected genes, whereas correlations persisted across causal chains. Validating the predicted interactions against the Pathway Commons database, gene ontology annotations, and semantic similarity, I found that pairwise MFIs contained different but a similar amount of mechanistic information relative to networks based on correlation. Furthermore, third-order interactions provided evidence of combinatorial regulation by transcription factors and immediate early genes. I then switched focus from mechanism to population structure. Each significant MFI can be assigned a set of single cells that most influence its value. Hierarchical clustering of the MFIs by cell assignment revealed substructures in the cell population corresponding to diverse cell states. This offered a new, purely data-driven view on cell states because the inferred states are not required to localise in gene expression space. Across the four data sets, I found 69 significant and biologically interpretable cell states, where only 9 could be obtained by standard approaches. I identified immature neurons among developing astrocytes and radial glial cells, D1 and D2 medium spiny neurons, D1 MSN subtypes, and cell-cycle related states present across four data sets. I further found evidence for states defined by genes associated to neuropeptide signalling, neuronal activity, myelin metabolism, and genomic imprinting. MFIs thus provide a new, statistically sound method to detect substructure in single-cell gene expression data, identifying cell types, subtypes, or states that can be delocalised in gene expression space and whose hierarchical structure provides a new view on the semantics of cell state. The estimation of the quasi-causal graph, the MFIs, and inference of the associated states is implemented as a publicly available Nextflow pipeline called Stator

    Learning Neural Graph Representations in Non-Euclidean Geometries

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    The success of Deep Learning methods is heavily dependent on the choice of the data representation. For that reason, much of the actual effort goes into Representation Learning, which seeks to design preprocessing pipelines and data transformations that can support effective learning algorithms. The aim of Representation Learning is to facilitate the task of extracting useful information for classifiers and other predictor models. In this regard, graphs arise as a convenient data structure that serves as an intermediary representation in a wide range of problems. The predominant approach to work with graphs has been to embed them in an Euclidean space, due to the power and simplicity of this geometry. Nevertheless, data in many domains exhibit non-Euclidean features, making embeddings into Riemannian manifolds with a richer structure necessary. The choice of a metric space where to embed the data imposes a geometric inductive bias, with a direct impact on the performance of the models. This thesis is about learning neural graph representations in non-Euclidean geometries and showcasing their applicability in different downstream tasks. We introduce a toolkit formed by different graph metrics with the goal of characterizing the topology of the data. In that way, we can choose a suitable target embedding space aligned to the shape of the dataset. By virtue of the geometric inductive bias provided by the structure of the non-Euclidean manifolds, neural models can achieve higher performances with a reduced parameter footprint. As a first step, we study graphs with hierarchical structures. We develop different techniques to derive hierarchical graphs from large label inventories. Noticing the capacity of hyperbolic spaces to represent tree-like arrangements, we incorporate this information into an NLP model through hyperbolic graph embeddings and showcase the higher performance that they enable. Second, we tackle the question of how to learn hierarchical representations suited for different downstream tasks. We introduce a model that jointly learns task-specific graph embeddings from a label inventory and performs classification in hyperbolic space. The model achieves state-of-the-art results on very fine-grained labels, with a remarkable reduction of the parameter size. Next, we move to matrix manifolds to work on graphs with diverse structures and properties. We propose a general framework to implement the mathematical tools required to learn graph embeddings on symmetric spaces. These spaces are of particular interest given that they have a compound geometry that simultaneously contains Euclidean as well as hyperbolic subspaces, allowing them to automatically adapt to dissimilar features in the graph. We demonstrate a concrete implementation of the framework on Siegel spaces, showcasing their versatility on different tasks. Finally, we focus on multi-relational graphs. We devise the means to translate Euclidean and hyperbolic multi-relational graph embedding models into the space of symmetric positive definite (SPD) matrices. To do so we develop gyrocalculus in this geometry and integrate it with the aforementioned framework

    Is the metric signature really electromagnetic in origin?

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    The programme of `pre-metric electromagnetism', developed by Hehl and collaborators, seeks to derive certain aspects of the spacetime geometry of the world (in particular, metrical signature) from elementary, empirically-informed axioms regarding electromagnetic fields. The programme should, therefore, be of profound interest to both empiricist and relationalist philosophers. Up to this point, however, pre-metric electromagnetism has received very little attention within the philosophy of physics; this paper seeks to rectify the situation, by engaging in a detailed foundational study of the programme. In particular, in this article, we (a) present a streamlined version of the programme, identifying key input assumptions, (b) consider the connections between this programme and other notable projects in the foundations of spacetime theories, e.g. (i) the dynamical approach to spacetime and (ii) constructive axiomatics, and (c) consider in detail the extent to which this programme can be generalised beyond electromagnetism. In achieving these tasks, we hope to open up to philosophers an extraordinarily fecund---but lamentably little-known!---project within the foundations of physics

    On Making in the Digital Humanities

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    On Making in the Digital Humanities fills a gap in our understanding of digital humanities projects and craft by exploring the processes of making as much as the products that arise from it. The volume draws focus to the interwoven layers of human and technological textures that constitute digital humanities scholarship. To do this, it assembles a group of well-known, experienced and emerging scholars in the digital humanities to reflect on various forms of making (we privilege here the creative and applied side of the digital humanities). The volume honours the work of John Bradley, as it is totemic of a practice of making that is deeply informed by critical perspectives. A special chapter also honours the profound contributions that this volume’s co-editor, Stéfan Sinclair, made to the creative, applied and intellectual praxis of making and the digital humanities. Stéfan Sinclair passed away on 6 August 2020. The chapters gathered here are individually important, but together provide a very human view on what it is to do the digital humanities, in the past, present and future. This book will accordingly be of interest to researchers, teachers and students of the digital humanities; creative humanities, including maker spaces and culture; information studies; the history of computing and technology; and the history of science and the humanities

    Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

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    Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science
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