Topological Hierarchies and Decomposition: From Clustering to Persistence

Hierarchical clustering is a class of algorithms commonly used in exploratory data analysis (EDA) and supervised learning. However, they suffer from some drawbacks, including the difficulty of interpreting the resulting dendrogram, arbitrariness in the choice of cut to obtain a flat clustering, and the lack of an obvious way of comparing individual clusters. In this dissertation, we develop the notion of a topological hierarchy on recursively-defined subsets of a metric space. We look to the field of topological data analysis (TDA) for the mathematical background to associate topological structures such as simplicial complexes and maps of covers to clusters in a hierarchy. Our main results include the definition of a novel hierarchical algorithm for constructing a topological hierarchy, and an implementation of the MAPPER algorithm and our topological hierarchies in pure Python code as well as a web app dashboard for exploratory data analysis. We show that the algorithm scales well to high-dimensional data due to the use of dimensionality reduction in most TDA methods, and analyze the worst-case time complexity of MAPPER and our hierarchical decomposition algorithm. Finally, we give a use case for exploratory data analysis with our techniques

CTC and International Research and Information Systems

There is a long history of creating digital libraries of legal materials in general and of international legal materials in particular. This article highlights the history of several noteworthy examples of earlier digital libraries. It then describes the creation of the Cape Town Convention Academic Project digital library. Finally, the article applies lessons learned from the histories of the earlier libraries to analyse issues the Cape Town Convention library may face in the future

Peri-pubertal exposure to testicular hormones organizes response to novel environments and social behaviour in adult male rats

Funding was received from the Wellcome Trust ISSF (grant ID 097831/Z/11/Z) scheme, awarded to the University of St Andrews.Previous research has shown that exposure to testicular hormones during the peri-pubertal period of life has long-term, organizational effects on adult sexual behaviour and underlying neural mechanisms in laboratory rodents. However, the organizational effects of peri-pubertal testicular hormones on other aspects of behaviour and brain function are less well understood. Here, we investigated the effects of manipulating peri-pubertal testicular hormone exposure on later behavioural responses to novel environments and on hormone receptors in various brain regions that are involved in response to novelty. Male rodents generally spend less time in the exposed areas of novel environments than females, and this sex difference emerges during the peri-pubertal period. Male Lister-hooded rats (Rattus norvegicus) were castrated either before puberty or after puberty, then tested in three novel environments (elevated plus-maze, light–dark box, open field) and in an object/social novelty task in adulthood. Androgen receptor (AR), oestrogen receptor (ER1) and corticotropin-releasing factor receptor (CRF-R2) mRNA expression were quantified in the hypothalamus, hippocampus and medial amygdala. The results showed that pre-pubertally castrated males spent more time in the exposed areas of the elevated-plus maze and light–dark box than post-pubertally castrated males, and also confirmed that peri-pubertal hormone exposure influences later response to an opposite-sex conspecific. Hormone receptor gene expression levels did not differ between pre-pubertally and post-pubertally castrated males in any of the brain regions examined. This study therefore demonstrates that testicular hormone exposure during the peri-pubertal period masculinizes later response to novel environments, although the neural mechanisms remain to be fully elucidated.Publisher PDFPeer reviewe

New experiments and a model-driven approach for interpreting Middle Stone Age Lithic Point Function using the Edge Damage Distribution Method

The Middle Stone Age (MSA) is associated with early evidence for symbolic material culture and complex technological innovations. However, one of the most visible aspects of MSA technologies are unretouched triangular stone points that appear in the archaeological record as early as 500,000 years ago in Africa and persist throughout the MSA. How these tools were being used and discarded across a changing Pleistocene landscape can provide insight into how MSA populations prioritized technological and foraging decisions. Creating inferential links between experimental and archaeological tool use helps to establish prehistoric tool function, but is complicated by the overlaying of post-depositional damage onto behaviorally worn tools. Taphonomic damage patterning can provide insight into site formation history, but may preclude behavioral interpretations of tool function. Here, multiple experimental processes that form edge damage on unretouched lithic points from taphonomic and behavioral processes are presented. These provide experimental distributions of wear on tool edges from known processes that are then quantitatively compared to the archaeological patterning of stone point edge damage from three MSA lithic assemblages--Kathu Pan 1, Pinnacle Point Cave 13B, and Die Kelders Cave 1. By using a model-fitting approach, the results presented here provide evidence for variable MSA behavioral strategies of stone point utilization on the landscape consistent with armature tips at KP1, and cutting tools at PP13B and DK1, as well as damage contributions from post-depositional sources across assemblages. This study provides a method with which landscape-scale questions of early modern human tool-use and site-use can be addressed

Examining Affect in Psychometric Schizotypy Using Behavioral Experience Sampling Methodology

poster abstractIn schizophrenia, patients often experience more negative emotions in the form of anger, sadness, and anxiety when compared to the general population. One unique way of measuring affect outside of the laboratory has been to use Experience Sampling Methods (ESM) to assess how individuals perceive current emotions in their daily life. However, these methods are still subject to self-report bias. In this study, we examined affect using traditional ESM methods while also implementing the Electronically Activated Recorder (EAR), a behaviorally-based ESM measure that provides real-world assessments of speech. To examine the EAR, we evaluated affect in schizotypy and non-schizotypy groups. Research shows that schizophrenia-like experiences, like increased negative affect, run along a continuum. Schizotypy is a category on the healthier end of the schizophrenia-spectrum; it applies to individuals who are thought to have a putative genetic liability for schizophrenia. Using the Linguistic Inquiry and Word Count (LIWC), we compared affective word usage among schizotypy and non-schizotypy groups to provide a real-world, behavioral ESM measure. When traditional ESM measures were used, we found individuals with schizotypy reported less negative emotions compared to the non-schizotypy group, but results did not reach the level of significance. We also observed that non-schizotypy individuals reported slightly higher positive emotions, and the schizotypy group reported slightly higher negative emotions. A similar pattern was observed when examining EAR data. Overall, results suggested that traditional and behavioral ESM measures of affect had significant overlap. In general, those with schizotypy demonstrated slightly more negative emotion and slightly less positive emotion than the non-schizotypy group. Findings did not reach the level of significance. This study demonstrates that the EAR provides behavioral ratings of affect that are on par with traditional ESM ratings. Future work should examine the EAR at different points on the schizophrenia-spectrum