BEYOND CLASSICAL CAUSAL MODELS: PATH DEPENDENCE, ENTANGLED MISSINGNESS AND GENERALIZED COARSENING

Classical causal models generally assume relatively simple settings like static observations, complete observability and independent and identically distributed (i.i.d.) data samples. For many systems of scientific interest, such assumptions are unrealistic. More recent work has explored models with complex properties including (time-invariant) temporal dynamics, data dependence, as well as missingness within the causal inference framework. Inspired by these advances, this dissertation goes beyond these classical causal inference models to explore the following complications that can arise in some causal systems – (i) path dependence, whereby systems exhibit state-specific causal relationships and a temporal evolution that could be counterfactually altered, (ii) entangled missingness, where missingness occurs in data together with causal dependence and finally, (iii) generalized coarsening, where systems entail causal processes operating at multiple timescales, and estimands of interest lie at a timescale different from that in which data is observed. In particular, we use the language of graphical causal models and discuss an important component of the causal inference pipeline, namely identification, which links the counterfactual of interest to the observed data via a set of assumptions. In some cases, we also discuss estimation, which allows us to obtain identified parameters from finite samples of data. We illustrate the use of these novel models on observational data obtained from biomedical and clinical settings

Automated Computer Program Evaluation and Projects -- Our Experiences

This paper provides a few approaches to automating computer programming and project submission tasks, that we have been following for the last six years and have found to be successful. The approaches include using CodeRunner with Learning Management System (LMS) integration for programming practice and evaluation, and Git (GitHub) for project submissions and automatic code evaluation. In this paper, we describe the details of how we set up the tools and customized those for computer science courses. Based on our experiences, we also provide a few insights on using these tools for effective learning.Comment: 14 pages, 15 figure

Stiles–Crawford effect of the first kind: assessment of photoreceptor alignments following dark patching

AbstractProperties of presumed mechanisms controlling photoreceptor alignments are partially defined. A phototropic mechanism normally dominates alignment, but do modest changes in orientations occur with dark patching? Here, new photopic Stiles–Crawford (SCE-I) determinations were made before patching (pre-patch), just after 8-days of dark-patching (post-patch), and 3 days after patch removal (recovery test). We tested at 0, 11 and 22° in the temporal retina of both eyes. Ten eyes of adult subjects were tested. SCE-I peak positions and Stile's parameter ‘rho’ were assessed. Dark-patching effects were small. Observations revealed meaningful corrective alignment overshoots with recovery in the light. Results suggest (1) the presence of multiple weak mechanisms affecting receptor alignments in the dark; (2) the phototropic mechanism to be dominant in the light; (3) the need for multiple test loci to be sampled in such studies, and (4) small changes in the SCE-I in the pupil plane can reflect meaningful events occurring at the retina

Reference Array and Design Consideration for the next-generation Event Horizon Telescope

We describe the process to design, architect, and implement a transformative enhancement of the Event Horizon Telescope (ngEHT). This program - the next-generation Event Horizon Telescope (ngEHT) - will form a networked global array of radio dishes capable of making high-fidelity real-time movies of supermassive black holes (SMBH) and their emanating jets. This builds upon the EHT principally by deploying additional modest-diameter dishes to optimized geographic locations to enhance the current global mm/submm wavelength Very Long Baseline Interferometric (VLBI) array, which has, to date, utilized mostly pre-existing radio telescopes. The ngEHT program further focuses on observing at three frequencies simultaneously for increased sensitivity and Fourier spatial frequency coverage. Here, the concept, science goals, design considerations, station siting and instrument prototyping are discussed, and a preliminary reference array to be implemented in phases is described.Comment: Submitted to the journal Galaxie

Skeletal muscle metabolic responses to physical activity are muscle type specific in a rat model of chronic kidney disease

Chronic kidney disease (CKD) leads to musculoskeletal impairments that are impacted by muscle metabolism. We tested the hypothesis that 10-weeks of voluntary wheel running can improve skeletal muscle mitochondria activity and function in a rat model of CKD. Groups included (n = 12–14/group): (1) normal littermates (NL); (2) CKD, and; (3) CKD-10 weeks of voluntary wheel running (CKD-W). At 35-weeks old the following assays were performed in the soleus and extensor digitorum longus (EDL): targeted metabolomics, mitochondrial respiration, and protein expression. Amino acid-related compounds were reduced in CKD muscle and not restored by physical activity. Mitochondrial respiration in the CKD soleus was increased compared to NL, but not impacted by physical activity. The EDL respiration was not different between NL and CKD, but increased in CKD-wheel rats compared to CKD and NL groups. Our results demonstrate that the soleus may be more susceptible to CKD-induced changes of mitochondrial complex content and respiration, while in the EDL, these alterations were in response the physiological load induced by mild physical activity. Future studies should focus on therapies to improve mitochondrial function in both types of muscle to determine if such treatments can improve the ability to adapt to physical activity in CKD