The Document Similarity Network: A Novel Technique for Visualizing Relationships in Text Corpora

With the abundance of written information available online, it is useful to be able to automatically synthesize and extract meaningful information from text corpora. We present a unique method for visualizing relationships between documents in a text corpus. By using Latent Dirichlet Allocation to extract topics from the corpus, we create a graph whose nodes represent individual documents and whose edge weights indicate the distance between topic distributions in documents. These edge lengths are then scaled using multidimensional scaling techniques, such that more similar documents are clustered together. Applying this method to several datasets, we demonstrate that these graphs are useful in visually representing high-dimensional document clustering in topic-space

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called ‘K*Sync’, in which alignments are generated by dynamic programming using a scoring function that combines information on many protein features, including a novel measure of how obligate a sequence region is to the protein fold. By systematically varying the weights on the different features that contribute to the alignment score, we generate very large ensembles of diverse alignments, each optimal under a particular constellation of weights. We investigate a variety of approaches to select the best models from the ensemble, including consensus of the alignments, a hydrophobic burial measure, low- and high-resolution energy functions, and combinations of these evaluation methods. The effect on model quality and selection resulting from loop modeling and backbone optimization is also studied. The performance of the method on a benchmark set is reported and shows the approach to be effective at both generating and selecting accurate alignments. The method serves as the foundation of the homology modeling module in the Robetta server

FlexType: Flexible Text Input with a Small Set of Input Gestures

In many situations, it may be impractical or impossible to enter text by selecting precise locations on a physical or touchscreen keyboard. We present an ambiguous keyboard with four character groups that has potential applications for eyes-free text entry, as well as text entry using a single switch or a brain-computer interface. We develop a procedure for optimizing these character groupings based on a disambiguation algorithm that leverages a long-span language model. We produce both alphabetically-constrained and unconstrained character groups in an offline optimization experiment and compare them in a longitudinal user study. Our results did not show a significant difference between the constrained and unconstrained character groups after four hours of practice. As expected, participants had significantly more errors with the unconstrained groups in the first session, suggesting a higher barrier to learning the technique. We therefore recommend the alphabetically-constrained character groups, where participants were able to achieve an average entry rate of 12.0 words per minute with a 2.03% character error rate using a single hand and with no visual feedback

On the cusp of cusps: a universal model for extreme scattering events in the ISM

The scattering structures in the ISM responsible for so-called ``extreme scattering events" (ESEs), observed in quasars and pulsars, remain enigmatic. Current models struggle to explain the high-frequency light curves of ESEs, and a recent analysis of a double lensing event in PSR\,B0834+06 reveals features of ESEs that may also be challenging to accommodate via existing models. We propose that these features arise naturally when the lens has a cusp-like profile, described by the elementary $A_3$ cusp catastrophe. This is an extension of previous work describing pulsar scintillation as arising from $A_2$ fold catastrophes in thin, corrugated plasma sheets along the line of sight. We call this framework of describing the lens potentials via elementary catastrophes ``doubly catastrophic lensing", as catastrophes (e.g. folds and cusps) have long been used to describe universal features in the light curves of lensing events that generically manifest, regardless of the precise details of the lens. Here, we argue that the lenses themselves may be described by these same elementary structures. If correct, the doubly catastrophic lensing framework would provide a unified description of scintillation and ESEs, where the lenses responsible for these scattering phenomena are universal and can be fully described by a small number of unfolding parameters. This could enable their application as giant cosmic lenses for precision measurements of coherent sources, including FRBs and pulsars.Comment: 10 pages, 10 figure

Disentangling Perceptions of Offensiveness: Cultural and Moral Correlates

Perception of offensiveness is inherently subjective, shaped by the lived experiences and socio-cultural values of the perceivers. Recent years have seen substantial efforts to build AI-based tools that can detect offensive language at scale, as a means to moderate social media platforms, and to ensure safety of conversational AI technologies such as ChatGPT and Bard. However, existing approaches treat this task as a technical endeavor, built on top of data annotated for offensiveness by a global crowd workforce without any attention to the crowd workers' provenance or the values their perceptions reflect. We argue that cultural and psychological factors play a vital role in the cognitive processing of offensiveness, which is critical to consider in this context. We re-frame the task of determining offensiveness as essentially a matter of moral judgment -- deciding the boundaries of ethically wrong vs. right language within an implied set of socio-cultural norms. Through a large-scale cross-cultural study based on 4309 participants from 21 countries across 8 cultural regions, we demonstrate substantial cross-cultural differences in perceptions of offensiveness. More importantly, we find that individual moral values play a crucial role in shaping these variations: moral concerns about Care and Purity are significant mediating factors driving cross-cultural differences. These insights are of crucial importance as we build AI models for the pluralistic world, where the values they espouse should aim to respect and account for moral values in diverse geo-cultural contexts

Scintillated microlensing: measuring cosmic distances with fast radio bursts

We propose a novel means of directly measuring cosmological distances using scintillated microlensing of fast radio bursts (FRBs). In standard strong lensing measurements of cosmic expansion, the main source of systematic uncertainty lies in modeling the mass profile of galactic halos. Using extra-galactic stellar microlensing to measure the Hubble constant avoids this systematic uncertainty as the lens potential of microlenses depends only on a single parameter: the mass of the lens. FRBs, which may achieve nanosecond precision on lensing time delays, are well-suited to precision measurements of stellar microlensing, for which the time delays are on the order of milliseconds. However, typical angular separations between the microlensed images on the order of microarcseconds make the individual images impossible to spatially resolve with ground-based telescopes. We propose leveraging scintillation in the ISM to resolve the microlensed images, effectively turning the ISM into an astrophysical-scale interferometer. Using this technique, we estimate a 6\% uncertainty on $H_0$ from a single observed scintillated microlensing event, with a sub-percent uncertainty on $H_0$ achievable with only 30 such events. With an optical depth for stellar microlensing of $10^{-3}$, this may be achievable in the near future with upcoming FRB telescopes

Concerto for Tenor Saxophone and Wind Ensemble

Title from PDF of title page viewed January 9, 2018Dissertation advisor: Chen YiVitaThesis (D.M.A.)--Conservatory of Music and Dance. University of Missouri--Kansas City, 2016I wrote CONCERTO FOR TENOR SAXOPHONE AND WIND ENSEMBLE in the tradition of the grand concerti of the nineteenth century, but incorporating a modern sense of harmony and rhythm. The spirit of the piece is very in the Romantic tradition with a soloist set against a large ensemble. However, the traditions surrounding form, harmony, and rhythm have been eschewed to give the piece a sense of freedom and unpredictability. Some general concepts from the concerto traditions have been retained though, so that the listener can hear the piece in the context of other concerti from the Western tradition; e.g. the fast-slow-fast structure of the movements. The solo part is designed to be approachable by an advanced graduate student. There will also be a version of the piece arranged for Saxophone, Piano, and Percussion, which could be performed on a chamber recital. The concerto is in three movements, and lasts about 20 minutes.Abstract -- Instrumentation -- Music score -- Vit

The isochromosome 20q abnormality of pluripotent cells interrupts germ layer differentiation

Chromosome 20 abnormalities are some of the most frequent genomic changes acquired by human pluripotent stem cell (hPSC) cultures worldwide. Yet their effects on differentiation remain largely unexplored. We investigated a recurrent abnormality also found on amniocentesis, the isochromosome 20q (iso20q), during a clinical retinal pigment epithelium differentiation. Here we show that the iso20q abnormality interrupts spontaneous embryonic lineage specification. Isogenic lines revealed that under conditions that promote the spontaneous differentiation of wild-type hPSCs, the iso20q variants fail to differentiate into primitive germ layers and to downregulate pluripotency networks, resulting in apoptosis. Instead, iso20q cells are highly biased for extra-embryonic/amnion differentiation following inhibition of DNMT3B methylation or BMP2 treatment. Finally, directed differentiation protocols can overcome the iso20q block. Our findings reveal in iso20q a chromosomal abnormality that impairs the developmental competency of hPSCs toward germ layers but not amnion, which models embryonic developmental bottlenecks in the presence of aberrations