Twin-width IV: ordered graphs and matrices

We establish a list of characterizations of bounded twin-width for hereditary, totally ordered binary structures. This has several consequences. First, it allows us to show that a (hereditary) class of matrices over a finite alphabet either contains at least $n!$ matrices of size $n \times n$, or at most $c^n$ for some constant $c$. This generalizes the celebrated Stanley-Wilf conjecture/Marcus-Tardos theorem from permutation classes to any matrix class over a finite alphabet, answers our small conjecture [SODA '21] in the case of ordered graphs, and with more work, settles a question first asked by Balogh, Bollob\'as, and Morris [Eur. J. Comb. '06] on the growth of hereditary classes of ordered graphs. Second, it gives a fixed-parameter approximation algorithm for twin-width on ordered graphs. Third, it yields a full classification of fixed-parameter tractable first-order model checking on hereditary classes of ordered binary structures. Fourth, it provides a model-theoretic characterization of classes with bounded twin-width.Comment: 53 pages, 18 figure

Vapnik-Chervonenkis density in some theories without the independence property, I

We recast the problem of calculating Vapnik-Chervonenkis (VC) density into one of counting types, and thereby calculate bounds (often optimal) on the VC density for some weakly o-minimal, weakly quasi-o-minimal, and $P$-minimal theories.Comment: 59

Pseudohyphal growth of the emerging pathogen Candida auris is triggered by genotoxic stress through the S phase checkpoint

We are grateful to Arunaloke Chakrabarti, Anuradha Chowdhary, Elizabeth Johnson (PHE), Takashi Kubota, and Shawn Lockhart (CDC) for providing strains. We thank Fei Long for skillful technical assistance. Flow cytometry was performed at the Iain Fraser Cytometry Centre (IFCC), University of Aberdeen (Raif Yuecel). Microscopy was done at the Microscopy & Histology Facility, University of Aberdeen (Kevin S. Mackenzie). This work was supported by a Wellcome Trust Seed Award to AL [grant number 212524/Z/18/Z], and the Medical Research Council (MRC) Centre for Medical Mycology at the University of Exeter [grant numbers MR/P501955/1, MR/N006364/1].Peer reviewedPreprin

Seismic stratigraphic investigation of the Ukpokiti Field Channel complex, Oml 108, offshore Nigeria, northwestern Niger Delta

Detailed seismic stratigraphic analyses and mapping show that a well defined Ukpokiti Field Channel complex (late Miocene) found on the up-thrown side of a major back-to-back fault system in the West Niger delta inner-continental shelf probably formed during a single eustatic fall. The channel (\u3e500 msec, 10 km wide) shows several tributaries entering the trunk axis from what was probably a surface of subaerial exposure. Slumping is prominent on the north flank of the trunk channel. No channel unconformity is evident in the down-thrown block. This investigation seeks to resolve the lack of down-dip correlative seismic expression across the major structural boundary and place the Ukpokiti Field channel complex within a sequence stratigraphic framework, thereby explaining the channel genesis. Seismic sequence analysis was performed in the LSU Subsurface Laboratory with the Landmark Graphics© software suite using standard workstation interpretation procedures. Ukpokiti Field reservoir interval appraisals, preloaded digital well logs, poststack synthetic seismograms, and multiple horizon maps were interpreted during the course of the study. Results show the down-thrown correlative channel base to be a depositional surface. Three internal channel fill seismic facies patterns (fluvial deposition, marine inundation, and deltaic progradation) are evident in both structural blocks. On the basis of available biostratigraphic age control, the channel base probably represents an incised valley created at the 6.3 Ma sequence boundary. The internal seismic facies units probably represent a single shoreline regression interval. Shoreline and fluvio-marine deposition occurred after incision. Next, estuarine and pro-delta deposition occurred when the channel was flooded. Last, deltaic deposition filled the valley. Observed slumping is probably a product of instability due to the rapid progradation of deltaic deposits in the final stage of channel evolution. The channel produces no resolvable lowstand basinfloor fan within the study area

Doctor of Philosophy

dissertationThis work presents the results of various investigations using various techniques of hyperpolarizing the nuclei of atoms. Hyperpolarization implies magnetic order in excess of the thermal order obtained naturally as described by Curie's law. The main portion of this work presents the results of a detailed experimental exploration of predictions arising from a new model of transverse nuclear spin relaxation in quantum systems, based on possible manifestations of microscopic chaos in quantum systems. Experiments have been carried out on a number of hyperpolarized xenon samples, each di ering in its relative percentage of xenon isotopes in order to vary the homonuclear and heteronuclear dipole couplings in the spin system. The experiments were performed under a variety of conditions in an attempt to observe the behaviors predicted by the model. Additionally, much more extensive measurements were made on a number of samples of solid CaF2 in both single crystal and powder forms. These samples, although thermally polarized, were observed with superior signal to noise ratios than even the hyperpolarized xenon solids, allowing for more precise measurements for comparison to the theory. This work thus contains the rst experimental evidence for the majority of the model's predictions. Additionally, this work contains the rst precise measurements of the frequency-shift enhancement parameters for 129Xe and krypton in the presence of spin-polarized Rb. The determination of these important numbers will be useful to many groups who utilize spinexchange optical pumping in their labs. This work built on the prior knowledge of a precise number for the frequency-shift enhancement parameter of 3He in Rb vapor. Finally, I detail work using NMR to detect nuclear-spin polarization enhancement in silicon phosphorus by a novel, photo-induced hyperpolarization technique developed by the Boehme research group at the University of Utah. Signiif cant nuclear polarization enhancements were observed by the Boehme group due to electron-photon interactions in semiconductor soilds; these enhancements were observed by their e ffects on the ambient electrons and measured with electron spin resonance techniques. The work described here details experiments to observe the enhanced nuclear polarization by directly measuring the intensity increase in an NMR measurement

Responsible and Regulatory Conform Machine Learning for Medicine: A Survey of Challenges and Solutions

Machine learning is expected to fuel significant improvements in medical care. To ensure that fundamental principles such as beneficence, respect for human autonomy, prevention of harm, justice, privacy, and transparency are respected, medical machine learning systems must be developed responsibly. Many high-level declarations of ethical principles have been put forth for this purpose, but there is a severe lack of technical guidelines explicating the practical consequences for medical machine learning. Similarly, there is currently considerable uncertainty regarding the exact regulatory requirements placed upon medical machine learning systems. This survey provides an overview of the technical and procedural challenges involved in creating medical machine learning systems responsibly and in conformity with existing regulations, as well as possible solutions to address these challenges. First, a brief review of existing regulations affecting medical machine learning is provided, showing that properties such as safety, robustness, reliability, privacy, security, transparency, explainability, and nondiscrimination are all demanded already by existing law and regulations - albeit, in many cases, to an uncertain degree. Next, the key technical obstacles to achieving these desirable properties are discussed, as well as important techniques to overcome these obstacles in the medical context. We notice that distribution shift, spurious correlations, model underspecification, uncertainty quantification, and data scarcity represent severe challenges in the medical context. Promising solution approaches include the use of large and representative datasets and federated learning as a means to that end, the careful exploitation of domain knowledge, the use of inherently transparent models, comprehensive out-of-distribution model testing and verification, as well as algorithmic impact assessments