Spherical and Hyperbolic Toric Topology-Based Codes On Graph Embedding for Ising MRF Models: Classical and Quantum Topology Machine Learning

The paper introduces the application of information geometry to describe the ground states of Ising models by utilizing parity-check matrices of cyclic and quasi-cyclic codes on toric and spherical topologies. The approach establishes a connection between machine learning and error-correcting coding. This proposed approach has implications for the development of new embedding methods based on trapping sets. Statistical physics and number geometry applied for optimize error-correcting codes, leading to these embedding and sparse factorization methods. The paper establishes a direct connection between DNN architecture and error-correcting coding by demonstrating how state-of-the-art architectures (ChordMixer, Mega, Mega-chunk, CDIL, ...) from the long-range arena can be equivalent to of block and convolutional LDPC codes (Cage-graph, Repeat Accumulate). QC codes correspond to certain types of chemical elements, with the carbon element being represented by the mixed automorphism Shu-Lin-Fossorier QC-LDPC code. The connections between Belief Propagation and the Permanent, Bethe-Permanent, Nishimori Temperature, and Bethe-Hessian Matrix are elaborated upon in detail. The Quantum Approximate Optimization Algorithm (QAOA) used in the Sherrington-Kirkpatrick Ising model can be seen as analogous to the back-propagation loss function landscape in training DNNs. This similarity creates a comparable problem with TS pseudo-codeword, resembling the belief propagation method. Additionally, the layer depth in QAOA correlates to the number of decoding belief propagation iterations in the Wiberg decoding tree. Overall, this work has the potential to advance multiple fields, from Information Theory, DNN architecture design (sparse and structured prior graph topology), efficient hardware design for Quantum and Classical DPU/TPU (graph, quantize and shift register architect.) to Materials Science and beyond.Comment: 71 pages, 42 Figures, 1 Table, 1 Appendix. arXiv admin note: text overlap with arXiv:2109.08184 by other author

Track Myself:a smartphone-based tool for monitoring Parkinson’s disease

Abstract. Parkinson disease (PD) is a fast-spreading neurological disorder that affects millions of people worldwide, it hinders its patients from performing daily activities with ease. Its symptoms may vary within hours and progress differently for each patient, and usually assessed clinically every six months. It requires customized treatment plan for each patient and demands adherence of patients to complex medication regimens. The goal of this thesis is to design, implement, and test a mobile app named “Track Myself” that can help people with Parkinson’s disease (PwP) resolve these issues. The app has two components that help PwP assess their symptoms level regularly, the first component is an accelerometer-based game that detects the patient’s hand movement and calculate a score for its accuracy, the second component is a self-report symptoms survey filled by the patient every day to rate their severity level. A medication journal is implemented in the app for the patients to log their medication intakes regularly, which are prescribed by their doctors using the app as well, this help keep track of the medication history and calculate the patient’s medication adherence. The app also contains a dashboard made of three charts, representing the medication time-adherence, symptom surveys, and game scores of the patient. The purpose of this dashboard is to help the doctors form relationships between the data in the charts and determine the best future treatment plan. The app was tested for two weeks by ten healthy participants, they were asked to act in the persona of a PD patient and perform certain tasks, where information about the disease and experiences of actual patients were provided for these participants. A questionnaire was sent to the participants after the study, it consists of open-ended questions, rating statements, as well as a validated mobile health app usability questionnaire (MAUQ). The participants rated the app as easy to use for PwP in most features with mean score of 6.04/7 and perceived the app as very useful in helping PwP with mean score of 6.18/7

Effects of specimen size reduction on the transition curve of the Charpy V-notch impact test

This study was undertaken to correlate the impact properties of ASTM standard full size Charpy V-notch impact specimens to the impact properties of subsize specimens. An ASTM A533-B quenched and tempered plate steel was examined. The fine grained martensitic material had a coarse prior austenite grain size, which resulted in a low upper shelf energy for this material. Three sizes of specimens were included. Specimens were irradiated in the TRIGA Reactor Facility operated by the U. S. Geological Survey in Denver, Colorado, to 1 x 1019 n/cm2 (E \u3e 1 MeV) at 150°C (302°F). Unirradiated and irradiated specimens were tested at several temperatures in an instrumented drop tower, and the load during impact was recorded as a function of time. Full transition curves of energy versus temperature were determined for the three sizes. The results are presented and compared. A method for correlating the upper shelf energies determined from subsize and full size specimens was developed. The method incorporated a normalizing factor proposed in earlier related studies, and the method is discussed in light of the new data. The estimates of upper shelf energy derived from the correlation agreed with the measured full size values within 10%. The correlation was found to be applicable to the subsize specimen data. The irradiation induced shift in the ductile to brittle transition temperature of the material was found to be independent of specimen size --Abstract, page iii

Medusan Morphospace: Phylogenetic Constraints, Biomechanical Solutions, and Ecological Consequences

Medusae were the earliest animals to evolve muscle-powered swimming in the seas. Although medusae have achieved diverse and prominent ecological roles throughout the world\u27s oceans, we argue that the primitive organization of cnidarian muscle tissue limits force production and, hence, the mechanical alternatives for swimming bell function. We use a recently developed model comparing the potential force production with the hydrodynamic requirements of jet propulsion, and conclude that jet production is possible only at relatively small bell diameters. In contrast, production of a more complex wake via what we term rowing propulsion permits much larger sizes but requires a different suite of morphological features. Analysis of morphometric data from all medusan taxa independently confirms size-dependent patterns of bell forms that correspond with model predictions. Further, morphospace analysis indicates that various lineages within the Medusozoa have proceeded along either of two evolutionary trajectories. The first alternative involved restriction of jet-propelled medusan bell diameters to small dimensions. These medusae may be either solitary individuals (characteristic of Anthomedusae and Trachymedusae) or aggregates of small individual medusan units into larger colonial forms (characteristic of the nectophores of many members of the Siphonophorae). The second trajectory involved use of rowing propulsion (characteristic of Scyphozoa and some hydromedusan lineages such as the Leptomedusae and Narcomedusae) that allows much larger bell sizes. Convergence on either of the differing propulsive alternatives within the Medusozoa has emerged via parallel evolution among different medusan lineages. The distinctions between propulsive modes have important ecological ramifications because swimming and foraging are interdependent activities for medusae. Rowing swimmers are characteristically cruising predators that select different prey types from those selected by jet-propelled medusae, which are predominantly ambush predators. These relationships indicate that the different biomechanical solutions to constraints on bell function have entailed ecological consequences that are evident in the prey selection patterns and trophic impacts of contemporary medusan lineages

Engineering data compendium. Human perception and performance, volume 3

The concept underlying the Engineering Data Compendium was the product of a research and development program (Integrated Perceptual Information for Designers project) aimed at facilitating the application of basic research findings in human performance to the design of military crew systems. The principal objective was to develop a workable strategy for: (1) identifying and distilling information of potential value to system design from existing research literature, and (2) presenting this technical information in a way that would aid its accessibility, interpretability, and applicability by system designers. The present four volumes of the Engineering Data Compendium represent the first implementation of this strategy. This is Volume 3, containing sections on Human Language Processing, Operator Motion Control, Effects of Environmental Stressors, Display Interfaces, and Control Interfaces (Real/Virtual)

High-throughput large-area plastic nanoelectronics

Large-area electronics (LAE) manufacturing has been a key focus of both academic and industrial research, especially within the last decade. The growing interest is born out of the possibility of adding attractive properties (flexibility, light weight or minimal thickness) at low cost to well-established technologies, such as photovoltaics, displays, sensors or enabling the realisation of emerging technologies such as wearable devices and the Internet of Things. As such there has been great progress in the development of materials specifically designed to be employed in solution processed (plastic) electronics, including organic, transparent metal oxide and nanoscale semiconductors, as well as progress in the deposition methods of these materials using low-cost high-throughput printing techniques, such as gravure printing, inkjet printing, and roll-to-roll vacuum deposition. Meanwhile, industry innovation driven by Moore’s law has pushed conventional silicon-based electronic components to the nanoscale. The processes developed for LAE must strive to reach these dimensions. Given that the complex and expensive patterning techniques employed by the semiconductor industry so far are not compatible with LAE, there is clearly a need to develop large-area high throughput nanofabrication techniques. This thesis presents progress in adhesion lithography (a-Lith), a nanogap electrode fabrication process that can be applied over large areas on arbitrary substrates. A-Lith is a self-alignment process based on the alteration of surface energies of a starting metal electrode which allows the removal of any overlap of a secondary metal electrode. Importantly, it is an inexpensive, scalable and high throughput technique, and, especially if combined with low temperature deposition of the active material, it is fundamentally compatible with large-area fabrication of nanoscale electronic devices on flexible (plastic) substrates. Herein, I present routes towards process optimisation with a focus on gap size reduction and yield maximisation. Asymmetric gaps with sizes below 10 nm and yields of > 90 % for hundreds of electrode pairs generated on a single substrate are demonstrated. These large width electrode nanogaps represent the highest aspect ratio nanogaps (up to 108) fabricated to date. As a next step, arrays of Schottky nanodiodes are fabricated by deposition of a suitable semiconductor from solution into the nanogap structures. Of principal interest is the wide bandgap transparent semiconductor, zinc oxide (ZnO). Lateral ZnO Schottky diodes show outstanding characteristics, with on-off ratios of up to 106 and forward current values up to 10 mA for obtained upon combining a-Lith with low-temperature solution processing. These unique devices are further investigated for application in rectifier circuits, and in particular for potential use in radio frequency identification (RFID) tag technology. The ZnO diodes are found to surpass the 13.56 MHz frequency bernchmark used in commercial applications and approach the ultra-high frequency (UHF) band (hundreds of megahertz), outperforming current state of the art printed diodes. Solution processed fullerene (C60) is also shown to approach the UHF band in this co-planar device configuration, highlighting the viability of a-Lith for enabling large-area flexible radio frequency nanoelectronics. Finally, resistive switching memory device arrays based on a-Lith patterned nanogap aluminium symmetric electrodes are demonstrated for the first time. These devices are based either on empty aluminium nanogap electrodes, or with the gap filled with a solution-processed semiconductor, the latter being ZnO, the semiconducting polymer poly(9,9-dioctylfluorene-alt-benzothiadiazole) (F8BT) or carbon nanotube/polyfluorene blends. The switching mechanism, retention time and switching speed are investigated and compared with published data. The fabrication of arrays of these devices illustrates the potential of a-Lith as a simple technique for the realisation of large-area high-density memory applications.Open Acces

Auringon historiallisten kirkkauskarttojen digitointi Metsähovin radio-observatoriolle

Metsähovi Radio Observatory has collected solar intensity maps since autumn 1978. The maps have been recorded with the main radio telescope at the observatory, which has a parabolic antenna with diameter 14 meters. The most common frequency is 37 GHz with beam diameter 2.4 arc minutes. Occasional observations have been conducted, for example, on 22 GHz and 77 GHz. The observational data were recorded on magnetic tapes or disks until 1987. The original data is lost, but the maps have survived as mechanically rendered contour plots, some of which were also published as report series by former Helsinki University of Technology, Metsähovi Radio Research Station. In order to convert scanned images of the maps into a more usable format, I have written a software as part of my master's thesis during spring 2018. After appropriate image ltering, all the markings on the maps can be interpreted using the methods described in my thesis. Contour lines can be converted into a matrix form, which represents the observed intensity in a rectangular grid. This is achieved by solving a Poisson's equation accosiated with the problem. The method is tolerant for various map defects, such as broken contours. In addition, I describe an algorithm for identifying bright and dim regions from these radio intensity map and show preliminary statistics based on the historical contour plots. The same algorithm is applicable to the modern maps as well, which are produced daily in Metsähovi.Metsähovin radio-observatorio on kerännyt Auringon kirkkauskarttoja syksystä 1978 alkaen. Kartat on kerätty observatorion pääradioteleskoopilla, jossa on 14-metrinen parabolinen antenni. Yleisin käytetty taajuus on 33 GHz, joka tuottaa halkaisijaltaan 2,4 kaariminuutin levyisen keilan. Yksittäisiä havaintoja on tehty mm. taajuuksilla 22 GHz ja 77 GHz. Havaintodata on tallennettu magneettisille nauhoille tai levyille vuoteen 1987 asti. Alkuperäinen data on kadonnut, mutta kartat ovat selvinneet mekaanisesti piirrettyinä korkeuskäyräkarttoina, joista osa on julkaistu silloisen TKK:n Metsä- hovin Radiotutkimusaseman sarjakokoelmissa. Jotta karttojen skannatut kuvat saataisiin paremmin hyödynnettävään muotoon, olen kirjoittanut ohjelmiston osana diplomityötäni keväällä 2018. Sopivan kuvansuodatuksen jälkeen kaikki kuvan merkinnät voidaan tunnistaa työssäni kuvatuilla menetelmillä. Korkeus- käyrät voidaan muuntaa matriisimuotoon, jossa havaittu kirkkaus on esitetty suorakulmaisessa verkossa. Tämä onnistuu ratkaisemalla ongelmaan liittyvä Poissonin yhtälö. Menetelmä sietää erilaisia karttavirheitä, kuten katkenneita korkeuskäyriä. Lisäksi kuvailen algoritmin, jolla tunnistetaan radiointensiteettikartoista kirkkaat ja himmeät alueet, sekä esittelen alustavia tilastoja historiallisista korkeus- käyräkartoista. Sama algoritmi soveltuu myös uusiin karttoihin, joita tuotetaan Metsähovissa päivittäin

A novel approach to handwritten character recognition

A number of new techniques and approaches for off-line handwritten character recognition are presented which individually make significant advancements in the field. First. an outline-based vectorization algorithm is described which gives improved accuracy in producing vector representations of the pen strokes used to draw characters. Later. Vectorization and other types of preprocessing are criticized and an approach to recognition is suggested which avoids separate preprocessing stages by incorporating them into later stages. Apart from the increased speed of this approach. it allows more effective alteration of the character images since more is known about them at the later stages. It also allows the possibility of alterations being corrected if they are initially detrimental to recognition. A new feature measurement. the Radial Distance/Sector Area feature. is presented which is highly robust. tolerant to noise. distortion and style variation. and gives high accuracy results when used for training and testing in a statistical or neural classifier. A very powerful classifier is therefore obtained for recognizing correctly segmented characters. The segmentation task is explored in a simple system of integrated over-segmentation. Character classification and approximate dictionary checking. This can be extended to a full system for handprinted word recognition. In addition to the advancements made by these methods. a powerful new approach to handwritten character recognition is proposed as a direction for future research. This proposal combines the ideas and techniques developed in this thesis in a hierarchical network of classifier modules to achieve context-sensitive. off-line recognition of handwritten text. A new type of "intelligent" feedback is used to direct the search to contextually sensible classifications. A powerful adaptive segmentation system is proposed which. when used as the bottom layer in the hierarchical network. allows initially incorrect segmentations to be adjusted according to the hypotheses of the higher level context modules

Enhancing Computational Methods for Strain Typing and Separating Strains of Mycoplasma bovis in Mixed Culture

There are no programs that allow a user to isolate strain-specific sequences within a complex assembly of mixed bacterial strains, unbiased by reference assembly. The tools that do exist each have a specialized focus, such as isolating small haplotype differences within strains, or have a reliance on reference genomes that may bias the sequences. For this purpose we have developed a tool called the Separator of Strain Inherent Sequences (SepSIS) that extracts sequences specific to each bacterial strain from the de novo assembly graph created using the SPAdes assembler. SepSIS is accompanied by a set of pre-processing scripts that form the “SepSIS pipeline”. The scripts are available at “https://github.com/MatthewWaldner/sepsis”. The SepSIS pipeline provides two functionalities, with each accepting a particular form of input data. The pipeline was designed for use with Illumina MiSeq paired-read data, but in theory, any read dataset compatible with SPAdes could function with SepSIS. The first function of the SepSIS pipeline accepts reads obtained from non-clonal bacterial isolates as input. It then attempts to isolate the complete strain-specific sequences using relative coverage levels of strain-specific subsequences in the assembly graph. It is marginally successful at this task. The second function of the SepSIS pipeline accepts reads from independently cultured isolates and mixes them in silico before assembly. After assembly, the contiguous sequences are analyzed by SepSIS using meta-information describing their strain of origin to produce lists of sequences specific to each strain. These sequences can then be studied and contrasted further. The second functionality of SepSIS was used to perform two primary investigations. The first investigation identifies unique sequences from sets of isolates, where each set was hypothesized to consist entirely of copies of a single strain. This investigation analyzed 10 sets of 5 independently sequenced isolates of Mycoplasma bovis, with all the isolates originating from a single culture spread on a growth plate. Despite originating from a single culture, it was found that many of the isolates had unique sequences; therefore, these isolates likely each represent an individual strain. The second investigation was based upon mixing two or more strains with contrasting phenotypic features allowing the second function of SepSIS to be applied to isolating sequences potentially responsible for each phenotype. By running multiple mixes with the same contrasting phenotypic combinations, the intersection of sequences common to a phenotype can be identified. This type of investigation was performed on 29 pairs of Mycoplasma bovis lung and stifle joint isolates, with each pair originating from a single animal. Infection location was considered a phenotype and sequences unique to each infection location were isolated and identified. The sequences with the strongest correlation to phenotype were variants of Mycoplasma bovis insertion sequences, or were from genes for variable surface lipoproteins and HAD-family hydrolases. The results show that SepSIS is useful when provided with reads sequenced from independently cultured isolates along with meta-information