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Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles

Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that uses self-organizing maps to translate high-dimensional expression profiles of time courses or sample classes into animated, coherent and robust mosaics images. GEDI facilitates identification of interesting patterns of molecular activity simultaneously across gene, time and sample space without prior assumption of any structure in the data, and then permits the user to retrieve genes of interest. Important changes in genome-wide activities may be quickly identified based on 'Gestalt' recognition and hence, GEDI may be especially useful for non-specialist end users, such as physicians. AVAILABILITY: GEDI v1.0 is written in Matlab, and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html Supplementary information: http://www.chip.org/~ge/gedihome.html.

Database Management Systems↗

Dark Energy Survey Year 6 Results: Redshift Calibration of the MagLim++ Lens Sample

In this work, we derive and calibrate the redshift distribution of the MagLim++ lens galaxy sample used in the Dark Energy Survey Year 6 (DES Y6) 3x2pt cosmology analysis. The 3x2pt analysis combines galaxy clustering from the lens galaxy sample and weak gravitational lensing. The redshift distributions are inferred using the SOMPZ method - a Self-Organizing Map framework that combines deep-field multi-band photometry, wide-field data, and a synthetic source injection (Balrog) catalog. Key improvements over the DES Year 3 (Y3) calibration include a noise-weighted SOM metric, an expanded Balrog catalogue, and an improved scheme for propagating systematic uncertainties, which allows us to generate O($10^8$) redshift realizations that collectively span the dominant sources of uncertainty. These realizations are then combined with independent clustering-redshift measurements via importance sampling. The resulting calibration achieves typical uncertainties on the mean redshift of 1-2%, corresponding to a 20-30% average reduction relative to DES Y3. We compress the $n(z)$ uncertainties into a small number of orthogonal modes for use in cosmological inference. Marginalizing over these modes leads to only a minor degradation in cosmological constraints. This analysis establishes the MagLim++ sample as a robust lens sample for precision cosmology with DES Y6 and provides a scalable framework for future surveys.

Giannini, G. [Chicago U., Astron. Astrophys. Ctr.;↗

Dark Energy Survey Year 6 Results: Redshift Calibration of the Weak Lensing Source Galaxies

Determining the distribution of redshifts for galaxies in wide-field photometric surveys is essential for robust cosmological studies of weak gravitational lensing. We present the methodology, calibrated redshift distributions, and uncertainties of the final Dark Energy Survey Year 6 (Y6) weak lensing galaxy data, divided into four redshift bins centered at $\langle z \rangle = [0.414, 0.538, 0.846, 1.157]$. We combine independent information from two methods on the full shape of redshift distributions: optical and near-infrared photometry within an improved Self-Organizing Map $p(z)$ (SOMPZ) framework, and cross-correlations with spectroscopic galaxy clustering measurements (WZ), which we demonstrate to be consistent both in terms of the redshift calibration itself and in terms of resulting cosmological constraints within 0.1$σ$. We describe the process used to produce an ensemble of redshift distributions that account for several known sources of uncertainty. Among these, imperfection in the calibration sample due to the lack of faint, representative spectra is the dominant factor. The final uncertainty on mean redshift in each bin is $σ_{\langle z\rangle} = [0.012, 0.008,0.009, 0.024]$. We ensure the robustness of the redshift distributions by leveraging new image simulations and a cross-check with galaxy shape information via the shear ratio (SR) method.

Yin, B. [Duke U.] (ORCID:0009000656049980)↗

The Power of DESI for Photometric Redshift Calibration: A Case Study with KiDS-1000

Accurate redshift estimates are a critical requirement for weak lensing surveys and one of the main uncertainties in constraints on dark energy and large-scale cosmic structure. In this paper, we study the potential to calibrate photometric redshift (photo-z) distributions for gravitational lensing using the Dark Energy Spectroscopic Instrument (DESI). Since beginning its science operations in 2021, DESI has collected more than 50 million redshifts, adding about one million monthly. In addition to its large-scale structure samples, DESI has also acquired over 256k high-quality spectroscopic redshifts (spec-zs) in the COSMOS and XMM and VVDS fields. This is already a factor of 3 larger than previous spec-z calibration compilations in these two regions. Here, we explore calibrating photo-zs for the subset of KiDS-1000 galaxies that fall into joint self-organizing map (SOM) cells overlapping the DESI COSMOS footprint using the DESI COSMOS observations. Estimating the redshift distribution in KiDS-1000 with the new DESI data, we find broad consistency with previously published results while also detecting differences in the mean redshift in some tomographic bins with an average shifts of Delta Mean(z) = -0.028 in the mean and Delta Median(z) = +0.011 in the median across tomographic bins. However, we also find that incompleteness per SOM cell, i.e., groups of galaxies with similar colors and magnitudes, can modify n(z) distributions. Finally, we comment on the fact that larger photometric catalogs, aligned with the DESI COSMOS and DESI XMM and VVDS footprints, would be needed to fully exploit the DESI dataset and would extend the coverage to nearly eight times the area of existing 9-band photometry.

Blanco, Diana [UC, Santa Cruz; UC, Santa Cruz, Ins↗

Communications and control for electric power systems: Power flow classification for static security assessment

This report investigates the classification of power system states using an artificial neural network model, Kohonen's self-organizing feature map. The ultimate goal of this classification is to assess power system static security in real-time. Kohonen's self-organizing feature map is an unsupervised neural network which maps N-dimensional input vectors to an array of M neurons. After learning, the synaptic weight vectors exhibit a topological organization which represents the relationship between the vectors of the training set. This learning is unsupervised, which means that the number and size of the classes are not specified beforehand. In the application developed in this report, the input vectors used as the training set are generated by off-line load-flow simulations. The learning algorithm and the results of the organization are discussed.

Niebur, D.↗

A Unified Photometric Redshift Calibration for Weak Lensing Surveys Using the Dark Energy Spectroscopic Instrument

The effective redshift distribution n(z) of galaxies is a critical component in the study of weak gravitational lensing. Here, we introduce a new method for determining n(z) for weak lensing surveys based on high-quality redshifts and neural-network-based importance weights. Additionally, we present the first unified photometric redshift calibration of the three leading stage-III weak lensing surveys, the Dark Energy Survey (DES), the Hyper Suprime-Cam (HSC) survey, and the Kilo-Degree Survey (KiDS), with state-of-the-art spectroscopic data from the Dark Energy Spectroscopic Instrument (DESI). We verify our method using a new, data-driven approach and obtain n(z) constraints with statistical uncertainties of the order of $σ_z$ ~ 0.01 and smaller. Our analysis is largely independent of previous photometric redshift calibrations and, thus, provides an important cross-check in light of recent cosmological tensions. Overall, we find excellent agreement with previously published results on the DES Y3 and HSC Y1 data sets, while there are some differences on the mean redshift with respect to the previously published KiDS-1000 results. We attribute the latter to mismatches in photometric noise properties in the COSMOS field compared to the wider KiDS self-organizing map-gold catalog. At the same time, the new n(z) estimates for KiDS do not significantly change estimates of cosmic structure growth from cosmic shear. Finally, we discuss how our method can be applied to future weak lensing calibrations with DESI data.

Lange, J. U. [American Univ., Washington, DC (Unit↗

Two generalizations of Kohonen clustering

The relationship between the sequential hard c-means (SHCM), learning vector quantization (LVQ), and fuzzy c-means (FCM) clustering algorithms is discussed. LVQ and SHCM suffer from several major problems. For example, they depend heavily on initialization. If the initial values of the cluster centers are outside the convex hull of the input data, such algorithms, even if they terminate, may not produce meaningful results in terms of prototypes for cluster representation. This is due in part to the fact that they update only the winning prototype for every input vector. The impact and interaction of these two families with Kohonen's self-organizing feature mapping (SOFM), which is not a clustering method, but which often leads ideas to clustering algorithms is discussed. Then two generalizations of LVQ that are explicitly designed as clustering algorithms are presented; these algorithms are referred to as generalized LVQ = GLVQ; and fuzzy LVQ = FLVQ. Learning rules are derived to optimize an objective function whose goal is to produce 'good clusters'. GLVQ/FLVQ (may) update every node in the clustering net for each input vector. Neither GLVQ nor FLVQ depends upon a choice for the update neighborhood or learning rate distribution - these are taken care of automatically. Segmentation of a gray tone image is used as a typical application of these algorithms to illustrate the performance of GLVQ/FLVQ.

Bezdek, James C.↗

Communications and control for electric power systems

The first section of the report describes the AbNET system, a hardware and software communications system designed for distribution automation (it can also find application in substation monitoring and control). The topology of the power system fixes the topology of the communications network, which can therefore be expected to include a larger number of branch points, tap points, and interconnections. These features make this communications network unlike any other. The network operating software has to solve the problem of communicating to all the nodes of a very complex network in as reliable a way as possible even if the network is damaged, and it has to do so with minimum transmission delays and at minimum cost. The design of the operating protocols is described within the framework of the seven-layer Open System Interconnection hierarchy of the International Standards Organization. Section 2 of the report describes the development and testing of a high voltage sensor based on an electro-optic polymer. The theory of operation is reviewed. Bulk fabrication of the polymer is discussed, as well as results of testing of the electro-optic coefficient of the material. Fabrication of a complete prototype sensor suitable for use in the range 1-20 kV is described. The electro-optic polymer is shown to be an important material for fiber optic sensing applications. Appendix A is theoretical support for this work. The third section of the report presents the application of an artificial neural network, Kohonen's self-organizing feature map, for the classification of power system states. This classifier maps vectors of an N-dimensional space to a 2-dimensional neural net in a nonlinear way preserving the topological order of the input vectors. These mappings are studied using a nonlinear power system model.

Kirkham, H.↗

Monitoring the Microgravity Environment Quality On-Board the International Space Station Using Soft Computing Techniques

This paper presents an artificial intelligence monitoring system developed by the NASA Glenn Principal Investigator Microgravity Services project to help the principal investigator teams identify the primary vibratory disturbance sources that are active, at any moment in time, on-board the International Space Station, which might impact the microgravity environment their experiments are exposed to. From the Principal Investigator Microgravity Services' web site, the principal investigator teams can monitor via a graphical display, in near real time, which event(s) is/are on, such as crew activities, pumps, fans, centrifuges, compressor, crew exercise, platform structural modes, etc., and decide whether or not to run their experiments based on the acceleration environment associated with a specific event. This monitoring system is focused primarily on detecting the vibratory disturbance sources, but could be used as well to detect some of the transient disturbance sources, depending on the events duration. The system has built-in capability to detect both known and unknown vibratory disturbance sources. Several soft computing techniques such as Kohonen's Self-Organizing Feature Map, Learning Vector Quantization, Back-Propagation Neural Networks, and Fuzzy Logic were used to design the system.

Jules, Kenol↗

An Intelligent System for Monitoring the Microgravity Environment Quality On-Board the International Space Station

An intelligent system for monitoring the microgravity environment quality on-board the International Space Station is presented. The monitoring system uses a new approach combining Kohonen's self-organizing feature map, learning vector quantization, and back propagation neural network to recognize and classify the known and unknown patterns. Finally, fuzzy logic is used to assess the level of confidence associated with each vibrating source activation detected by the system.

Lin, Paul P.↗

Monitoring the Microgravity Environment Quality On-board the International Space Station Using Soft Computing Techniques: Preliminary System Performance Results - Part 2

This paper presents the preliminary performance results of the artificial intelligence monitoring system in full operational mode using near real time acceleration data downlinked from the International Space Station. Preliminary microgravity environment characterization analysis result for the International Space Station (Increment-2), using the monitoring system is presented. Also, comparison between the system predicted performance based on ground test data for the US laboratory "Destiny" module and actual on-orbit performance, using measured acceleration data from the U.S. laboratory module of the International Space Station is presented. Finally, preliminary on-orbit disturbance magnitude levels are presented for the Experiment of Physics of Colloids in Space, which are compared with on ground test data. The ground test data for the Experiment of Physics of Colloids in Space were acquired from the Microgravity Emission Laboratory, located at the NASA Glenn Research Center, Cleveland, Ohio. The artificial intelligence was developed by the NASA Glenn Principal Investigator Microgravity Services Project to help the principal investigator teams identify the primary vibratory disturbance sources that are active, at any moment of time, on-board the International Space Station, which might impact the microgravity environment their experiments are exposed to. From the Principal Investigator Microgravity Services' web site, the principal investigator teams can monitor via a dynamic graphical display, implemented in Java, in near real time, which event(s) is/are on, such as crew activities, pumps, fans, centrifuges, compressor, crew exercise, structural modes, etc., and decide whether or not to run their experiments, whenever that is an option, based on the acceleration magnitude and frequency sensitivity associated with that experiment. This monitoring system detects primarily the vibratory disturbance sources. The system has built-in capability to detect both known and unknown vibratory disturbance sources. Several soft computing techniques such as Kohonen's Self-Organizing Feature Map, Learning Vector Quantization, Back-Propagation Neural Networks, and Fuzzy Logic were used to design the system.

Jules, Kenol↗

Real Time On-line Space Research Laboratory Environment Monitoring with Off-line Trend and Prediction Analysis

One of the responsibilities of the NASA Glenn Principal Investigator Microgravity Services is to support NASA sponsored investigators in the area of reduced-gravity acceleration data analysis, interpretation and the monitoring of the reduced-gravity environment on-board various carriers. With the International Space Station currently operational, a significant amount of acceleration data is being down-linked and processed on ground for both the space station onboard environment characterization (and verification) and scientific experiments. Therefore, to help principal investigator teams monitor the acceleration level on-board the International Space Station to avoid undesirable impact on their experiment, when possible, the NASA Glenn Principal Investigator Microgravity Services developed an artificial intelligence monitoring system, which detects in near real time any change in the environment susceptible to affect onboard experiments. The main objective of the monitoring system is to help research teams identify the vibratory disturbances that are active at any instant of time onboard the International Space Station that might impact the environment in which their experiment is being conducted. The monitoring system allows any space research scientist, at any location and at any time, to see the current acceleration level on-board the Space Station via the World Wide Web. From the NASA Glenn s Exploration Systems Division web site, research scientists can see in near real time the active disturbances, such as pumps, fans, compressor, crew exercise, re-boost, extra-vehicular activity, etc., and decide whether or not to continue operating or stopping (or making note of such activity for later correlation with science results) their experiments based on the g-level associated with that specific event. A dynamic graphical display accessible via the World Wide Web shows the status of all the vibratory disturbance activities with their degree of confidence as well as their g-level contribution to the environment. The system can detect both known and unknown vibratory disturbance activities. It can also perform trend analysis and prediction by analyzing past data over many Increments of the space station for selected disturbance activities. This feature can be used to monitor the health of onboard mechanical systems to detect and prevent potential system failure as well as for use by research scientists during their science results analysis. Examples of both real time on-line vibratory disturbance detection and off-line trend analysis are presented in this paper. Several soft computing techniques such as Kohonen s Self-Organizing Feature Map, Learning Vector Quantization, Back-Propagation Neural Networks, and Fuzzy Logic were used to design the system.

Jules, Kenol↗

The performance evaluation of a new neural network based traffic management scheme for a satellite communication network

A neural-network-based traffic management scheme for a satellite communication network is described. The scheme consists of two levels of management. The front end of the scheme is a derivation of Kohonen's self-organization model to configure maps for the satellite communication network dynamically. The model consists of three stages. The first stage is the pattern recognition task, in which an exemplar map that best meets the current network requirements is selected. The second stage is the analysis of the discrepancy between the chosen exemplar map and the state of the network, and the adaptive modification of the chosen exemplar map to conform closely to the network requirement (input data pattern) by means of Kohonen's self-organization. On the basis of certain performance criteria, whether a new map is generated to replace the original chosen map is decided in the third stage. A state-dependent routing algorithm, which arranges the incoming call to some proper path, is used to make the network more efficient and to lower the call block rate. Simulation results demonstrate that the scheme, which combines self-organization and the state-dependent routing mechanism, provides better performance in terms of call block rate than schemes that only have either the self-organization mechanism or the routing mechanism.

Ansari, Nirwan↗

Self-organization and clustering algorithms

Kohonen's feature maps approach to clustering is often likened to the k or c-means clustering algorithms. Here, the author identifies some similarities and differences between the hard and fuzzy c-Means (HCM/FCM) or ISODATA algorithms and Kohonen's self-organizing approach. The author concludes that some differences are significant, but at the same time there may be some important unknown relationships between the two methodologies. Several avenues of research are proposed.

Bezdek, James C.↗

Adding dynamic rules to self-organizing fuzzy systems

This paper develops a Dynamic Self-Organizing Fuzzy System (DSOFS) capable of adding, removing, and/or adapting the fuzzy rules and the fuzzy reference sets. The DSOFS background consists of a self-organizing neural structure with neuron relocation features which will develop a map of the input-output behavior. The relocation algorithm extends the topological ordering concept. Fuzzy rules (neurons) are dynamically added or released while the neural structure learns the pattern. The DSOFS advantages are the automatic synthesis and the possibility of parallel implementation. A high adaptation speed and a reduced number of neurons is needed in order to keep errors under some limits. The computer simulation results are presented in a nonlinear systems modelling application.

Buhusi, Catalin V.↗

Emergent topological polarization textures in relaxor ferroelectrics

Relaxor ferroelectrics underpin high-performance actuators and sensors, yet the nature of polar heterogeneities driving their broadband dielectric response remains debated. Using a unified, multimodal structural refinement framework— simultaneously fitting complementary X-ray and neutron total scattering, X-ray absorption spectra, and diffuse scattering—we reconstruct 3D mesoscale polarization maps in the classic relaxor system PbMg 1/3 Nb 2/3 O 3 –PbTiO 3 . We uncover self-organized swirling polarization textures with half-skyrmion (meron) vortices, challenging models of independent polar nanoregions. These textures, characterized by smooth changes in the polarization direction, originate from overlapping volumes in which the projections of locally correlated polarization vectors onto each volume’s long axis share the same sign. Vortex cores correlate strongly with local charge and strain gradients imposed by compositional heterogeneities. In this work, our results suggest that chemical disorder, acting via depolarizing and strain fields, stabilizes topological vortex textures of the polarization field, offering a route for engineering new dielectric and ferroelectric functionalities.

Eremenko, Maksim [National Institute of Standards ↗

An evaluation of ISOCLS and CLASSY clustering algorithms for forest classification in northern Idaho

Both the iterative self-organizing clustering system (ISOCLS) and the CLASSY algorithms were applied to forest and nonforest classes for one 1:24,000 quadrangle map of northern Idaho and the classification and mapping accuracies were evaluated with 1:30,000 color infrared aerial photography. Confusion matrices for the two clustering algorithms were generated and studied to determine which is most applicable to forest and rangeland inventories in future projects. In an unsupervised mode, ISOCLS requires many trial-and-error runs to find the proper parameters to separate desired information classes. CLASSY tells more in a single run concerning the classes that can be separated, shows more promise for forest stratification than ISOCLS, and shows more promise for consistency. One major drawback to CLASSY is that important forest and range classes that are smaller than a minimum cluster size will be combined with other classes. The algorithm requires so much computer storage that only data sets as small as a quadrangle can be used at one time.

Werth, L. F.↗

Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators

Multicomponent polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures, molecular dynamics simulations are typically infeasible at the spatial scales required to study the stability of mesophase structure. Polymer field theories offer an attractive alternative, but analytical calculations are only tractable for mean-field theories and nearby perturbations, constraints that become especially problematic for fluctuation-induced effects such as coacervation. Here, we show that a recently developed technique for obtaining numerical solutions to partial differential equations based on operator learning, neural operators, lends itself to a highly scalable training strategy by parallelizing per-species operator maps. We illustrate the efficacy of our approach on six-component mixtures with randomly selected compositions and that it significantly outperforms the state-of-the-art pseudospectral integrators for field-theoretic simulations, especially as polymer lengths become long.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗