Initial public release of scGRMC: Graph-refined representation learning for single-cell multi-omics clustering. Included Source code for autoencoder pretraining and multi-omics clustering Support for paired RNA + ADT and RNA + ATAC data InHouse example dataset, pretrained checkpoint, and test script Installation, parameter, dataset-format, and reproducibility documentation Apache License 2.0 and third-party software notices Data The processed datasets are archived at Zenodo: https://doi.org/10.5281/zenodo.22172578
fish· Zenodo (CERN European Organi...· 0 citations
This paper establishes the observer as a physical node embedded in the causal graph and resolves the conceptual relation between General Relativity and Quantum Mechanics within the N.E.A. (Network Emergent Architecture) framework. The Mens Protocol defines the observer as a self-referential sampling operator, subject to the same finite bandwidth B=1 as every other node. The Stride-10 sampling window imposes a Nyquist limit on perceptual resolution. An SVD spectral audit reveals that over 95% of perceptual energy is concentrated in a single dominant mode across all tested lattice sizes — the topological origin of the subjective flow of time. This dominant mode is not a saturation plateau claim; the trend is monotonic and robust, with verification on larger lattices left as future numerical work. Three spatial dimensions are inherited from the d=3 efficiency plateau (H); the temporal dimension is inherited from the dominant singular mode of the directed sampling operator. Special and General Relativity are shown to be the geometry of bandwidth allocation on the causal graph (hardware). Motion is defined as the re-indexing of adjacency edges; the Pythagorean constraint f_int^2 + f_ext^2 = B^2 yields time dilation as an algebraic necessity. The 1/r gravitational potential is the Discrete Green's Function of the 3D graph Laplacian — a topological fingerprint of three-dimensional space. Quantum Mechanics describes the information-theoretic limits of observing that hardware with finite resources (software). The wavefunction arises as a beat envelope from aliased sampling, inheriting linearity from hardware unitarity. Measurement collapse is bandwidth hijacking. The uncertainty principle is the Nyquist limit, with a dimensionless uncertainty floor from the bandwidth constraint. Pauli exclusion is buffer-overflow protection with spin-±1/2 as time-division multiplexing. Entanglement is interpreted as a candidate topological trace on the 1D causal skeleton mandated by the Being Tax — a hypothesis, not yet a derivation. These two descriptions are not contradictory but are descriptively orthogonal, dynamically coupled layers of a single computational stack governed by the Pythagorean bandwidth constraint. The contradiction dissolves upon recognizing that physicists have been attempting to locate hardware bus specifications within software rendering algorithms. The observer's sampling rent is quantitatively denominated in Zhangyu (ZY): H_obs ≈ 1.0117 ZY as a preliminary numerical estimate. The hydrogen atom spectrum is reproduced on the discrete C8 lattice, converging to the continuum Schrödinger limit with 0.0024% deviation. ħ is demoted from fundamental status: ħ = Z × t_Tick, the product of bandwidth currency and the Tick. The preferred basis problem (OP-8), the first-principles derivation of the GR coefficient 2GM/c² (OP-O1), and Bell statistics for skeletal entanglement (OP-24) are honestly marked as open problems. The Born rule is identified as a maximum-entropy hypothesis, not yet a formal derivation from graph topology. A complete Scope and Logical Boundaries declaration is included, alongside extended classical references (Nyquist, Shannon, Born, Einstein, Bell).
Yu Zhang· Zenodo (CERN European Organi...· 0 citations
A guaranteed-coverage confidence interval for the two-sample standardized effect William J. Dwyer, MD, MPH, FAAP — Department of Mathematics and Statistics, University of Massachusetts Lowell. ORCID 0009-0004-0855-7222. Concept DOI (always resolves to the latest version): minted on first publication. What this is The reproducibility deposit for the m01te methods paper: a guaranteed-coverage confidence interval for the two-sample standardized effect (Cohen's d) at the skewed, unequal-variance, small-n corner where the textbook interval silently under-covers. The noncentral-t inversion assumes normal data and equal variances; at a lognormal, four-to-one variance-ratio, n = 10 design its realized coverage falls to 0.81 against a nominal 0.95, and a naive percentile bootstrap of dfalls further, to 0.78 — a joint failure of the mean-difference reference and the variance estimate that standardizes it, which resampling does not repair. The paper gives a three-tier recommendation, mirroring the companion two-sample test and the one-way effect-size paper: Classical — the noncentral-t / normal-approximation interval, the everyday default, liberal at the corner. Calibrated middle tier — the guaranteed two-sample test T_BB inverted for the mean difference at the full level, divided by the plug-in pooled scale. Closed-form and deterministic (no resampling), with near-nominal worst-case coverage 0.93 at about 1.6× the classical width. It keeps the mean-difference deflation that repairs the actual under-coverage while treating the scale at its point estimate; the over-covering numerator and the under-covering plugged-in scale roughly cancel to near nominal. Guaranteed floor — a Bonferroni combination of the T_BB-inverted mean-difference interval with a distribution-free bootstrap scale interval, carrying a proved finite-sample coverage floor (worst-case 0.97) at about 4× the classical width. What the deposit contains Manuscript (author + anonymized markdown; built .docx/.pdf, including a cross-reference–hyperlinked variant) and the derivations (D1–D6): the estimand and its d_av scale; the T_BB-inverted mean-difference interval; the exact Bonferroni coverage floor of the ratio interval; why the classical standard error under-covers off its normal/equal-variance premise; the deterministic-simulation confirmation; and the calibrated middle tier with its compensation argument. Reproducibility runner — rerun/rc_m01te_coverage.py computes, for each design cell across the parent-distribution × sample-size × variance-ratio × effect grid, the realized coverage and mean width of all four intervals (classical, percentile-bootstrap, calibrated middle, guaranteed floor). Every number regenerates from this deterministically-seeded script (seed 20260826); its locked output CSV is deposited. Figure — figures/m01te_coverage.png (built by make_m01te_figure.py): the four coverage curves cell by cell across the grid, the classical and bootstrap curves sliding below nominal at the corner, the calibrated curve tracking near it, and the guaranteed curve holding above it. All evaluation is simulation-based. Code is released under the MIT License; text and figures under CC BY 4.0. How to cite Please cite this deposit if you use the package or the method. Citing the concept DOI references the work in general and always resolves to the latest version; cite a specific version DOI to point at an exact snapshot. Dwyer, W. J. (2026). A guaranteed-coverage confidence interval for the two-sample standardized effect: reproducibility deposit (Version 1.0.0) [Software]. Zenodo. https://doi.org/⟨concept DOI⟩
William Dwyer· Zenodo (CERN European Organi...· 0 citations
Software and derived tables for partitioning every record of the BOLD public data package into three provenance states: imported from INSDC, native to BOLD but deposited into INSDC, and exclusive to BOLD. For the median taxonomic class, 79% of BOLD records are also held by INSDC. Includes the audit that adjudicates the provenance criterion, and a null simulation for testing associations between ratios that share a denominator.
F. Patti· Zenodo (CERN European Organi...· 0 citations
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This second section of the study addresses the design and fabrication of the equipment developed for the preparation and shaping of rocket propellant. Two primary pieces of equipment were developed within the scope of the study: a Temperature-Controlled Fryer and a Propellant Shaping Stand. The Temperature-Controlled Fryer was designed to maintain the temperature of the container in which the rocket propellant is prepared at the desired value through a microcontroller (MCU – PIC). The Propellant Shaping Stand is used to shape the prepared propellant into the desired form. These pieces of equipment were developed as a result of extensive testing and design studies and also allow different design approaches to be implemented. The study additionally addresses the importance of indirect and controlled heating and explains the fundamental operating principles of the equipment employed. By presenting the design drawings, fabrication stages, electronic circuits, and software as an integrated part of the study, the design and manufacturing processes of the developed systems are examined.
ercan koçlar· Zenodo (CERN European Organi...· 0 citations
This second section of the study addresses the design and fabrication of the equipment developed for the preparation and shaping of rocket propellant. Two primary pieces of equipment were developed within the scope of the study: a Temperature-Controlled Fryer and a Propellant Shaping Stand. The Temperature-Controlled Fryer was designed to maintain the temperature of the container in which the rocket propellant is prepared at the desired value through a microcontroller (MCU – PIC). The Propellant Shaping Stand is used to shape the prepared propellant into the desired form. These pieces of equipment were developed as a result of extensive testing and design studies and also allow different design approaches to be implemented. The study additionally addresses the importance of indirect and controlled heating and explains the fundamental operating principles of the equipment employed. By presenting the design drawings, fabrication stages, electronic circuits, and software as an integrated part of the study, the design and manufacturing processes of the developed systems are examined.
ercan koçlar· Zenodo (CERN European Organi...· 0 citations
This reproducibility-focused software archive provides the Residual-on-Inertia Curve–Event Transformer (RICE-Former) materials used in the manuscript RICE-Former: A Residual-on-Inertia Curve–Event Transformer for Event-Aware 1–4 h Glucose Trajectory and Glycemic Event Forecasting. The repository supports independent audit of the study's four connected designs: (1) typed event marks that retain each meal, bolus, correction, and basal record; (2) wall-clock lag encoding relative to the prediction origin; (3) a residual-on-inertia connection that generates a 48-point 1–4 h trajectory over a persistence reference; and (4) a curve–event dual-branch decoder that produces the trajectory and 16 event–horizon scores from shared memory. Included materials RICE-Former method code: marked-event adapters, shared encoder, residual-on-inertia curve generation, and dual-branch event queries (CEQT is the retained engineering codename) Locked protocol and splits: prediction horizons, event thresholds, leakage checks, and the frozen AZT1D participant allocation Evaluation and baseline code for the staged experiment pipeline Privacy-preserving aggregate result tables for AZT1D, OhioT1DM, and DiaTrend curve, event, ablation, slice, and mechanism summaries Aggregate analysis tables for subject-level metrics and paired statistical tests Manuscript figures used in the paper, including the illustrative trajectory panels Documentation for data access, reproducibility, and GitHub–Zenodo release steps Repository layout src/ceqt/: model, data adapters, training, evaluation, baselines, and staged experiment code results/tables/: locked protocol, split identifiers, aggregate performance tables, and leakage-test report results/analysis/: aggregate subject-level metrics and paired tests results/figures/: manuscript figures scripts/: subject-level aggregate analysis exports docs/: data access, reproducibility, and release instructions Install and verify conda env create -f environment.yml conda activate rice-former export PYTHONPATH="$PWD/src" Obtain AZT1D, OhioT1DM, and DiaTrend from their original providers, arrange them as described in docs/data-access.md, and run selected stages with python -m ceqt.phases.run --from P0 --to P9. Data and privacy boundary The datasets analyzed in the study are available from their original sources: AZT1D (Mendeley Data, 10.17632/gk9m674wcx.1), OhioT1DM (Marling and Bunescu, 2020), and DiaTrend (Synapse, 10.7303/syn38187184). This deposit archives method and evaluation code, locked protocol files, aggregate result tables, analysis tables, and manuscript figures. Raw CGM records, participant event logs, the numeric extract behind the illustrative trajectory figure, credentials, trained weights, and caches are not redistributed. Details are provided in docs/data-access.md. Citation Please cite this software archive as: Liu Q, Yang M, Wang Z, Wang S, An X, Lu S, Yang Q, Liu M, Wu Z, Huang D. RICE-Former: a curve–event Transformer. Zenodo. https://doi.org/10.5281/zenodo.22171786 Citation metadata are also provided in CITATION.cff. Please cite the accompanying manuscript when referring to the scientific findings. Software repository: https://github.com/modalfuse/rice-former
Qiang Liu, Ming Yang, Zijiaqi Wang et al.· Zenodo (CERN European Organi...· 0 citations
This dataset contains the 6-month Standardized Precipitation Index (SPI-6) monthly time series for all 331 Divisional Secretariat (DS) divisions of Sri Lanka, spanning 1981 to 2024. SPI-6 values were computed using the SPI_SL_6.exe software, developed in line with World Meteorological Organization (WMO) recommendations, from monthly precipitation data interpolated across the 331 DS-divisions via Kriging from 62 meteorological stations operated by the Department of Meteorology, Sri Lanka. The dataset supports the manuscript "SPI-Based Spatiotemporal Drought Frequency and Trends across the Divisional Secretariat Divisions in Sri Lanka" (Pramudi et al., submitted to Natural Hazards and Earth System Sciences, manuscript ID egusphere-2026-5234), which uses these SPI-6 values to derive drought frequency across five severity categories and to assess long-term monotonic trends at the DS-division scale using the Mann–Kendall test and Sen's slope estimator.
D.G.L. Pramudi, U. T. G. Perera, F. Ruzaik et al.· Zenodo (CERN European Organi...· 0 citations
This release contains the versioned software, frozen experiment records, automated tests, publication figures, and bilingual manuscript sources associated with an identifiability-aware method for selecting shared finite-memory models from sparse grouped observations. The method fits candidate positive-rate realizations with rates shared across independent specimens or material groups and unit-specific amplitudes and offsets. A candidate order is retained only when information gain, held-unit early-to-late prediction, foldwise log-rate stability, and adjacent-rate resolution support the same interpretation. When these criteria disagree, the model order is reported as unresolved. The archive corresponds to GitHub commit 13001874f788f9de9b49632961166d3713561f7b. It includes source code, 151 automated tests, frozen machine-readable results, experiment drivers, vector figures, and English and Chinese AMM manuscript sources. Third-party public datasets are not redistributed. Persistent source identifiers, frozen SHA-256 digests, and a verified downloader are included so that the public inputs can be retrieved from their authoritative repositories. The software is released under the MIT License. Dataset licenses and attribution requirements remain those of the original data providers.
Haitao Duan, Ning Hu, Shuqun Li et al.· Zenodo (CERN European Organi...· 0 citations
The Machine with Two Levers is a standalone WidiVision exploration of Expanded Halving and Doubling (EHD). A museum-story Vignette introduces a machine with two principal motions—MEDIATE and DUPLICATE—and a small REMEMBER tray. The following Illumination reorganizes addition, subtraction, multiplication, and division as different journeys through a common architecture of descent, ascent, parity memory, comparison, selection, and reconstruction. The purpose is conceptual rather than computational speed. The publication does not claim novelty for the classical halving-and-doubling methods used in multiplication and division. Its contribution is a unified WidiVision reading that makes relationships among the four basic operations visible to a general reader. Multiplication and division are closed within the system by reusing EHD addition and subtraction as nested journeys rather than silently importing the ordinary operations. The deposit includes Computational Exploration EHD.1 — The Two-Lever Laboratory, a self-contained offline browser instrument. Readers may enter their own numbers, advance through structural events one step at a time, inspect the memory record, and reconstruct results for a single number, addition, subtraction, multiplication, and division. Bill Widi conceived EHD and directed its development as a WidiVision exploration. ChatGPT (OpenAI) assisted with formalization, drafting, software implementation and testing, and editorial refinement. Bill Widi reviewed the work and takes responsibility for its final form.
Bill Widi· Zenodo (CERN European Organi...· 0 citations
The aim of this study is to determine the levels of organizational deviance behaviors among employees in the banking sector, to identify the sub-dimensions of organizational deviance, and to examine whether these behaviors differ according to employees’ demographic characteristics. The population of the study consists of employees working in public and private banks operating in the city center and districts of Konya. Within the scope of the sample determined based on a 95% confidence level and a 5% margin of error, data were collected from 470 bank employees using a survey method. To measure organizational deviance behaviors, the “Workplace Deviance Scale” developed by Bennett and Robinson (2000) and adapted into Turkish was utilized. The collected data were analyzed using the SPSS 22 statistical software package; descriptive statistics, factor analysis, reliability analysis, t-test, ANOVA, Kruskal–Wallis, and correlation analyses were employed. The findings indicate that organizational deviance behaviors are more strongly associated with organizational processes and work environment–related factors rather than individual demographic characteristics. By examining organizational deviance behaviors within the context of the banking sector, this study contributes to the literature and provides important implications for managers regarding the evaluation of employee behaviors within the framework of preventive and developmental human resource policies.
Fatih İbrahim Kurşunmaden· Selçuk Üniversitesi Sosyal B...· 0 citations
This record contains the corrected deterministic implementation freeze for HLV-R-MECH-001. The controlling scientific protocol is: Krūger, M. (2026). HLV-R-MECH-001: Prospective Triangle-Matched Mechanism Test of the Surviving Degree-Preserving Rewire Spectral Residual — Pre-Execution Protocol Freeze v0.1.0. Zenodo. DOI: 10.5281/zenodo.22166283 The public predecessor implementation is: Krūger, M. (2026). HLV-R-MECH-001: Deterministic One-Click Engine for Triangle-Matched Rewire Mechanism Testing — Implementation Freeze v0.1.0 [Computer software]. Zenodo. DOI: 10.5281/zenodo.22166434 Version v0.1.1 corrects only the numerical-runtime bootstrap of the One-Click Colab launcher. The first locked execution under v0.1.0 terminated before any scientific evaluation because the assigned Google Colab runtime exposed: NumPy 2.1.3 SciPy 1.16.3 while the frozen scientific implementation requires: NumPy 2.3.5 SciPy 1.17.0. The resulting machine state was: RMECH001_INCONCLUSIVE_NUMERICAL with spectral_computation_started = false. Therefore the stopped execution did not evaluate the confirmatory R_DEG or R_TRI spectra, did not compute target QSPEC or RRESP scores, and did not produce a scientific HLV-R-MECH-001 mechanism verdict. The scientific engine itself has not been changed. The v0.1.1 launcher contains the exact byte-identical scientific engine used in public implementation freeze v0.1.0. Frozen scientific engine SHA-256: 317df650991120f686768ffc07d12f044f58e38ce8f2c47c083901bf1d7a8a14 The corrected launcher now performs the following runtime bootstrap before starting the unchanged scientific engine: 1. inspect the assigned host numerical environment; 2. if the host already provides exactly NumPy 2.3.5 and SciPy 1.17.0, use that environment directly; 3. otherwise create an isolated Python virtual environment; 4. install exact binary versions: NumPy 2.3.5 SciPy 1.17.0; 5. verify the installed versions explicitly; 6. verify the embedded scientific-engine SHA-256; 7. only after these checks execute the unchanged frozen HLV-R-MECH-001 scientific engine. The correction occurs entirely outside the scientific engine. No scientific rule has been modified. In particular, v0.1.1 does not change: - the DG-001 target; - the target graph identity; - the R_DEG control family; - the R_TRI control family; - confirmatory seed streams; - candidate ordering; - accepted-swap counts; - proposal caps; - structural admission rules; - the 40–45% edge-replacement-depth requirement; - the 31-control family size; - exact degree-sequence preservation; - exact global triangle preservation T = 6960 in R_TRI; - the between-family rewiring-depth gate; - QSPEC; - RRESP; - spectral bands; - leave-one-out scoring; - the robust-margin threshold; - numerical scientific hard gates; - or scientific machine-verdict logic. The frozen mechanism design therefore remains identical to the controlling protocol DOI 10.5281/zenodo.22166283. The two confirmatory control families remain: R_DEG: fresh degree-preserving structural rewires of the fixed DG-001 target graph. R_TRI: fresh rewires preserving both the exact labelled target degree sequence and the exact global triangle count T = 6960. Each family requires 31 accepted controls. The structural firewall remains unchanged: the complete R_DEG and R_TRI control banks must be generated, structurally validated, written to disk, and hash-fixed before any confirmatory spectral calculation is permitted. No control may be admitted or rejected using eigenvalues, QSPEC, RRESP, spectral-band distances, target-control scores, or scientific verdict information. The corrected implementation was validated only with burned development seeds and synthetic numerical checks. Correction validation confirmed: - exact protocol verification: PASS; - NumPy 2.3.5 / SciPy 1.17.0 environment validation: PASS; - burned R_DEG generation: PASS; - exact labelled degree-sequence preservation: PASS; - burned R_TRI generation with 10,000 accepted swaps: PASS; - exact triangle preservation T = 6960: PASS; - connectivity: PASS; - approximately 40–45% edge replacement: PASS; - deterministic replay: PASS; - synthetic QSPEC/RRESP implementation checks: PASS. No confirmatory HLV-R-MECH-001 seed stream was used during correction validation. No confirmatory target spectrum was computed. No confirmatory target QSPEC or RRESP score was computed. No scientific HLV-R-MECH-001 verdict was generated. The corrected One-Click notebook SHA-256 is: e8d1f516bc7a600039b44a7f2de8bdf5ecdc51a739d39aaf1e839d97d7e4bc95 The corrected implementation-freeze PDF SHA-256 is: e75aee3a4c790fefafda41aee93c6c267c814b66739bd1070355b519eb98452c The corrected implementation package SHA-256 is: d6e2d6ef3bf0b315bcbf7270c3be591bca28b7c13ef5730af30cb9bbead70b0f The unchanged scientific engine SHA-256 is: 317df650991120f686768ffc07d12f044f58e38ce8f2c47c083901bf1d7a8a14 This record supersedes implementation freeze v0.1.0 only with respect to numerical-environment bootstrapping. It does not supersede or alter the scientific protocol. HLV-R-MECH-001 remains a finite graph-mechanism test. Neither this corrected implementation nor any later HLV-R-MECH-001 result can by itself establish unique HLV geometry, physical selection of the golden ratio, extra dimensions, spacetime, particle physics, an absolute energy scale, gravity, dark matter, dark energy, cosmology, or experimental validation. The purpose of this corrected implementation freeze is solely to ensure that the prospectively frozen scientific engine can execute in a numerically reproducible environment despite changes in the externally assigned Colab runtime.
Marcel Krüger· Zenodo (CERN European Organi...· 0 citations
A USAF cadet and a Lincoln Laboratory researcher found AI chatbots can help nontechnical service members produce viable software applications for their unique problems.
