% ===================================================================== % Theodor Spiro — publications % Bibliography file for al-folio Jekyll site % ===================================================================== % % Conventions used here: % - @article for preprints with a DOI (or under review at a venue) % - @misc for in-prep manuscripts and tool/dataset releases % - selected = {true} — surfaces on the /about page under "Selected work" % - bibtex_show = {true} — adds a "BibTeX" button next to the entry % - code = {url} — adds a code-link button % - abbr — venue badge shown next to the title % - status — internal note on stage; not rendered, used for sorting % % Author identity: all entries are by Theodor Spiro (ORCID 0009-0004-5382-9346). % ===================================================================== % ===================================================================== % CELLULAR PERCEPTION — FRAMEWORK AND TOOLKIT % ===================================================================== @software{spiro2026perceptome, abbr = {toolkit}, title = {perceptome: a Python toolkit for cellular perception analysis}, author = {Spiro, Theodor}, year = {2026}, version = {0.3}, doi = {10.5281/zenodo.20113468}, url = {https://doi.org/10.5281/zenodo.20113468}, code = {https://github.com/mool32/perceptome}, abstract = {A Python toolkit treating 44 cellular signaling pathways (NF-kB, mTOR, UPR, p53, nuclear receptors, ...) as a cell's perceptual repertoire. Three capabilities other tools don't directly provide: (1) a 9-PC eigenspace derived from 154 normal human cell types (Human Protein Atlas) where any cell can be located on the same map; (2) a capacity-floor predictor that says whether a cell type and pathway will ramp under stimulus or is already saturated; (3) a validity scorecard with three null controls (random-gene panel, housekeeping, cell cycle) that catches common perturbation artifacts before interpretation. Headline empirical result: an 8-cell attractor cluster (gastric chief, pancreatic acinar, parietal, megakaryocytes, cytotrophoblasts, migrating cytotrophoblasts, late primary spermatocytes, gastric progenitor) toward which 11 cancers from 11 organ systems converge during transformation — independently replicated on the Sun et al. 2021 paired HCC cohort. The tool implements only what the underlying multi-year pre-registered research program validated and deliberately excludes operations that were tested and falsified.}, selected = {true}, bibtex_show = {true}, status = {public-release-v0.3} } % ===================================================================== % BIOLOGY / AGING BIOMARKERS % ===================================================================== @article{spiro2026ecg, abbr = {bioRxiv}, title = {Spectral exponents of the twelve-lead ECG reveal the anatomy of cardiac conduction disorders and a bifurcation between aging and disease}, author = {Spiro, Theodor}, journal = {bioRxiv}, year = {2026}, doi = {10.5281/zenodo.19945065}, url = {https://doi.org/10.5281/zenodo.19945065}, code = {https://github.com/mool32/ecg-spectral-exponents}, pdf = {ecg_spectral_exponents_spiro_2026.pdf}, abstract = {Spectral exponent beta extracted from 412,730 twelve-lead recordings across three continents (PTB-XL, Chapman-Shaoxing, CODE-15). beta is diagnostic of cardiac conduction anatomy: CLBBB vs CRBBB AUC=0.982 (Germany), 0.982 (China), 0.979 (Brazil), versus 0.688 for QRS duration alone. Aging flattens the spectrum; disease steepens it. Honest null on independent mortality prediction (HR=1.02, p=0.83).}, selected = {true}, bibtex_show = {true}, status = {preprint-submitted, bioRxiv ID BIORXIV/2026/717157} } @article{spiro2026waveform, abbr = {Front. Aging Neurosci.}, title = {Waveform asymmetry as a biomarker of neural aging: spatial degradation of oscillatory cycle shape across two independent cohorts}, author = {Spiro, Theodor}, journal = {Frontiers in Aging Neuroscience (under review)}, year = {2026}, doi = {10.5281/zenodo.19912202}, url = {https://doi.org/10.5281/zenodo.19912202}, code = {https://github.com/mool32/waveform-asymmetry-aging}, pdf = {waveform_asymmetry_spiro_2026.pdf}, abstract = {Peak-trough asymmetry of EEG oscillations across five frequency bands in 215 (LEMON) and 608 (Dortmund Vital Study) adults, with 208-subject 5-year longitudinal follow-up. Beta-band asymmetry decreases with age (r=-0.326 LEMON, r=-0.314 Dortmund); effect size exceeds classical alpha slowing. Theta spatial entropy predicts memory independent of age.}, selected = {true}, bibtex_show = {true}, status = {under-review, Frontiers in Aging Neuroscience} } @article{spiro2026pitissue, abbr = {bioRxiv}, title = {Transcriptomic noise accumulates within tissue identity across human aging: a systemic signature distinct from cell-composition drift}, author = {Spiro, Theodor}, journal = {bioRxiv}, year = {2026}, doi = {10.5281/zenodo.19944444}, url = {https://doi.org/10.5281/zenodo.19944444}, code = {https://github.com/mool32/pi-tissue-aging}, pdf = {pi_tissue_spiro_2026.pdf}, abstract = {Three-level variance decomposition of bulk transcriptomes from 263 GTEx v8 donors (ages 20-79) plus single-cell data from Tabula Muris Senis, Calico rat caloric-restriction atlas, and a rhesus macaque cross-species atlas. Tissue identity is preserved across forty years of aging; the signature is systemic noise, not selective accumulation. Caloric restriction acts as a noise filter, not a structure restorer. Cross-species lifespan scaling (alpha=-1.02, R^2=0.90).}, selected = {true}, bibtex_show = {true}, status = {preprint-submitted, post-review v4} } @misc{spiro2026oscillatorycancer, abbr = {preprint}, title = {Temporal architecture of signaling oscillations predicts cancer gene function across pathways}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Preprint}, code = {https://github.com/mool32/oscillatory-cancer-framework}, pdf = {oscillatory_cancer_framework_spiro_2026.pdf}, abstract = {157 genes across 14 oscillatory signaling pathways classified into rise-phase and recovery-phase components by temporal role only. Rise genes enriched for oncogenes, recovery for tumor suppressors (OR=27.5, p=3.6e-9). 12/12 pathways with testable cancer genes match the prediction; 12 anti-coupled cases in growth-inhibitory pathways (p53, TGF-beta) match the predicted inversion. On 22 divergent cases between temporal and naive biochemical classification, temporal framework correct in 19/22 (86 percent). GoF drug targets concentrated in rise arm (28/33 = 85 percent, p=3.3e-5).}, bibtex_show = {true}, status = {preprint-public-on-github, github-public} } @misc{spiro2026nflcancer, abbr = {preprint}, title = {Negative feedback loop architecture as a modular predictor of cancer vulnerability across signaling pathways}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Manuscript, in preparation}, code = {https://github.com/mool32/oscillatory-nfl-cancer}, pdf = {oscillatory_nfl_cancer_spiro_2026.pdf}, abstract = {Algorithmic extraction of all short negative-feedback loops (NFLs) from 159 KEGG signaling networks. 128 unique motifs collapse into 14 pathway-level oscillatory modules; NFL genes are 59-fold enriched for Cancer Gene Census membership compared to non-NFL genes in the same pathways (Fisher exact p=9e-44). Conservation gradient from universal eukaryotic loops (ERK/DUSP, Ca2+/SERCA, ~1500 Mya) to vertebrate-specific (Notch, JAK-STAT, ~435 Mya). Irreversible Authority (IA) metric predicts cancer gene fraction across modules with Spearman rho=0.83. Eigenspace projection identifies 20 novel cancer gene candidates, 13 (65 percent) IntOGen-validated.}, bibtex_show = {true}, status = {manuscript-in-preparation, github-public} } % ===================================================================== % CROSS-DOMAIN: LLM <-> BIOLOGY BRIDGE % ===================================================================== @misc{spiro2026clonalcrystallization, abbr = {preprint}, title = {Clonal crystallization as a shared signature of bone-marrow aging and neural-network training}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Manuscript, in preparation}, code = {https://github.com/mool32/clonal-crystallization-aging}, pdf = {clonal_crystallization_spiro_2026.pdf}, abstract = {A two-metric framework (Gini coefficient and effective number of contributing components, eff_N) applied jointly to cell-type proportion distributions in mouse tissues and to head-importance distributions across Pythia-410M training. Pythia moves through (Delta-Gini, Delta-eff_N) by (+0.145, -45.5) over 143k training steps; mouse bone marrow on FACS and Droplet platforms moves in the same quadrant of the plane (+0.088, -2.19 / +0.038, -0.54). Kidney and Limb Muscle also crystallize at coarse granularity; Lung and Spleen disperse, replicated on Kimmel 2019. Granularity is a primary parameter: Kidney TMS sub-cell-type analysis shows podocytes crystallize while macrophages disperse. Caloric restriction in rat bone marrow rescues 64 percent of the Gini drift and 57 percent of the eff_N drift (P(rescue greater than 0) = 1.000). A specific substrate-independent compositional signature, narrower than full DFE universality (companion paper arXiv:2604.10571).}, selected = {true}, bibtex_show = {true}, status = {manuscript-in-preparation, github-public} } % ===================================================================== % LLM RESEARCH % ===================================================================== @misc{spiro2026functionaldifferentiation, abbr = {preprint}, title = {Functional differentiation generates universal fitness-effect distributions in neural networks}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Preprint}, code = {https://github.com/mool32/functional-differentiation-dfe}, pdf = {functional_differentiation_dfe_spiro_2026.pdf}, abstract = {Ablation studies of 144 identity-tracked attention heads, 24 transformer layers, and 30 distributed-noise perturbations at each of 8 checkpoints (step 512 to step 143000) of Pythia 410M-deduped. 1,584 ablations total; the DFE shape converges to a universal form during training.}, selected = {true}, bibtex_show = {true}, status = {preprint, paper-2-llm-track} } @misc{spiro2026epistasisheads, abbr = {in prep}, title = {Epistasis mapping in transformer attention heads: cross-model multi-checkpoint ablation interactions}, author = {Spiro, Theodor}, year = {2026}, howpublished = {In preparation}, code = {https://github.com/mool32/epistasis-transformer-heads}, abstract = {Pairwise head-ablation interaction maps (epsilon_AB = Delta_AB - (Delta_A + Delta_B)) on Pythia 410M and OLMo2 1B across the full training trajectory. Extends the functional-differentiation DFE work with a population-genetics tool: epistasis. 78 percent of significant top-30 pairs in Pythia 410M show epsilon_loss greater than 0 (synthetic-lethal-like in Costanzo's terminology).}, bibtex_show = {true}, status = {phase-2-in-progress} } @article{spiro2026aievolution, abbr = {arXiv}, title = {Universal statistical signatures of evolution in artificial intelligence architectures}, author = {Spiro, Theodor}, journal = {arXiv}, year = {2026}, eprint = {2604.10571}, archivePrefix = {arXiv}, primaryClass = {cs.LG}, doi = {10.48550/arXiv.2604.10571}, url = {https://arxiv.org/abs/2604.10571}, code = {https://github.com/mool32/ai-evolution-universal-signatures}, abstract = {935 ablation experiments compiled from 161 publications. The distribution of fitness effects of architectural modifications matches biological DFEs across multiple organisms (heavy-tailed Student's t; 68 percent deleterious / 19 percent neutral / 13 percent beneficial for major ablations, n=568); architectural diversification follows logistic dynamics with punctuated equilibria matching paleontological radiation patterns; 14 architectural traits were independently invented 3-5 times in parallel with biological convergences. Evolutionary statistics are shaped by fitness-landscape topology, not selection mechanism.}, selected = {true}, bibtex_show = {true}, status = {preprint-on-arxiv} } % ===================================================================== % AI EPISTEMICS % ===================================================================== @misc{spiro2026oraclefingerprint, abbr = {preprint}, title = {The Oracle's Fingerprint: correlated AI forecasting errors and the limits of bias transmission}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Manuscript, in preparation}, code = {https://github.com/mool32/ai-oracle-fingerprint}, pdf = {oracle_fingerprint_spiro_2026.pdf}, abstract = {Three studies on whether the "wisdom of crowds" survives consultation of a small set of LLMs. Study 1: GPT-4o, Claude, and Gemini show pairwise error correlation r=0.78 on 568 resolved binary Metaculus forecasts. Study 2: human community forecasts move in the LLM-predicted direction (r=0.20, p=0.007), but the shift is fully explained by rational updating toward ground truth (post-control beta=0.023, p=0.36, NS). Study 3: pre-ChatGPT human biases already strongly resembled the LLM pattern (r=0.87); post-ChatGPT the resemblance weakened (r=-0.28). LLMs inherited human biases rather than introducing novel ones; epistemic monoculture is built but not yet activated.}, selected = {true}, bibtex_show = {true}, status = {manuscript-in-preparation, github-public} } % ===================================================================== % COGNITION / METHODS % ===================================================================== @misc{spiro2026datru, abbr = {manuscript}, title = {21,000 attempts to think differently: a large-scale Russian adaptation of the Divergent Association Task reveals practice resistance and lexical predictors of semantic creativity}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Manuscript}, code = {https://github.com/mool32/dat-ru-paper}, url = {https://mool32.github.io/dat-ru/}, abstract = {Russian-language adaptation of the Divergent Association Task (Olson et al., 2021). 21,159 submissions; Cronbach's alpha=0.899; split-half reliability 0.696; no measurable practice effect (i.i.d. sampling model preferred over mixed-effects). Strongest predictor: semantic category diversity (r=0.47). Theoretical ceiling 110.5 (best human attempt: 104.8).}, selected = {true}, bibtex_show = {true}, status = {manuscript-ready, live-instrument-on-github-pages} } % ===================================================================== % NEGATIVE RESULTS / METHODS % ===================================================================== @misc{spiro2026cci, abbr = {report}, title = {Connectivity Contrast Index across five EEG datasets: an honest non-replication and a methods note on universal comprehension biomarkers}, author = {Spiro, Theodor}, year = {2026}, howpublished = {Technical report}, code = {https://github.com/mool32/eeg-connectivity-contrast}, abstract = {18 candidate connectivity and spectral metrics tested across 5 independent EEG datasets totaling 126 subjects, after a promising initial finding (CCI d=+0.564 on a small distance-learning dataset). No metric replicated across datasets; the strongest follow-up signal (wPLI alpha CV on DERCo, p=0.015) reversed direction on ZuCo and showed null effects on two other datasets. Negative result with implications for proposed universal EEG biomarkers of comprehension.}, bibtex_show = {true}, status = {report-ready, write-up-only} }