| # Brain–language-model alignment: ds006239 (roi-language) |
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| Wang et al. 2025 — word-level phonological and semantic reading tasks in children and adolescents aged 10–17. |
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| - Paper: https://www.sciencedirect.com/science/article/pii/S2352340925009692 |
| - Data: https://openneuro.org/datasets/ds006239/versions/1.0.5 |
| - Generated: 2026-09-10 |
| - Pipeline: https://github.com/suchirsalhan/cdl-representations-brains-babylms |
| - Masking: **roi-language** -- see DATASETS.md section 10 for the three-level standard (phonology/language/all) this is part of, and how it differs from the whole-brain reference. |
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| ## Read this first: does the measurement work? |
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| Every alignment number in this dataset is only as meaningful as the brain |
| RDMs it was computed against. So before any model result, the same |
| pipeline is asked whether *anything* stimulus-driven correlates with those |
| RDMs — stimulus duration, intensity, word length, frequency, phoneme and |
| syllable counts, an acoustic model of the audio where the stimuli are |
| audio, and the study's own condition contrast — each tested by a |
| permutation test that shuffles stimulus identity. |
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| **GATE: FAILED. 0/38 stimulus tests are significant** after Holm |
| correction — not the acoustic model of the audio the children actually |
| heard, not the study's own experimental contrast. |
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| **The alignment numbers below are therefore uninterpretable as |
| evidence about language models.** They measure a representational |
| geometry that does not demonstrably encode the stimuli. They are |
| published for completeness and for whoever fixes the estimator, not as |
| a result. Do not cite them as evidence that models fail to align with |
| the developing brain. |
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| Measured cause, from `control/`: |
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| - RDM effective rank: **61** of 84 stimuli |
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| Note that this is NOT ds003604's failure mode. There, the RDM |
| effective rank was ~3 of 40-48 stimuli -- near-degenerate betas |
| that could not express stimulus-level structure at all. The rank |
| recorded above is a large fraction of the stimulus count, so these |
| RDMs do carry stimulus structure and the control failing here means |
| the specific controls tested did not reach significance, not that |
| the measurement is uninterpretable. Check `control/` for which |
| controls ran: an acoustic or visual control needs the dataset's |
| stimulus files present, and reports zero features if they are not. |
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|
| ## What was built |
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| 8 task × session cells, each an RDM over the stimuli |
| shared by that cell's subjects, with voxel patterns z-scored **within |
| run** before aggregation (without that, the RDM measures scanner drift |
| rather than language) and an inter-subject noise ceiling. |
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|
| | task | session | n_stim | ceiling_lower | ceiling_upper | ceiling_n | |
| |:---------|:----------|---------:|----------------:|----------------:|------------:| |
| | Orth | ses-11+ | 96 | 0.565363 | 0.596556 | 48 | |
| | Orth | ses-11 | 96 | 0.525637 | 0.564327 | 39 | |
| | Phon | ses-11+ | 96 | 0.565363 | 0.596556 | 48 | |
| | Phon | ses-11 | 96 | 0.525637 | 0.564327 | 39 | |
| | Sem | ses-11+ | 72 | 0.390139 | 0.433242 | 50 | |
| | Sem | ses-11 | 72 | 0.351029 | 0.405242 | 39 | |
| | SemLocal | ses-11+ | 48 | 0.310001 | 0.359958 | 49 | |
| | SemLocal | ses-11 | 48 | 0.26477 | 0.331669 | 34 | |
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| Model grid: **15 families**, 2096 alignment rows across 8 cells. |
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| | | | |
| |---|---| |
| | mean noise ceiling | 0.437 | |
| | best alignment anywhere | 0.0691 | |
| | as a fraction of ceiling | 19.7% | |
| | families equivalent to zero (TOST ±0.05) | 15/15 | |
| | Pythia scale trend | ρ = -0.348, p = 0.03 | |
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|
| ### Per family |
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| | family | n_checkpoints | rsa_mean | rsa_sd | rsa_abs_max | frac_of_ceiling_abs_max | p_equivalence_tost | |
| |:----------------------|----------------:|-----------:|---------:|--------------:|--------------------------:|---------------------:| |
| | pico-decoder-tiny | 21 | 0.0053 | 0.0058 | 0.0538 | 0.119 | 0 | |
| | pico-decoder-small | 21 | 0.0035 | 0.0125 | 0.0522 | 0.1971 | 0 | |
| | babylm-gpt2 | 9 | 0.002 | 0.0104 | 0.0389 | 0.0997 | 0 | |
| | pico-decoder-large | 21 | 0.0015 | 0.009 | 0.0474 | 0.162 | 0 | |
| | pico-decoder-medium | 21 | -0.0007 | 0.0086 | 0.0476 | 0.1798 | 0 | |
| | beetle-humanscale-eng | 18 | -0.0014 | 0.0122 | 0.0423 | 0.1365 | 0 | |
| | pythia-70m-full | 21 | -0.0016 | 0.0103 | 0.0382 | 0.1389 | 0 | |
| | pythia-410m-full | 21 | -0.0046 | 0.0102 | 0.0458 | 0.1479 | 0 | |
| | beetle-fineweb3-eng | 19 | -0.0057 | 0.0119 | 0.0504 | 0.1905 | 0 | |
| | pythia-1b-full | 21 | -0.0098 | 0.0045 | 0.0461 | 0.1455 | 0 | |
| | pythia-160m-full | 21 | -0.0116 | 0.0058 | 0.0423 | 0.1598 | 0 | |
| | pythia-1.4b-full | 21 | -0.0135 | 0.0044 | 0.0595 | 0.1642 | 0 | |
| | babylm-gpt2-5 | 9 | -0.0262 | 0.0336 | 0.0663 | 0.1262 | 0.0427 | |
| | babylm-gpt2-7 | 9 | -0.0265 | 0.034 | 0.0691 | 0.1314 | 0.0457 | |
| | babylm-gpt2-3 | 9 | -0.027 | 0.0336 | 0.067 | 0.1275 | 0.0471 | |
| |
| ## Dataset-specific notes |
| |
| Contains **LocalSem**, the only genuinely run/stimulus-CROSSED language cell across all four datasets in this project: its stimuli recur across runs, so run identity and stimulus identity are separable and the scanner-run confound that invalidated the first ds003604 analysis cannot arise. Per-subject age is NOT recoverable from the release — participants.tsv has birthdate but no scan date and there are no *_scans.tsv files — so this dataset is cohort-level only and cannot carry the developmental axis as published. |
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| ## Files |
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| | path | what | present here | |
| |---|---|---| |
| | `alignment_by_checkpoint.csv` | every model × checkpoint × cell, with ceiling | ✓ | |
| | `alignment_by_family.csv` | per family, with equivalence tests | ✓ | |
| | `alignment_by_cell.csv` | per task × session | ✓ | |
| | `ceilings_ds006239.csv` | noise ceiling per cell | ✓ | |
| | `control/` | the positive control and RDM dimensionality — the gate | ✓ | |
| | `scale_ladder.csv` | the Pythia 70M→1.4B scale test | ✓ | |
| | `fig_*.pdf, fig_*.png` | figures | ✓ | |
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| ## Method |
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| Representational similarity analysis. For each cell, a brain RDM over |
| stimuli (correlation distance between per-stimulus GLM beta patterns, |
| within-run z-scored, aggregated across subjects) is compared by Spearman |
| correlation with a model RDM over the same stimuli, taken from each |
| checkpoint's hidden states. Alignment is reported raw and as a fraction of |
| the inter-subject noise ceiling, and judged against a null built from the |
| PARC suite — 18 models differing only by random seed, which is what 'no |
| effect' looks like on this measurement. |
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| Null and fixation trials are excluded from the stimulus set. For paired |
| designs the stimulus identity is the pair, not either word alone. |
