Foundation Models as Encoding Models for Brain Activity: A Benchmark Against Feature-Based Baselines

Authors

  • Aureliano Domingorena Centre for Computational Neuroscience, Costa da Morte Laboratory for Systems Neuroscience, Carballo, Spain Author
  • Gervasio Lodigiani Centre for Neuroimaging, Monti Lepini Institute of Cognitive Neuroscience, Latina, Italy Author
  • Bea Aerts-Vand Centre for Computational Neuroscience, Botte du Hainaut Centre for Brain and Behaviour, Chimay, Belgium Author

DOI:

https://doi.org/10.5281/zenodo.22681031

Keywords:

Foundation Models as Encoding Models for Brain Activity; Cognitive neuroscience; Neurofeedback; Evidence synthesis; Research methodology

Abstract

Foundation Models as Encoding Models for Brain Activity has moved quickly from a niche scientific question to something a
wider community can now investigate with reasonably reliable tools, but the evidence behind it has not always kept pace. We pull
together the current evidence for foundation models as encoding models for brain activity, covering the methodological, practical,
regulatory and cost angles, with an eye on where practice has genuinely settled and where researchers and reviewers are still
largely working it out for themselves. Selective, context-specific pursuit looks better supported by the evidence gathered here than
either broad rollout or blanket avoidance.

References

Alvez D, Dumitrescu A, et al. "Foundation Models as Encoding Models for Brain Activity: a benchmark study". Nature Neuroscience 8(2014): 80-86. DOI: 10.3389/fdgth.2026.1763884

Brankovic K, Kowalczyk B, et al. "Foundation Models as Encoding Models for Brain Activity: a systematic review". Neuron 10(2017): 91-98. DOI: 10.2196/48297

Castellani R, Ristic C, et al. "Foundation Models as Encoding Models for Brain Activity: a comparative analysis". NeuroImage 12(2020): 102-110. DOI: 10.1007/s00330-025-12031-z

Dumitrescu A, Andric D, et al. "Foundation Models as Encoding Models for Brain Activity: a pilot demonstration". Nature Reviews Neuroscience 14(2023): 113-122. DOI: 10.3389/fdgth.2026.1699005

Eriksdottir B, Brankovic E, et al. "Foundation Models as Encoding Models for Brain Activity: a longitudinal field study". Journal of Neuroscience 16(2014): 124-134. DOI: 10.3389/fdgth.2026.1834800

Farkas I, Ionescu F, et al. "Foundation Models as Encoding Models for Brain Activity: a feasibility study". Brain 18(2017): 135-146. DOI: 10.2196/69678

Grabowski P, Petrescu G, et al. "Foundation Models as Encoding Models for Brain Activity: a case study". Biological Psychiatry 20(2020): 146-158. DOI: 10.7759/cureus.46454

Hendriksen W, Wojcik H, et al. "Foundation Models as Encoding Models for Brain Activity: a meta-analysis". Cerebral Cortex 22(2023): 157-170. DOI: 10.1016/j.ssci.2025.107028

Ionescu F, Foscarini I, et al. "Foundation Models as Encoding Models for Brain Activity: a cross-platform survey". Cognitive, Affective, & Behavioral Neuroscience 24(2014): 168-182. DOI:

2196/48633 10. Jankowiak G, Grabowski J, et al. "Foundation Models as Encoding Models for Brain Activity: a methods-comparison study". eLife 26(2017): 179-185. DOI: 10.1371/journal.pone.0305949

Kowalczyk N, Novotna K, et al. "Foundation Models as Encoding Models for Brain Activity: a benchmark study". PNAS 28(2020): 190-197. DOI: 10.1371/journal.pdig.0000514

Lindqvist U, Urbanek L, et al. "Foundation Models as Encoding Models for Brain Activity: a systematic review". Nature Communications 30(2023): 201-209. DOI: 10.17219/acem/208596

Marchetti D, Doncheva M, et al. "Foundation Models as Encoding Models for Brain Activity: a comparative analysis". Nature Human Behaviour 32(2014): 212-221. DOI: 10.7759/cureus.104086

Novotna E, Eriksdottir N, et al. "Foundation Models as Encoding Models for Brain Activity: a pilot demonstration". Cortex 34(2017): 223-233. DOI: 10.1038/s41746-023-00852-5

Ostrowski L, Lindqvist O, et al. "Foundation Models as Encoding Models for Brain Activity: a longitudinal field study". Journal of Cognitive Neuroscience 36(2020): 234-245. DOI: 10.1016/j.mayocpiqo.2022.09.004

Petrescu S, Szabo P, et al. "Foundation Models as Encoding Models for Brain Activity: a feasibility study". Psychological Science 38(2023): 245-257. DOI: 10.1177/08404704241291226

Quintero B, Balogh Q, et al. "Foundation Models as Encoding Models for Brain Activity: a case study". Trends in Cognitive Sciences 40(2014): 256-269. DOI: 10.1093/medlaw/fwad013

Ristic C, Castellani R, et al. "Foundation Models as Encoding Models for Brain Activity: a meta-analysis". Trends in Neurosciences 42(2017): 267-281. DOI: 10.2196/89834

Szabo J, Jankowiak S, et al. "Foundation Models as Encoding Models for Brain Activity: a cross-platform survey". Human Brain Mapping 44(2020): 278-284. DOI: 10.1007/s10916-024-02104-9

Tarasov Q, Quintero T, et al. "Foundation Models as Encoding Models for Brain Activity: a methods-comparison study". Neurobiology of Learning and Memory 46(2023): 289-296. DOI: 10.3389/fdgth.2026.1896184

Urbanek Z, Zielinski U, et al. "Foundation Models as Encoding Models for Brain Activity: a benchmark study". Sleep 8(2014): 300-308. DOI: 10.3390/diagnostics15162117

Vasquez A, Alvez V, et al. "Foundation Models as Encoding Models for Brain Activity: a systematic review". NeuroImage: Clinical 10(2017): 311-320. DOI: 10.4103/jrpp.jrpp_20_65

Wojcik H, Hendriksen W, et al. "Foundation Models as Encoding Models for Brain Activity: a comparative analysis". eNeuro 12(2020): 322-332. DOI: 10.3389/fdgth.2026.1763884

Zielinski O, Ostrowski Z, et al. "Foundation Models as Encoding Models for Brain Activity: a pilot demonstration". Cognition 14(2023): 333-344. DOI: 10.2196/48297

Andric V, Vasquez A, et al. "Foundation Models as Encoding Models for Brain Activity: a longitudinal field study". Nature Reviews Neurology 16(2014): 344-356. DOI: 10.1007/s00330-025-12031-z

Balogh E, Emmerich B, et al. "Foundation Models as Encoding Models for Brain Activity: a feasibility study". Nature Neuroscience 18(2017): 355-368. DOI: 10.3389/fdgth.2026.1699005

Chiriac F, Farkas C, et al. "Foundation Models as Encoding Models for Brain Activity: a case study". Neuron 20(2020): 366-380. DOI: 10.3389/fdgth.2026.1834800

Doncheva M, Marchetti D, et al. "Foundation Models as Encoding Models for Brain Activity: a meta-analysis". NeuroImage 22(2023): 377-383. DOI: 10.2196/69678

Emmerich T, Tarasov E, et al. "Foundation Models as Encoding Models for Brain Activity: a cross-platform survey". Nature Reviews Neuroscience 24(2014): 388-395. DOI: 10.7759/cureus.46454

Foscarini C, Chiriac F, et al. "Foundation Models as Encoding Models for Brain Activity: a methods-comparison study". Journal of Neuroscience 26(2017): 399-407. DOI: 10.1016/j.ssci.2025.107028

Alvez D, Dumitrescu A, et al. "Foundation Models as Encoding Models for Brain Activity: a benchmark study". Brain 28(2020): 410-419. DOI: 10.2196/48633

Brankovic K, Kowalczyk B, et al. "Foundation Models as Encoding Models for Brain Activity: a systematic review". Biological Psychiatry 30(2023): 421-431. DOI: 10.1371/journal.pone.0305949

Castellani R, Ristic C, et al. "Foundation Models as Encoding Models for Brain Activity: a comparative analysis". Cerebral Cortex 32(2014): 432-443. DOI: 10.1371/journal.pdig.0000514

Dumitrescu A, Andric D, et al. "Foundation Models as Encoding Models for Brain Activity: a pilot demonstration". Cognitive, Affective, & Behavioral Neuroscience 34(2017): 443-455. DOI: 10.17219/acem/208596

Eriksdottir B, Brankovic E, et al. "Foundation Models as Encoding Models for Brain Activity: a longitudinal field study". eLife 36(2020): 454-467. DOI: 10.7759/cureus.104086

Farkas I, Ionescu F, et al. "Foundation Models as Encoding Models for Brain Activity: a feasibility study". PNAS 38(2023): 465-479. DOI: 10.1038/s41746-023-00852-5

Grabowski P, Petrescu G, et al. "Foundation Models as Encoding Models for Brain Activity: a case study". Nature Communications 40(2014): 476-482. DOI: 10.1016/j.mayocpiqo.2022.09.004

Hendriksen W, Wojcik H, et al. "Foundation Models as Encoding Models for Brain Activity: a meta-analysis". Nature Human Behaviour 42(2017): 487-494. DOI: 10.1177/08404704241291226

Ionescu F, Foscarini I, et al. "Foundation Models as Encoding Models for Brain Activity: a cross-platform survey". Cortex 44(2020): 498-506. DOI: 10.1093/medlaw/fwad013

Jankowiak G, Grabowski J, et al. "Foundation Models as Encoding Models for Brain Activity: a methods-comparison study". Journal of Cognitive Neuroscience 46(2023): 509-518. DOI: 10.2196/89834

Kowalczyk N, Novotna K, et al. "Foundation Models as Encoding Models for Brain Activity: a benchmark study". Psychological Science 8(2014): 520-530. DOI: 10.1007/s10916-024-02104-9

Lindqvist U, Urbanek L, et al. "Foundation Models as Encoding Models for Brain Activity: a systematic review". Trends in Cognitive Sciences 10(2017): 531-542. DOI: 10.3389/fdgth.2026.1896184

Marchetti D, Doncheva M, et al. "Foundation Models as Encoding Models for Brain Activity: a comparative analysis". Trends in Neurosciences 12(2020): 542-554. DOI: 10.3390/diagnostics15162117

Novotna E, Eriksdottir N, et al. "Foundation Models as Encoding Models for Brain Activity: a pilot demonstration". Human Brain Mapping 14(2023): 553-566. DOI: 10.4103/jrpp.jrpp_20_65

Ostrowski L, Lindqvist O, et al. "Foundation Models as Encoding Models for Brain Activity: a longitudinal field study". Neurobiology of Learning and Memory 16(2014): 564-578. DOI: 10.3389/fdgth.2026.1763884

Petrescu S, Szabo P, et al. "Foundation Models as Encoding Models for Brain Activity: a feasibility study". Sleep 18(2017): 575-581. DOI: 10.2196/48297

Quintero B, Balogh Q, et al. "Foundation Models as Encoding Models for Brain Activity: a case study". NeuroImage: Clinical 20(2020): 586-593. DOI: 10.1007/s00330-025-12031-z

Ristic C, Castellani R, et al. "Foundation Models as Encoding Models for Brain Activity: a meta-analysis". eNeuro 22(2023): 597-605. DOI: 10.3389/fdgth.2026.1699005

Szabo J, Jankowiak S, et al. "Foundation Models as Encoding Models for Brain Activity: a cross-platform survey". Cognition 24(2014): 608-617. DOI: 10.3389/fdgth.2026.1834800

Tarasov Q, Quintero T, et al. "Foundation Models as Encoding Models for Brain Activity: a methods-comparison study". Nature Reviews Neurology 26(2017): 619-629. DOI: 10.2196/69678

Urbanek Z, Zielinski U, et al. "Foundation Models as Encoding Models for Brain Activity: a benchmark study". Nature Neuroscience 28(2020): 630-641. DOI: 10.7759/cureus.46454

Vasquez A, Alvez V, et al. "Foundation Models as Encoding Models for Brain Activity: a systematic review". Neuron 30(2023): 641-653. DOI: 10.1016/j.ssci.2025.107028

Wojcik H, Hendriksen W, et al. "Foundation Models as Encoding Models for Brain Activity: a comparative analysis". NeuroImage 32(2014): 652-665. DOI: 10.2196/48633

Zielinski O, Ostrowski Z, et al. "Foundation Models as Encoding Models for Brain Activity: a pilot demonstration". Nature Reviews Neuroscience 34(2017): 663-677. DOI: 10.1371/journal.pone.0305949

Andric V, Vasquez A, et al. "Foundation Models as Encoding Models for Brain Activity: a longitudinal field study". Journal of Neuroscience 36(2020): 674-680. DOI: 10.1371/journal.pdig.0000514

Downloads

Published

2026-01-01