Skip to main content

Feature Fallacy: Complications with Interpreting Linear Decoding Weights in fMRI

  • Chapter
  • First Online:
Explainable AI: Interpreting, Explaining and Visualizing Deep Learning

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 11700))

Abstract

Decoding and encoding models are popular multivariate approaches used to study representations in functional neuroimaging data. Encoding approaches seek to predict brain activation patterns using aspects of the stimuli as features. Decoding models, in contrast, utilize measured brain responses as features to make predictions about experimental manipulations or behavior. Both approaches have typically included linear classification components. Ideally, decoding and encoding models could be used for the dual purpose of prediction and neuroscientific knowledge gain. However, even within a linear framework, interpretation can be difficult. Encoding models suffer from feature fallacy; multiple combinations of features derived from a stimulus may describe measured brain responses equally well. Interpreting linear decoding models also requires great care, particularly when informative predictor variables (e.g., fMRI voxels) are present in great quantity (redundant) and correlated with noise measurements. In certain cases, noise channels may be assigned a stronger weight than channels that contain relevant information. Although corrections for this problem exist, there are certain noise sources - common to functional neuroimaging recordings - that may complicate corrective approaches, even after regularization is applied. Here, we review potential pitfalls for making inferences based on encoding and decoding hypothesis testing, and suggest a form of feature fallacy also extends to the decoding framework.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Alpaydin, E.: Introduction to Machine Learning, 3rd edn. MIT Press, Cambridge (2014)

    MATH  Google Scholar 

  2. Anderson, A., Han, D., Douglas, P.K., Bramen, J., Cohen, M.S.: Real-time functional MRI classification of brain states using Markov-SVM hybrid models: peering inside the rt-fMRI black box. In: Langs, G., Rish, I., Grosse-Wentrup, M., Murphy, B. (eds.) MLINI 2011. LNCS (LNAI), vol. 7263, pp. 242–255. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-34713-9_31

    Chapter  Google Scholar 

  3. Blankertz, B., Lemm, S., Treder, M., Haufe, S., Müller, K.R.: Single-trial analysis and classification of ERP components – a tutorial. NeuroImage 56, 814–825 (2011)

    Google Scholar 

  4. Bruce, D.: Fifty years since lashley’s in search of the Engram: refutations and conjectures. J. Hist. Neurosci. 10, 308–318 (2001)

    Google Scholar 

  5. Chu, C., Hsu, A.L., Chou, K.H., Bandettini, P., Lin, C.: Does feature selection improve classification accuracy? Impact of sample size and feature selection on classification using anatomical magnetic resonance images. NeuroImage 60, 59–70 (2012)

    Google Scholar 

  6. Colby, J.B., Rudie, J.D., Brown, J.A., Douglas, P.K., Cohen, M.S., Shehzad, Z.: Insights into multimodal imaging classification of ADHD. Front. Syst. Neurosci. 6, 59 (2012)

    Google Scholar 

  7. Cox, D.D., Savoy, R.L.: Functional magnetic resonance imaging (fMRI) ‘brain reading’: detecting and a classifying distributed patterns of fMRI activity in human visual cortex. NeuroImage 19, 261–270 (2003)

    Google Scholar 

  8. Cukur, T., Huth, A.G., Nishimoto, S., Gallant, J.L.: Functional subdomains within human FFA. J. Neurosci. 33, 16748–16766 (2013)

    Google Scholar 

  9. De Angelis, V., De Martino, F., Moerel, M., Santoro, R., Hausfeld, L., Formisano, E.: Cortical processing of pitch: model-based encoding and decoding of auditory fMRI responses to real-life sounds. NeuroImage 180, 291–300 (2018)

    Google Scholar 

  10. DiCarlo, J.J., Zoccolan, D., Rust, N.C.: How does the brain solve visual object recognition? Neuron 73, 415–434 (2012)

    Google Scholar 

  11. Diedrichsen, J., Kriegeskorte, N.: Representational models: a common framework for understanding encoding, pattern-component, and representational-similarity analysis. bioRxiv 071472 (2016)

    Google Scholar 

  12. Diedrichsen, J., Wiestler, T., Krakauer, J.W.: Two distinct ipsilateral cortical representations for individuated finger movements. Cereb. Cortex 23, 1362–1377 (2013)

    Google Scholar 

  13. Douglas, P.K., Anderson, A.: Interpreting fMRI decoding weights: additional considerations. In: NIPS, Interpretable Machine Learning Workshop (2017)

    Google Scholar 

  14. Douglas, P.K., Harris, S., Cohen, M.S.: Naive Bayes classification of belief and disbelief using event related functional neuroimaging data. In: Human Brain Mapping Conference Poster (2009)

    Google Scholar 

  15. Douglas, P.K., Harris, S., Yuille, A., Cohen, M.S.: Performance comparison of machine learning algorithms and number of independent components used in fMRI decoding of belief vs. disbelief. NeuroImage 56, 544–553 (2011)

    Google Scholar 

  16. Douglas, P.K., et al.: Single trial decoding of belief decision making from EEG and fMRI data using independent components features. Front. Hum. Neurosci. 7, 392 (2013)

    Google Scholar 

  17. Friston, K.J.: Modalities, modes, and models in functional neuroimaging. Science 326, 399–403 (2009)

    Google Scholar 

  18. Gazzaniga, M.S.: Regional differences in cortical organization. Science 289, 1887–1888 (2000)

    Google Scholar 

  19. Gotsopoulos, A., et al.: Reproducibility of importance extraction methods in neural network based fMRI classification. NeuroImage 181, 44–54 (2018)

    Google Scholar 

  20. Gross, C.G.: Genealogy of the “grandmother cell”. Neurosci. 8, 512–518 (2002)

    Google Scholar 

  21. Güçü, U., van Gerven, M.A.J.: Deep neural networks reveal a gradient in the complexity of neural representations across the ventral stream. J. Neurosci. 35, 10005–10014 (2015)

    Google Scholar 

  22. Guyon, I., Elisseeff, A.: An introduction to variable and feature selection. J. Mach. Learn. Res. 3, 1157–1182 (2003)

    MATH  Google Scholar 

  23. Hampton, A.N., O’Doherty, J.P.: Decoding the neural substrates of reward-related decision making with functional MRI. Proc. Natl. Acad. Sci. 104, 1377–1382 (2007)

    Google Scholar 

  24. Handwerker, D.A., Ollinger, J.M., D’Esposito, M.: Variation of BOLD hemodynamic responses across subjects and brain regions and their effects on statistical analyses. NeuroImage 21, 1639–1651 (2004)

    Google Scholar 

  25. Haufe, S., et al.: On the interpretation of weight vectors of linear models in multivariate neuroimaging. NeuroImage 87, 96–110 (2014)

    Google Scholar 

  26. Haxby, J.V.: Distributed and overlapping representations of faces and objects in ventral temporal cortex. Science 293, 2425–2430 (2001)

    Google Scholar 

  27. Haynes, J.D.: A primer on pattern-based approaches to fMRI: principles, pitfalls, and perspectives. Neuron 87, 257–270 (2015)

    Google Scholar 

  28. Haynes, J.D., Rees, G.: Predicting the stream of consciousness from activity in human visual cortex. Curr. Biol 15, 1301–1307 (2005)

    Google Scholar 

  29. Haynes, J.D., Rees, G.: Decoding mental states from brain activity in humans. Nat. Rev. Neurosci. 7, 523–534 (2006)

    Google Scholar 

  30. Hodgkin, A.L., Huxley, A.F.: A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. 117, 500–544 (1952)

    Google Scholar 

  31. Hong, H., Yamins, D.L.K., Majaj, N.J., DiCarlo, J.J.: Explicit information for category-orthogonal object properties increases along the ventral stream. Nat. Neurosci. 19, 613–622 (2016)

    Google Scholar 

  32. Huth, A.G., de Heer, W.A., Griffiths, T.L., Theunissen, F.E., Gallant, J.L.: Natural speech reveals the semantic maps that tile human cerebral cortex. Nature 532, 453–458 (2016)

    Google Scholar 

  33. Kamitani, Y., Tong, F.: Decoding the visual and subjective contents of the human brain. Nat. Neurosci. 8, 679–685 (2005)

    Google Scholar 

  34. Kanwisher, N., Yovel, G.: The fusiform face area: a cortical region specialized for the perception of faces. Philos. Trans. Roy. Soc. B: Biol. Sci. 361, 2109–2128 (2006)

    Google Scholar 

  35. Kay, K.N., Naselaris, T., Prenger, R.J., Gallant, J.L.: Identifying natural images from human brain activity. Nature 452, 352–355 (2008)

    Google Scholar 

  36. Kerr, W.T., Douglas, P.K., Anderson, A., Cohen, M.S.: The utility of data-driven feature selection: Re: Chu et al. 2012. NeuroImage 84, 1107–1110 (2014)

    Google Scholar 

  37. Khaligh-Razavi, S.M., Kriegeskorte, N.: Deep supervised, but not unsupervised, models may explain IT cortical representation. PLOS Comput. Biol. 10(11), e1003915 (2014)

    Google Scholar 

  38. Khaligh-Razavi, S., Kriegeskorte, N.: Object-vision models that better explain IT also categorize better, but all models fail at both. Cosyne Abstracts (2013)

    Google Scholar 

  39. Koopmans, P.J., Barth, M., Orzada, S., Norris, D.G.: Multi-echo fMRI of the cortical laminae in humans at 7T. NeuroImage 56, 1276–1285 (2011)

    Google Scholar 

  40. Kriegeskorte, N.: Deep neural networks: a new framework for modeling biological vision and brain information processing. Ann. Rev. Vis. Sci. 1, 417–446 (2015)

    Google Scholar 

  41. Kriegeskorte, N.: Pattern-information analysis: from stimulus decoding to computational-model testing. NeuroImage 56, 411–421 (2011)

    Google Scholar 

  42. Kriegeskorte, N., Douglas, P.K.: Cognitive computational neuroscience. Nat. Neurosci. 21, 1148–1160 (2018)

    Google Scholar 

  43. Kriegeskorte, N., Douglas, P.K.: Interpreting encoding and decoding models. arXiv:1812.00278 (2018)

  44. Lee, A.T., Glover, G.H., Meyer, C.H.: Discrimination of large venous vessels in time-course spiral blood-oxygen-level-dependent magnetic-resonance functional neuroimaging. Magn. Reson. Med. 33, 745–754 (1995)

    Google Scholar 

  45. Lemm, S., Blankertz, B., Dickhaus, T., Müller, K.R.: Introduction to machine learning for brain imaging. NeuroImage 56, 387–399 (2011)

    Google Scholar 

  46. Logothetis, N.K., Pauls, J., Augath, M., Trinath, T., Oeltermann, A.: Neurophysiological investigation of the basis of the fMRI signal. Nature 412, 150–157 (2001)

    Google Scholar 

  47. Meshkat, N., Kuo, C.E., DiStefano, J.: On finding and using identifiable parameter combinations in nonlinear dynamic systems biology models and COMBOS: a novel web implementation. PLoS One 9, e110261 (2014)

    Google Scholar 

  48. Mikl, M., et al.: Effects of spatial smoothing on fMRI group inferences. Magn. Reson. Imaging 26, 490–503 (2008)

    Google Scholar 

  49. Naselaris, T., Kay, K.N.: Resolving ambiguities of MVPA using explicit models of representation. Trends Cogn. Sci. 19, 551–554 (2015)

    Google Scholar 

  50. Naselaris, T., Kay, K.N., Nishimoto, S., Gallant, J.L.: Encoding and decoding in fMRI. NeuroImage 56, 400–410 (2011)

    Google Scholar 

  51. Naselaris, T., Prenger, R.J., Kay, K.N., Oliver, M., Gallant, J.L.: Bayesian reconstruction of natural images from human brain activity. Neuron 63, 902–915 (2009)

    Google Scholar 

  52. Norman, K.A., Polyn, S.M., Detre, G.J., Haxby, J.V.: Beyond mind-reading: multi-voxel pattern analysis of fMRI data. Trends Cogn. Sci. (Regul. Ed.) 10, 424–430 (2006)

    Google Scholar 

  53. de Beeck, H.P.O.: Against hyperacuity in brain reading: spatial smoothing does not hurt multivariate fMRI analyses? NeuroImage 49, 1943–1948 (2010)

    Google Scholar 

  54. Poldrack, R.A.: Can cognitive processes be inferred from neuroimaging data? Trends Cogn. Sci. (Regul. Ed.) 10, 59–63 (2006)

    Google Scholar 

  55. Pouget, A., Dayan, P., Zemel, R.: Information processing with population codes. Nat. Rev. Neurosci. 1, 125–132 (2000)

    Google Scholar 

  56. Power, J.D., Mitra, A., Laumann, T.O., Snyder, A.Z., Schlaggar, B.L., Petersen, S.E.: Methods to detect, characterize, and remove motion artifact in resting state fMRI. NeuroImage 84, 320–341 (2014)

    Google Scholar 

  57. Quiroga, R.Q., Reddy, L., Kreiman, G., Koch, C., Fried, I.: Invariant visual representation by single neurons in the human brain. Nature 435, 1102–1107 (2005)

    Google Scholar 

  58. Selemon, L., Goldman-Rakic, P.: Common cortical and subcortical targets of the dorsolateral prefrontal and posterior parietal cortices in the rhesus monkey: evidence for a distributed neural network subserving spatially guided behavior. J. Neurosci. 8, 4049–4068 (1988)

    Google Scholar 

  59. Sturm, I., Lapuschkin, S., Samek, W., Müller, K.R.: Interpretable deep neural networks for single-trial EEG classification. J. Neurosci. Methods 274, 141–145 (2016)

    Google Scholar 

  60. Thomas, A.W., Heekeren, H.R., Müller, K.R., Samek, W.: Analyzing neuroimaging data through recurrent deep learning models. arXiv:1810.09945 (2018)

  61. Tomsett, R., et al.: Why the failure? How adversarial examples can provide insights for interpretable machine learning. In: 21st International Conference on Information Fusion (2018)

    Google Scholar 

  62. VanRullen, R., Reddy, L.: Reconstructing faces from fMRI patterns using deep generative neural networks. arXiv:1810.03856 (2018)

  63. Varoquaux, G., Raamana, P.R., Engemann, D.A., Hoyos-Idrobo, A., Schwartz, Y., Thirion, B.: Assessing and tuning brain decoders: cross-validation, caveats, and guidelines. NeuroImage 145, 166–179 (2017)

    Google Scholar 

  64. Worsley, K.J., Marrett, S., Neelin, P., Vandal, A.C., Friston, K.J., Evans, A.C.: A unified statistical approach for determining significant signals in images of cerebral activation. Hum. Brain Mapp. 4, 58–73 (1996)

    Google Scholar 

  65. Wu, G.R., Liao, W., Stramaglia, S., Ding, J.R., Chen, H., Marinazzo, D.: A blind deconvolution approach to recover effective connectivity brain networks from resting state fMRI data. Med. Image Anal. 17, 365–374 (2013)

    Google Scholar 

  66. Xie, J., Douglas, P.K., Wu, Y., Anderson, A.: Decoding the Encoding of functional brain networks: an fMRI classification comparison of non-negative matrix factorization (NMF), independent component analysis (ICA), and sparse coding algorithms. Int. J. Imaging Syst. Technol. 21, 223–231 (2016)

    Google Scholar 

  67. Zhao, S., et al.: Automatic recognition of fMRI-derived functional networks using 3D convolutional neural networks. IEEE Trans. Biomed. Eng. 65(9), 1975–1984 (2017)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Pamela K. Douglas .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Douglas, P.K., Anderson, A. (2019). Feature Fallacy: Complications with Interpreting Linear Decoding Weights in fMRI. In: Samek, W., Montavon, G., Vedaldi, A., Hansen, L., Müller, KR. (eds) Explainable AI: Interpreting, Explaining and Visualizing Deep Learning. Lecture Notes in Computer Science(), vol 11700. Springer, Cham. https://doi.org/10.1007/978-3-030-28954-6_20

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-28954-6_20

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-28953-9

  • Online ISBN: 978-3-030-28954-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics