Insights from an autism imaging biomarker challenge: Promises and threats to biomarker discovery.

MRI has been extensively used to identify anatomical and functional differences in Autism Spectrum Disorder (ASD). Yet, many of these findings have proven difficult to replicate because studies rely on small cohorts and are built on many complex, undisclosed, analytic choices. We conducted an international challenge to predict ASD diagnosis from MRI data, where we provided preprocessed anatomical and functional MRI data from > 2,000 individuals. Evaluation of the predictions was rigorously blinded. 146 challengers submitted prediction algorithms, which were evaluated at the end of the challenge using unseen data and an additional acquisition site. On the best algorithms, we studied the importance of MRI modalities, brain regions, and sample size. We found evidence that MRI could predict ASD diagnosis: the 10 best algorithms reliably predicted diagnosis with AUC∼0.80 - far superior to what can be currently obtained using genotyping data in cohorts 20-times larger. We observed that functional MRI was more important for prediction than anatomical MRI, and that increasing sample size steadily increased prediction accuracy, providing an efficient strategy to improve biomarkers. We also observed that despite a strong incentive to generalise to unseen data, model development on a given dataset faces the risk of overfitting: performing well in cross-validation on the data at hand, but not generalising. Finally, we were able to predict ASD diagnosis on an external sample added after the end of the challenge (EU-AIMS), although with a lower prediction accuracy (AUC=0.72). This indicates that despite being based on a large multisite cohort, our challenge still produced biomarkers fragile in the face of dataset shifts.

Categorical Perception: A Groundwork for Deep Learning.

Classification is one of the major tasks that deep learning is successfully tackling. Categorization is also a fundamental cognitive ability. A well-known perceptual consequence of categorization in humans and other animals, categorical perception, is notably characterized by a within-category compression and a between-category separation: two items, close in input space, are perceived closer if they belong to the same category than if they belong to different categories. Elaborating on experimental and theoretical results in cognitive science, here we study categorical effects in artificial neural networks. We combine a theoretical analysis that makes use of mutual and Fisher information quantities and a series of numerical simulations on networks of increasing complexity. These formal and numerical analyses provide insights into the geometry of the neural representation in deep layers, with expansion of space near category boundaries and contraction far from category boundaries. We investigate categorical representation by using two complementary approaches: one mimics experiments in psychophysics and cognitive neuroscience by means of morphed continua between stimuli of different categories, while the other introduces a categoricality index that, for each layer in the network, quantifies the separability of the categories at the neural population level. We show on both shallow and deep neural networks that category learning automatically induces categorical perception. We further show that the deeper a layer, the stronger the categorical effects. As an outcome of our study, we propose a coherent view of the efficacy of different heuristic practices of the dropout regularization technique. More generally, our view, which finds echoes in the neuroscience literature, insists on the differential impact of noise in any given layer depending on the geometry of the neural representation that is being learned, that is, on how this geometry reflects the structure of the categories.

Efficient Communication in Written and Performed Music.

Since its inception, Shannon's information theory has attracted interest for the study of language and music. Recently, a wide range of converging studies have shown how efficient communication pervades language, from phonetics to syntax. Efficient principles imply that more resources should be assigned to highly informative items. For instance, average information content was shown to be a better predictor of word length than frequency, revisiting the famous Zipf's law. However, in spite of the success of the efficient communication framework in the study of language and speech, very little work has investigated its relevance in the analysis of music. Here, we examine the organization of harmonic information in two large corpora of Western music, one made of MIDI files directly sequenced from scores, and the other made of MIDI recordings of live performances of highly skilled piano players. We show that there is a clear positive relationship between (contextual) information content of harmonic sequences and two essential musical properties, namely duration and loudness: the more unexpected a harmonic event is, the longer and the louder it is.

Epidemiological modelling of the 2005 French riots: a spreading wave and the role of contagion.

As a large-scale instance of dramatic collective behaviour, the 2005 French riots started in a poor suburb of Paris, then spread in all of France, lasting about three weeks. Remarkably, although there were no displacements of rioters, the riot activity did travel. Access to daily national police data has allowed us to explore the dynamics of riot propagation. Here we show that an epidemic-like model, with just a few parameters and a single sociological variable characterizing neighbourhood deprivation, accounts quantitatively for the full spatio-temporal dynamics of the riots. This is the first time that such data-driven modelling involving contagion both within and between cities (through geographic proximity or media) at the scale of a country, and on a daily basis, is performed. Moreover, we give a precise mathematical characterization to the expression "wave of riots", and provide a visualization of the propagation around Paris, exhibiting the wave in a way not described before. The remarkable agreement between model and data demonstrates that geographic proximity played a major role in the propagation, even though information was readily available everywhere through media. Finally, we argue that our approach gives a general framework for the modelling of the dynamics of spontaneous collective uprisings.

Perception of categories: from coding efficiency to reaction times.

Reaction-times in perceptual tasks are the subject of many experimental and theoretical studies. With the neural decision making process as main focus, most of these works concern discrete (typically binary) choice tasks, implying the identification of the stimulus as an exemplar of a category. Here we address issues specific to the perception of categories (e.g. vowels, familiar faces, …), making a clear distinction between identifying a category (an element of a discrete set) and estimating a continuous parameter (such as a direction). We exhibit a link between optimal Bayesian decoding and coding efficiency, the latter being measured by the mutual information between the discrete category set and the neural activity. We characterize the properties of the best estimator of the likelihood of the category, when this estimator takes its inputs from a large population of stimulus-specific coding cells. Adopting the diffusion-to-bound approach to model the decisional process, this allows to relate analytically the bias and variance of the diffusion process underlying decision making to macroscopic quantities that are behaviorally measurable. A major consequence is the existence of a quantitative link between reaction times and discrimination accuracy. The resulting analytical expression of mean reaction times during an identification task accounts for empirical facts, both qualitatively (e.g. more time is needed to identify a category from a stimulus at the boundary compared to a stimulus lying within a category), and quantitatively (working on published experimental data on phoneme identification tasks).

Word Durations in Non-Native English.

In this study, we compare the effects of English lexical features on word duration for native and non-native English speakers and for non-native speakers with different L1s and a range of L2 experience. We also examine whether non-native word durations lead to judgments of a stronger foreign accent. We measured word durations in English paragraphs read by 12 American English (AE), 20 Korean, and 20 Chinese speakers. We also had AE listeners rate the `accentedness' of these non-native speakers. AE speech had shorter durations, greater within-speaker word duration variance, greater reduction of function words, and less between-speaker variance than non-native speech. However, both AE and non-native speakers showed sensitivity to lexical predictability by reducing second mentions and high frequency words. Non-native speakers with more native-like word durations, greater within-speaker word duration variance, and greater function word reduction were perceived as less accented. Overall, these findings identify word duration as an important and complex feature of foreign-accented English.

Neural coding of categories: information efficiency and optimal population codes.

This paper deals with the analytical study of coding a discrete set of categories by a large assembly of neurons. We consider population coding schemes, which can also be seen as instances of exemplar models proposed in the literature to account for phenomena in the psychophysics of categorization. We quantify the coding efficiency by the mutual information between the set of categories and the neural code, and we characterize the properties of the most efficient codes, considering different regimes corresponding essentially to different signal-to-noise ratio. One main outcome is to find that, in a high signal-to-noise ratio limit, the Fisher information at the population level should be the greatest between categories, which is achieved by having many cells with the stimulus-discriminating parts (steepest slope) of their tuning curves placed in the transition regions between categories in stimulus space. We show that these properties are in good agreement with both psychophysical data and with the neurophysiology of the inferotemporal cortex in the monkey, a cortex area known to be specifically involved in classification tasks.