We introduce an efficient algorithmic framework for model selection in online learning, also known as parameter-free online learning. Departing from previous work, which has focused on highly structured function classes such as nested balls in Hilbert space, we propose a generic meta-algorithm framework that achieves online model selection oracle inequalities under minimal structural assumptions. We give the first computationally efficient parameter-free algorithms that work in arbitrary Banach spaces under mild smoothness assumptions; previous results applied only to Hilbert spaces. We further derive new oracle inequalities for matrix classes, non-nested convex sets, and $\mathbb{R}^{d}$ with generic regularizers. Finally, we generalize these results by providing oracle inequalities for arbitrary non-linear classes in the online supervised learning model. These results are all derived through a unified meta-algorithm scheme using a novel multi-scale algorithm for prediction with expert advice based on random playout, which may be of independent interest.

A fundamental goal in network neuroscience is to understand how activity in one brain region drives activity elsewhere, a process referred to as effective connectivity. Here we propose to model this causal interaction using integro-differential equations and causal kernels that allow for a rich analysis of effective connectivity. The approach combines the tractability and flexibility of autoregressive modeling with the biophysical interpretability of dynamic causal modeling. The causal kernels are learned nonparametrically using Gaussian process regression, yielding an efficient framework for causal inference. We construct a novel class of causal covariance functions that enforce the desired properties of the causal kernels, an approach which we call GP CaKe. By construction, the model and its hyperparameters have biophysical meaning and are therefore easily interpretable. We demonstrate the efficacy of GP CaKe on a number of simulations and give an example of a realistic application on magnetoencephalography (MEG) data.

We develop a nonparametric and online learning algorithm that estimates the triggering functions of a multivariate Hawkes process (MHP). The approach we take approximates the triggering function $f_{i,j}(t)$ by functions in a reproducing kernel Hilbert space (RKHS), and maximizes a time-discretized version of the log-likelihood, with Tikhonov regularization. Theoretically, our algorithm achieves an $\calO(\log T)$ regret bound. Numerical results show that our algorithm offers a competing performance to that of the nonparametric batch learning algorithm, with a run time comparable to the parametric online learning algorithm.

Cognitive neuroscience is enjoying rapid increase in extensive public brain-imaging datasets. It opens the door to large-scale statistical models. Finding a unified perspective for all available data calls for scalable and automated solutions to an old challenge: how to aggregate heterogeneous information on brain function into a universal cognitive system that relates mental operations/cognitive processes/psychological tasks to brain networks? We cast this challenge in a machine-learning approach to predict conditions from statistical brain maps across different studies. For this, we leverage multi-task learning and multi-scale dimension reduction to learn low-dimensional representations of brain images that carry cognitive information and can be robustly associated with psychological stimuli. Our multi-dataset classification model achieves the best prediction performance on several large reference datasets, compared to models without cognitive-aware low-dimension representations; it brings a substantial performance boost to the analysis of small datasets, and can be introspected to identify universal template cognitive concepts.

Neuroscientists classify neurons into different types that perform similar computations at different locations in the visual field. Traditional methods for neural system identification do not capitalize on this separation of "what" and "where". Learning deep convolutional feature spaces that are shared among many neurons provides an exciting path forward, but the architectural design needs to account for data limitations: While new experimental techniques enable recordings from thousands of neurons, experimental time is limited so that one can sample only a small fraction of each neuron's response space. Here, we show that a major bottleneck for fitting convolutional neural networks (CNNs) to neural data is the estimation of the individual receptive field locations - a problem that has been scratched only at the surface thus far. We propose a CNN architecture with a sparse readout layer factorizing the spatial (where) and feature (what) dimensions. Our network scales well to thousands of neurons and short recordings and can be trained end-to-end. We evaluate this architecture on ground-truth data to explore the challenges and limitations of CNN-based system identification. Moreover, we show that our network model outperforms current state-of-the art system identification models of mouse primary visual cortex.

Adaptive stimulus selection methods in neuroscience have primarily focused on maximizing the firing rate of a single recorded neuron. When recording from a population of neurons, it is usually not possible to find a single stimulus that maximizes the firing rates of all neurons. This motivates optimizing an objective function that takes into account the responses of all recorded neurons together. We propose "Adept," an adaptive stimulus selection method that can optimize population objective functions. In simulations, we first confirmed that population objective functions elicited more diverse stimulus responses than single-neuron objective functions. Then, we tested Adept in a closed-loop electrophysiological experiment in which population activity was recorded from macaque V4, a cortical area known for mid-level visual processing. To predict neural responses, we used the outputs of a deep convolutional neural network model as feature embeddings. Images chosen by Adept elicited mean neural responses that were 20% larger than those for randomly-chosen natural images, and also evoked a larger diversity of neural responses. Such adaptive stimulus selection methods can facilitate experiments that involve neurons far from the sensory periphery, for which it is often unclear which stimuli to present.

Brain processes occur at various timescales, ranging from milliseconds (neurons) to minutes and hours (behavior). Characterizing functional coupling among brain regions at these diverse timescales is key to understanding how the brain produces behavior. Here, we apply instantaneous and lag-based measures of conditional linear dependence, based on Granger-Geweke causality (GC), to infer network connections at distinct timescales from functional magnetic resonance imaging (fMRI) data. Due to the slow sampling rate of fMRI, it is widely held that GC produces spurious and unreliable estimates of functional connectivity when applied to fMRI data. We challenge this claim with simulations and a novel machine learning approach. First, we show, with simulated fMRI data, that instantaneous and lag-based GC identify distinct timescales and complementary patterns of functional connectivity. Next, we analyze fMRI scans from 500 subjects and show that a linear classifier trained on either instantaneous or lag-based GC connectivity reliably distinguishes task versus rest brain states, with ~80-85% cross-validation accuracy. Importantly, instantaneous and lag-based GC exploit markedly different spatial and temporal patterns of connectivity to achieve robust classification. Our approach enables identifying functionally connected networks that operate at distinct timescales in the brain.

Designing optimal treatment plans for patients with comorbidities requires accurate cause-specific mortality prognosis. Motivated by the recent availability of linked electronic health records, we develop a nonparametric Bayesian model for survival analysis with competing risks, which can be used for jointly assessing a patient's risk of multiple (competing) adverse outcomes. The model views a patient's survival times with respect to the competing risks as the outputs of a deep multi-task Gaussian process (DMGP), the inputs to which are the patients' covariates. Unlike parametric survival analysis methods based on Cox and Weibull models, our model uses DMGPs to capture complex non-linear interactions between the patients' covariates and cause-specific survival times, thereby learning flexible patient-specific and cause-specific survival curves, all in a data-driven fashion without explicit parametric assumptions on the hazard rates. We propose a variational inference algorithm that is capable of learning the model parameters from time-to-event data while handling right censoring. Experiments on synthetic and real data show that our model outperforms the state-of-the-art survival models.

We study minimax strategies for the online prediction problem with expert advice. It has been conjectured that a simple adversary strategy, called COMB, is near optimal in this game for any number of experts. Our results and new insights make progress in this direction by showing that, up to a small additive term, COMB is minimax optimal in the finite-time three expert problem. In addition, we provide for this setting a new near minimax optimal COMB-based learner. Prior to this work, in this problem, learners obtaining the optimal multiplicative constant in their regret rate were known only when $K=2$ or $K\rightarrow\infty$. We characterize, when $K=3$, the regret of the game scaling as $\sqrt{8/(9\pi)T}\pm \log(T)^2$ which gives for the first time the optimal constant in the leading ($\sqrt{T}$) term of the regret.

We study online learning with the general notion of transductive regret, that is regret with modification rules applying to expert sequences (as opposed to single experts) that are representable by weighted finite-state transducers. We show how transductive regret generalizes existing notions of regret, including: (1) external regret; (2) internal regret; (3) swap regret; and (4) conditional swap regret. We present a general and efficient online learning algorithm for minimizing transductive regret. We further extend that to design efficient algorithms for the time-selection and sleeping expert settings. A by-product of our study is an algorithm for swap regret, which, under mild assumptions, is more efficient than existing ones, and a substantially more efficient algorithm for time selection swap regret.