Natural language contains information at multiple timescales. To understand how the human brain represents this information, one approach is to build encoding models that predict fMRI responses to natural language using representations extracted from neural network language models (LMs). However, these LM-derived representations do not explicitly separate information at different timescales, making it difficult to interpret the encoding models. In this work we construct interpretable multi-timescale representations by forcing individual units in an LSTM LM to integrate information over specific temporal scales. This allows us to explicitly and directly map the timescale of information encoded by each individual fMRI voxel. Further, the standard fMRI encoding procedure does not account for varying temporal properties in the encoding features. We modify the procedure so that it can capture both short- and long-timescale information. This approach outper-forms other encoding models, particularly for voxels that represent long-timescale information. It also provides a finer-grained map of timescale information in the human language pathway. This serves as a framework for future work investigating temporal hierarchies across artificial and biological language systems.

Functional magnetic resonance imaging (fMRI) offers a rich source of data for studying the neural basis of cognition. Here, we describe the Brain Imaging Analysis Kit (BrainIAK), an open-source, free Python package that provides computationally optimized solutions to key problems in advanced fMRI analysis. A variety of techniques are presently included in BrainIAK: intersubject correlation (ISC) and intersubject functional connectivity (ISFC), functional alignment via the shared response model (SRM), full correlation matrix analysis (FCMA), a Bayesian version of representational similarity analysis (BRSA), event segmentation using hidden Markov models, topographic factor analysis (TFA), inverted encoding models (IEMs), an fMRI data simulator that uses noise characteristics from real data (fmrisim), and some emerging methods. These techniques have been optimized to leverage the efficiencies of high-performance compute (HPC) clusters, and the same code can be seamlessly transferred from a laptop to a cluster. For each of the aforementioned techniques, we describe the data analysis problem that the technique is meant to solve and how it solves that problem; we also include an example Jupyter notebook for each technique and an annotated bibliography of papers that have used and/or described that technique. In addition to the sections describing various analysis techniques in BrainIAK, we have included sections describing the future applications of BrainIAK to real-time fMRI, tutorials that we have developed and shared online to facilitate learning the techniques in BrainIAK, computational innovations in BrainIAK, and how to contribute to BrainIAK. We hope that this manuscript helps readers to understand how BrainIAK might be useful in their research.

Among the many ways to model signals, a recent approach that draws considerable attention is sparse representation modeling. In this model, the signal is assumed to be generated as a random linear combination of a few atoms from a pre-specified dictionary. In this work we analyze two Bayesian denoising algorithms -the Maximum-Aposteriori Probability (MAP) and the Minimum-Mean-Squared-Error (MMSE) estimators, under the assumption that the dictionary is unitary. It is well known that both these estimators lead to a scalar shrinkage on the transformed coefficients, albeit with a different response curve. In this work we start by deriving closed-form expressions for these shrinkage curves and then analyze their performance. Upper bounds on the MAP and the MMSE estimation errors are derived. We tie these to the error obtained by a so-called oracle estimator, where the support is given, establishing a worst-case gain-factor between the MAP/MMSE estimation errors and the oracle's performance. These denoising algorithms are demonstrated on synthetic signals and on true data (images).

Solving l 1 regularized optimization problems is common in the fields of computational biology, signal processing and machine learning. Such l 1 regularization is utilized to find sparse minimizers of convex functions. A well-known example is the LASSO problem, where the l 1 norm regularizes a quadratic function. A multilevel framework is presented for solving such l 1 regularized sparse optimization problems efficiently. We take advantage of the expected sparseness of the solution, and create a hierarchy of problems of similar type, which is traversed in order to accelerate the optimization process. This framework is applied for solving two problems: (1) the sparse inverse covariance estimation problem, and (2) l 1 -regularized logistic regression. In the first problem, the inverse of an unknown covariance matrix of a multivariate normal distribution is estimated, under the assumption that it is sparse. To this end, an l 1 regularized log-determinant optimization problem needs to be solved. This task is challenging especially for large-scale datasets, due to time and memory limitations. In the second problem, the l 1 -regularization is added to the logistic regression classification objective to reduce overfitting to the data and obtain a sparse model. Numerical experiments demonstrate the efficiency of the multilevel framework in accelerating existing iterative solvers for both of these problems.

The scale of functional magnetic resonance image data is rapidly increasing as large multi-subject datasets are becoming widely available and high-resolution scanners are adopted. The inherent low-dimensionality of the information in this data has led neuroscientists to consider factor analysis methods to extract and analyze the underlying brain activity. In this work, we consider two recent multi-subject factor analysis methods: the Shared Response Model and Hierarchical Topographic Factor Analysis. We perform analytical, algorithmic, and code optimization to enable multi-node parallel implementations to scale. Single-node improvements result in 99× and 1812× speedups on these two methods, and enables the processing of larger datasets. Our distributed implementations show strong scaling of 3.3× and 5.5× respectively with 20 nodes on real datasets. We also demonstrate weak scaling on a synthetic dataset with 1024 subjects, on up to 1024 nodes and 32,768 cores.