Network structure mediates functional reorganization induced by optogenetic stimulation of non-human primate sensorimotor cortex.

Because aberrant network-level functional connectivity underlies a variety of neural disorders, the ability to induce targeted functional reorganization would be a profound development toward therapies for neural disorders. Brain stimulation has been shown to induce large-scale network-wide functional connectivity changes (FCC), but the mapping from stimulation to the induced changes is unclear. Here, we develop a model which jointly considers the stimulation protocol and the cortical network structure to accurately predict network-wide FCC in response to optogenetic stimulation of non-human primate primary sensorimotor cortex. We observe that the network structure has a much stronger effect than the stimulation protocol on the resulting FCC. We also observe that the mappings from these input features to the FCC diverge over frequency bands and successive stimulations. Our framework represents a paradigm shift for targeted neural stimulation and can be used to interrogate, improve, and develop stimulation-based interventions for neural disorders.

A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series.

The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.

Label-Embedding for Image Classification.

Attributes act as intermediate representations that enable parameter sharing between classes, a must when training data is scarce. We propose to view attribute-based image classification as a label-embedding problem: each class is embedded in the space of attribute vectors. We introduce a function that measures the compatibility between an image and a label embedding. The parameters of this function are learned on a training set of labeled samples to ensure that, given an image, the correct classes rank higher than the incorrect ones. Results on the Animals With Attributes and Caltech-UCSD-Birds datasets show that the proposed framework outperforms the standard Direct Attribute Prediction baseline in a zero-shot learning scenario. Label embedding enjoys a built-in ability to leverage alternative sources of information instead of or in addition to attributes, such as, e.g., class hierarchies or textual descriptions. Moreover, label embedding encompasses the whole range of learning settings from zero-shot learning to regular learning with a large number of labeled examples.

Good practice in large-scale learning for image classification.

We benchmark several SVM objective functions for large-scale image classification. We consider one-versus-rest, multiclass, ranking, and weighted approximate ranking SVMs. A comparison of online and batch methods for optimizing the objectives shows that online methods perform as well as batch methods in terms of classification accuracy, but with a significant gain in training speed. Using stochastic gradient descent, we can scale the training to millions of images and thousands of classes. Our experimental evaluation shows that ranking-based algorithms do not outperform the one-versus-rest strategy when a large number of training examples are used. Furthermore, the gap in accuracy between the different algorithms shrinks as the dimension of the features increases. We also show that learning through cross-validation the optimal rebalancing of positive and negative examples can result in a significant improvement for the one-versus-rest strategy. Finally, early stopping can be used as an effective regularization strategy when training with online algorithms. Following these "good practices," we were able to improve the state of the art on a large subset of 10K classes and 9M images of ImageNet from 16.7 percent Top-1 accuracy to 19.1 percent.

Temporal localization of actions with actoms.

We address the problem of localizing actions, such as opening a door, in hours of challenging video data. We propose a model based on a sequence of atomic action units, termed "actoms," that are semantically meaningful and characteristic for the action. Our actom sequence model (ASM) represents an action as a sequence of histograms of actom-anchored visual features, which can be seen as a temporally structured extension of the bag-of-features. Training requires the annotation of actoms for action examples. At test time, actoms are localized automatically based on a nonparametric model of the distribution of actoms, which also acts as a prior on an action's temporal structure. We present experimental results on two recent benchmarks for action localization "Coffee and Cigarettes" and the "DLSBP" dataset. We also adapt our approach to a classification-by-localization set-up and demonstrate its applicability on the challenging "Hollywood 2" dataset. We show that our ASM method outperforms the current state of the art in temporal action localization, as well as baselines that localize actions with a sliding window method.