Fast non-negative deconvolution for spike train inference from population calcium imaging

Calcium imaging for observing spiking activity from large populations of neurons are quickly gaining popularity. While the raw data are fluorescence movies, the underlying spike trains are of interest. This work presents a fast non-negative deconvolution filter to infer the approximately most likely spike train for each neuron, given the fluorescence observations. This algorithm outperforms optimal linear deconvolution (Wiener filtering) on both simulated and biological data. The performance gains come from restricting the inferred spike trains to be positive (using an interior-point method), unlike the Wiener filter. The algorithm is fast enough that even when imaging over 100 neurons, inference can be performed on the set of all observed traces faster than real-time. Performing optimal spatial filtering on the images further refines the estimates. Importantly, all the parameters required to perform the inference can be estimated using only the fluorescence data, obviating the need to perform joint electrophysiological and imaging calibration experiments.Comment: 22 pages, 10 figure

ACCAMS: Additive Co-Clustering to Approximate Matrices Succinctly

Matrix completion and approximation are popular tools to capture a user's preferences for recommendation and to approximate missing data. Instead of using low-rank factorization we take a drastically different approach, based on the simple insight that an additive model of co-clusterings allows one to approximate matrices efficiently. This allows us to build a concise model that, per bit of model learned, significantly beats all factorization approaches to matrix approximation. Even more surprisingly, we find that summing over small co-clusterings is more effective in modeling matrices than classic co-clustering, which uses just one large partitioning of the matrix. Following Occam's razor principle suggests that the simple structure induced by our model better captures the latent preferences and decision making processes present in the real world than classic co-clustering or matrix factorization. We provide an iterative minimization algorithm, a collapsed Gibbs sampler, theoretical guarantees for matrix approximation, and excellent empirical evidence for the efficacy of our approach. We achieve state-of-the-art results on the Netflix problem with a fraction of the model complexity.Comment: 22 pages, under review for conference publicatio

Inferring Interpersonal Relations in Narrative Summaries

Characterizing relationships between people is fundamental for the understanding of narratives. In this work, we address the problem of inferring the polarity of relationships between people in narrative summaries. We formulate the problem as a joint structured prediction for each narrative, and present a model that combines evidence from linguistic and semantic features, as well as features based on the structure of the social community in the text. We also provide a clustering-based approach that can exploit regularities in narrative types. e.g., learn an affinity for love-triangles in romantic stories. On a dataset of movie summaries from Wikipedia, our structured models provide more than a 30% error-reduction over a competitive baseline that considers pairs of characters in isolation

Inferring monopartite projections of bipartite networks: an entropy-based approach

Bipartite networks are currently regarded as providing a major insight into the organization of many real-world systems, unveiling the mechanisms driving the interactions occurring between distinct groups of nodes. One of the most important issues encountered when modeling bipartite networks is devising a way to obtain a (monopartite) projection on the layer of interest, which preserves as much as possible the information encoded into the original bipartite structure. In the present paper we propose an algorithm to obtain statistically-validated projections of bipartite networks, according to which any two nodes sharing a statistically-significant number of neighbors are linked. Since assessing the statistical significance of nodes similarity requires a proper statistical benchmark, here we consider a set of four null models, defined within the exponential random graph framework. Our algorithm outputs a matrix of link-specific p-values, from which a validated projection is straightforwardly obtainable, upon running a multiple hypothesis testing procedure. Finally, we test our method on an economic network (i.e. the countries-products World Trade Web representation) and a social network (i.e. MovieLens, collecting the users' ratings of a list of movies). In both cases non-trivial communities are detected: while projecting the World Trade Web on the countries layer reveals modules of similarly-industrialized nations, projecting it on the products layer allows communities characterized by an increasing level of complexity to be detected; in the second case, projecting MovieLens on the films layer allows clusters of movies whose affinity cannot be fully accounted for by genre similarity to be individuated.Comment: 16 pages, 9 figure