7 research outputs found
Simple connectome inference from partial correlation statistics in calcium imaging
In this work, we propose a simple yet effective solution to the problem of
connectome inference in calcium imaging data. The proposed algorithm consists
of two steps. First, processing the raw signals to detect neural peak
activities. Second, inferring the degree of association between neurons from
partial correlation statistics. This paper summarises the methodology that led
us to win the Connectomics Challenge, proposes a simplified version of our
method, and finally compares our results with respect to other inference
methods
Rebuilding a realistic corticostriatal “social network” from dissociated cells
Many of the methods available for the study of cortical influences on striatal neurons have serious problems. In vivo the connectivity is so complex that the study of input from an individual cortical neuron to a single striatal cell is nearly impossible. Mixed corticostriatal cultures develop many connections from striatal cells to cortical cells, in striking contrast to the fact that only connections from cortical cells to striatal cells are present in vivo. Furthermore, interneuron populations are over-represented in organotypic cultures. For these reasons, we have developed a method for growing cortical and striatal neurons in separated compartments that allows cortical neurons to innervate striatal cells in culture. The method works equally well for acutely dissociated or cryopreserved neurons and allows a number of manipulations that are not otherwise possible. Either cortical or striatal compartments can be transfected with channel rhodopsins. The activity of both areas can be recorded in multielectrode arrays or individual patch recordings from pairs of cells. Finally, corticostriatal connections can be severed acutely. This procedure enables determination of the importance of corticostriatal interaction in the resting pattern of activity. These cultures also facilitate development of sensitive analytical network methods to track connectivity
Simple connectome inference from partial correlation statistics in calcium imaging
peer reviewedIn this work, we propose a simple yet effective solution to the problem of connectome inference in calcium imaging data. The proposed algorithm consists of two steps. First, processing the raw signals to detect neural peak activities. Second, inferring the degree of association between neurons from partial correlation statistics. This paper summarises the methodology that led us to win the Connectomics Challenge, proposes a simplified version of our method, and finally compares our results with respect to other inference methods
Understanding Random Forests: From Theory to Practice
Data analysis and machine learning have become an integrative part of the
modern scientific methodology, offering automated procedures for the prediction
of a phenomenon based on past observations, unraveling underlying patterns in
data and providing insights about the problem. Yet, caution should avoid using
machine learning as a black-box tool, but rather consider it as a methodology,
with a rational thought process that is entirely dependent on the problem under
study. In particular, the use of algorithms should ideally require a reasonable
understanding of their mechanisms, properties and limitations, in order to
better apprehend and interpret their results.
Accordingly, the goal of this thesis is to provide an in-depth analysis of
random forests, consistently calling into question each and every part of the
algorithm, in order to shed new light on its learning capabilities, inner
workings and interpretability. The first part of this work studies the
induction of decision trees and the construction of ensembles of randomized
trees, motivating their design and purpose whenever possible. Our contributions
follow with an original complexity analysis of random forests, showing their
good computational performance and scalability, along with an in-depth
discussion of their implementation details, as contributed within Scikit-Learn.
In the second part of this work, we analyse and discuss the interpretability
of random forests in the eyes of variable importance measures. The core of our
contributions rests in the theoretical characterization of the Mean Decrease of
Impurity variable importance measure, from which we prove and derive some of
its properties in the case of multiway totally randomized trees and in
asymptotic conditions. In consequence of this work, our analysis demonstrates
that variable importances [...].Comment: PhD thesis. Source code available at
https://github.com/glouppe/phd-thesi