546 research outputs found
Statistical Physics and Representations in Real and Artificial Neural Networks
This document presents the material of two lectures on statistical physics
and neural representations, delivered by one of us (R.M.) at the Fundamental
Problems in Statistical Physics XIV summer school in July 2017. In a first
part, we consider the neural representations of space (maps) in the
hippocampus. We introduce an extension of the Hopfield model, able to store
multiple spatial maps as continuous, finite-dimensional attractors. The phase
diagram and dynamical properties of the model are analyzed. We then show how
spatial representations can be dynamically decoded using an effective Ising
model capturing the correlation structure in the neural data, and compare
applications to data obtained from hippocampal multi-electrode recordings and
by (sub)sampling our attractor model. In a second part, we focus on the problem
of learning data representations in machine learning, in particular with
artificial neural networks. We start by introducing data representations
through some illustrations. We then analyze two important algorithms, Principal
Component Analysis and Restricted Boltzmann Machines, with tools from
statistical physics
Physics of epigenetic landscapes and statistical inference by cells
Biology is currently in the midst of a revolution. Great technological advances have led to unprecedented quantitative data at the whole genome level. However, new techniques are needed to deal with this deluge of high-dimensional data. Therefore, statistical physics has the potential to help develop systems biology level models that can incorporate complex data. Additionally, physicists have made great strides in understanding non-equilibrium thermodynamics. However, the consequences of these advances have yet to be fully incorporated into biology.
There are three specific problems that I address in my dissertation. First, a common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. I introduce a framework for explicitly constructing epigenetic landscapes that combines genomic data with techniques from spin-glass physics. The model reproduces known reprogramming protocols and identifies candidate transcription factors for reprogramming to novel cell fates, suggesting epigenetic landscapes are a powerful paradigm for understanding cellular identity.
Second, I examine the dynamics of cellular reprogramming. By reanalyzing all available time-series data, I show that gene expression dynamics during reprogramming follow a simple one-dimensional reaction coordinate that is independent of both the time and details of experimental protocol used. I show that such a reaction coordinate emerges naturally from epigenetic landscape models of cell identity where cellular reprogramming is viewed as a "barrier-crossing" between the starting and ending cell fates. Overall, the analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an "optimal path"' in gene expression space for reprogramming.
Third, an important task of cells is to perform complex computations in response to external signals. Intricate networks are required to sense and process signals, and since cells are inherently non-equilibrium systems, these networks naturally consume energy. Since there is a deep connection between thermodynamics, computation, and information, a natural question is what constraints does thermodynamics place on statistical estimation and learning. I modeled a single chemical receptor and established the first fundamental relationship between the energy consumption and statistical accuracy of a receptor in a cell
Emergence of Compositional Representations in Restricted Boltzmann Machines
Extracting automatically the complex set of features composing real
high-dimensional data is crucial for achieving high performance in
machine--learning tasks. Restricted Boltzmann Machines (RBM) are empirically
known to be efficient for this purpose, and to be able to generate distributed
and graded representations of the data. We characterize the structural
conditions (sparsity of the weights, low effective temperature, nonlinearities
in the activation functions of hidden units, and adaptation of fields
maintaining the activity in the visible layer) allowing RBM to operate in such
a compositional phase. Evidence is provided by the replica analysis of an
adequate statistical ensemble of random RBMs and by RBM trained on the
handwritten digits dataset MNIST.Comment: Supplementary material available at the authors' webpag
In All Likelihood, Deep Belief Is Not Enough
Statistical models of natural stimuli provide an important tool for
researchers in the fields of machine learning and computational neuroscience. A
canonical way to quantitatively assess and compare the performance of
statistical models is given by the likelihood. One class of statistical models
which has recently gained increasing popularity and has been applied to a
variety of complex data are deep belief networks. Analyses of these models,
however, have been typically limited to qualitative analyses based on samples
due to the computationally intractable nature of the model likelihood.
Motivated by these circumstances, the present article provides a consistent
estimator for the likelihood that is both computationally tractable and simple
to apply in practice. Using this estimator, a deep belief network which has
been suggested for the modeling of natural image patches is quantitatively
investigated and compared to other models of natural image patches. Contrary to
earlier claims based on qualitative results, the results presented in this
article provide evidence that the model under investigation is not a
particularly good model for natural image
Equilibrium Propagation: Bridging the Gap Between Energy-Based Models and Backpropagation
We introduce Equilibrium Propagation, a learning framework for energy-based
models. It involves only one kind of neural computation, performed in both the
first phase (when the prediction is made) and the second phase of training
(after the target or prediction error is revealed). Although this algorithm
computes the gradient of an objective function just like Backpropagation, it
does not need a special computation or circuit for the second phase, where
errors are implicitly propagated. Equilibrium Propagation shares similarities
with Contrastive Hebbian Learning and Contrastive Divergence while solving the
theoretical issues of both algorithms: our algorithm computes the gradient of a
well defined objective function. Because the objective function is defined in
terms of local perturbations, the second phase of Equilibrium Propagation
corresponds to only nudging the prediction (fixed point, or stationary
distribution) towards a configuration that reduces prediction error. In the
case of a recurrent multi-layer supervised network, the output units are
slightly nudged towards their target in the second phase, and the perturbation
introduced at the output layer propagates backward in the hidden layers. We
show that the signal 'back-propagated' during this second phase corresponds to
the propagation of error derivatives and encodes the gradient of the objective
function, when the synaptic update corresponds to a standard form of
spike-timing dependent plasticity. This work makes it more plausible that a
mechanism similar to Backpropagation could be implemented by brains, since
leaky integrator neural computation performs both inference and error
back-propagation in our model. The only local difference between the two phases
is whether synaptic changes are allowed or not
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