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Model-based targeted dimensionality reduction for neuronal population data

Neural Information Processing Systems

Summarizing high-dimensional data using a small number of parameters is a ubiquitous first step in the analysis of neuronal population activity. Recently developed methods use targeted approaches that work by identifying multiple, distinct low-dimensional subspaces of activity that capture the population response to individual experimental task variables, such as the value of a presented stimulus or the behavior of the animal. These methods have gained attention because they decompose total neural activity into what are ostensibly different parts of a neuronal computation. However, existing targeted methods have been developed outside of the confines of probabilistic modeling, making some aspects of the procedures ad hoc, or limited in flexibility or interpretability. Here we propose a new model-based method for targeted dimensionality reduction based on a probabilistic generative model of the population response data.


Model-based targeted dimensionality reduction for neuronal population data

Neural Information Processing Systems

Summarizing high-dimensional data using a small number of parameters is a ubiquitous first step in the analysis of neuronal population activity. Recently developed methods use "targeted" approaches that work by identifying multiple, distinct low-dimensional subspaces of activity that capture the population response to individual experimental task variables, such as the value of a presented stimulus or the behavior of the animal. These methods have gained attention because they decompose total neural activity into what are ostensibly different parts of a neuronal computation. However, existing targeted methods have been developed outside of the confines of probabilistic modeling, making some aspects of the procedures ad hoc, or limited in flexibility or interpretability. Here we propose a new model-based method for targeted dimensionality reduction based on a probabilistic generative model of the population response data.


Reviews: Model-based targeted dimensionality reduction for neuronal population data

Neural Information Processing Systems

Supervised dimensionality reduction has become a topic of interest in the systems neuroscience community over the last few years. Here, the authors suggested a very sensible extension to demixed PCA and targeted dimensionality reduction (TDR), which are recently developed but well-known and impactful methods in the field. However, I am disappointed that it heavily relies on simulated data rather than real biological datasets for its results. In particular, all datasets examined by the demixed PCA paper (in eLife) are freely available, so I feel that at least one of those datasets should have been analyzed for the purpose of comparison. I am not convinced that the proposed model would produce qualitatively different results from those already published. That being said, I think the proposed modeling framework is more straightforward than demixed PCA and offers the possibility of interesting future extensions.


Model-based Cleaning of the QUILT-1M Pathology Dataset for Text-Conditional Image Synthesis

Aubreville, Marc, Ganz, Jonathan, Ammeling, Jonas, Kaltenecker, Christopher C., Bertram, Christof A.

arXiv.org Artificial Intelligence

The QUILT-1M dataset is the first openly available dataset containing images harvested from various online sources. While it provides a huge data variety, the image quality and composition is highly heterogeneous, impacting its utility for text-conditional image synthesis. We propose an automatic pipeline that provides predictions of the most common impurities within the images, e.g., visibility of narrators, desktop environment and pathology software, or text within the image. Additionally, we propose to use semantic alignment filtering of the image-text pairs. Our findings demonstrate that by rigorously filtering the dataset, there is a substantial enhancement of image fidelity in text-to-image tasks.


Curriculum Learning for Graph Neural Networks: A Multiview Competence-based Approach

Vakil, Nidhi, Amiri, Hadi

arXiv.org Artificial Intelligence

A curriculum is a planned sequence of learning materials and an effective one can make learning efficient and effective for both humans and machines. Recent studies developed effective data-driven curriculum learning approaches for training graph neural networks in language applications. However, existing curriculum learning approaches often employ a single criterion of difficulty in their training paradigms. In this paper, we propose a new perspective on curriculum learning by introducing a novel approach that builds on graph complexity formalisms (as difficulty criteria) and model competence during training. The model consists of a scheduling scheme which derives effective curricula by accounting for different views of sample difficulty and model competence during training. The proposed solution advances existing research in curriculum learning for graph neural networks with the ability to incorporate a fine-grained spectrum of graph difficulty criteria in their training paradigms. Experimental results on real-world link prediction and node classification tasks illustrate the effectiveness of the proposed approach.


Model-based targeted dimensionality reduction for neuronal population data

Aoi, Mikio, Pillow, Jonathan W.

Neural Information Processing Systems

Summarizing high-dimensional data using a small number of parameters is a ubiquitous first step in the analysis of neuronal population activity. Recently developed methods use "targeted" approaches that work by identifying multiple, distinct low-dimensional subspaces of activity that capture the population response to individual experimental task variables, such as the value of a presented stimulus or the behavior of the animal. These methods have gained attention because they decompose total neural activity into what are ostensibly different parts of a neuronal computation. However, existing targeted methods have been developed outside of the confines of probabilistic modeling, making some aspects of the procedures ad hoc, or limited in flexibility or interpretability. Here we propose a new model-based method for targeted dimensionality reduction based on a probabilistic generative model of the population response data.


Model-based clustering and segmentation of time series with changes in regime

Samé, Allou, Chamroukhi, Faicel, Govaert, Gérard, Aknin, Patrice

arXiv.org Machine Learning

Mixture model-based clustering, usually applied to multidimensional data, has become a popular approach in many data analysis problems, both for its good statistical properties and for the simplicity of implementation of the Expectation-Maximization (EM) algorithm. Within the context of a railway application, this paper introduces a novel mixture model for dealing with time series that are subject to changes in regime. The proposed approach consists in modeling each cluster by a regression model in which the polynomial coefficients vary according to a discrete hidden process. In particular, this approach makes use of logistic functions to model the (smooth or abrupt) transitions between regimes. The model parameters are estimated by the maximum likelihood method solved by an Expectation-Maximization algorithm. The proposed approach can also be regarded as a clustering approach which operates by finding groups of time series having common changes in regime. In addition to providing a time series partition, it therefore provides a time series segmentation. The problem of selecting the optimal numbers of clusters and segments is solved by means of the Bayesian Information Criterion (BIC). The proposed approach is shown to be efficient using a variety of simulated time series and real-world time series of electrical power consumption from rail switching operations.


Model-based clustering with Hidden Markov Model regression for time series with regime changes

Chamroukhi, Faicel, Samé, Allou, Aknin, Patrice, Govaert, Gérard

arXiv.org Machine Learning

This paper introduces a novel model-based clustering approach for clustering time series which present changes in regime. It consists of a mixture of polynomial regressions governed by hidden Markov chains. The underlying hidden process for each cluster activates successively several polynomial regimes during time. The parameter estimation is performed by the maximum likelihood method through a dedicated Expectation-Maximization (EM) algorithm. The proposed approach is evaluated using simulated time series and real-world time series issued from a railway diagnosis application. Comparisons with existing approaches for time series clustering, including the stand EM for Gaussian mixtures, $K$-means clustering, the standard mixture of regression models and mixture of Hidden Markov Models, demonstrate the effectiveness of the proposed approach.