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Tristan Sylvain

Alumni

Publications

Learning to rank for censored survival data
Margaux Luck
Tristan Sylvain
Joseph Paul Cohen
Heloise Cardinal
Andrea Lodi
Yoshua Bengio
Survival analysis is a type of semi-supervised ranking task where the target output (the survival time) is often right-censored. Utilizing t… (voir plus)his information is a challenge because it is not obvious how to correctly incorporate these censored examples into a model. We study how three categories of loss functions, namely partial likelihood methods, rank methods, and our classification method based on a Wasserstein metric (WM) and the non-parametric Kaplan Meier estimate of the probability density to impute the labels of censored examples, can take advantage of this information. The proposed method allows us to have a model that predict the probability distribution of an event. If a clinician had access to the detailed probability of an event over time this would help in treatment planning. For example, determining if the risk of kidney graft rejection is constant or peaked after some time. Also, we demonstrate that this approach directly optimizes the expected C-index which is the most common evaluation metric for ranking survival models.
2018-06-06
ArXiv (prépublication)
arxiv.org
arxiv.org
Diet Networks: Thin Parameters for Fat Genomics
Adriana Romero Soriano
Pierre Luc Carrier
Akram Erraqabi
Tristan Sylvain
Alex Auvolat
Étienne Dejoie
Marc-André Legault
Marie-Pierre Dubé
Julie Hussin
Yoshua Bengio
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (voir plus) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in medical research, more specifically in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer (number of input features times number of hidden units): each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed in data), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation (based on the feature's identity not its value) to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). This approach views the problem of producing the parameters associated with each feature as a multi-task learning problem. We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
2017-01-01
ICLR.cc/2017/conference (poster)
openreview.net
openreview.net
Diet Networks: Thin Parameters for Fat Genomics
Adriana Romero Soriano
Pierre Luc Carrier
Akram Erraqabi
Tristan Sylvain
Alex Auvolat
Étienne Dejoie
Marc-André Legault
Marie-Pierre Dubé
Julie Hussin
Yoshua Bengio
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (voir plus) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in medical research, more specifically in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer (number of input features times number of hidden units): each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed in data), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation (based on the feature's identity not its value) to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). This approach views the problem of producing the parameters associated with each feature as a multi-task learning problem. We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
2017-01-01
ICLR.cc/2017/conference (poster)
openreview.net
openreview.net
Diet Networks: Thin Parameters for Fat Genomic
Adriana Romero Soriano
Pierre Luc Carrier
Akram Erraqabi
Tristan Sylvain
Alex Auvolat
Étienne Dejoie
Marc-André Legault
M. Dubé
Julie Hussin
Yoshua Bengio
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (voir plus) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer: each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
2016-11-04
ArXiv (prépublication)
arxiv.org
arxiv.org