Models, code, and papers for "Pierre P":

Recently, multi-task networks have shown to both offer additional estimation capabilities, and, perhaps more importantly, increased performance over single-task networks on a "main/primary" task. However, balancing the optimization criteria of multi-task networks across different tasks is an area of active exploration. Here, we extend a previously proposed 3D attention-based network with four additional multi-task subnetworks for the detection of lung cancer and four auxiliary tasks (diagnosis of asthma, chronic bronchitis, chronic obstructive pulmonary disease, and emphysema). We introduce and evaluate a learning policy, Periodic Focusing Learning Policy (PFLP), that alternates the dominance of tasks throughout the training. To improve performance on the primary task, we propose an Internal-Transfer Weighting (ITW) strategy to suppress the loss functions on auxiliary tasks for the final stages of training. To evaluate this approach, we examined 3386 patients (single scan per patient) from the National Lung Screening Trial (NLST) and de-identified data from the Vanderbilt Lung Screening Program, with a 2517/277/592 (scans) split for training, validation, and testing. Baseline networks include a single-task strategy and a multi-task strategy without adaptive weights (PFLP/ITW), while primary experiments are multi-task trials with either PFLP or ITW or both. On the test set for lung cancer prediction, the baseline single-task network achieved prediction AUC of 0.8080 and the multi-task baseline failed to converge (AUC 0.6720). However, applying PFLP helped multi-task network clarify and achieved test set lung cancer prediction AUC of 0.8402. Furthermore, our ITW technique boosted the PFLP enabled multi-task network and achieved an AUC of 0.8462 (McNemar test, p < 0.01).

Annual low dose computed tomography (CT) lung screening is currently advised for individuals at high risk of lung cancer (e.g., heavy smokers between 55 and 80 years old). The recommended screening practice significantly reduces all-cause mortality, but the vast majority of screening results are negative for cancer. If patients at very low risk could be identified based on individualized, image-based biomarkers, the health care resources could be more efficiently allocated to higher risk patients and reduce overall exposure to ionizing radiation. In this work, we propose a multi-task (diagnosis and prognosis) deep convolutional neural network to improve the diagnostic accuracy over a baseline model while simultaneously estimating a personalized cancer-free progression time (CFPT). A novel Censored Regression Loss (CRL) is proposed to perform weakly supervised regression so that even single negative screening scans can provide small incremental value. Herein, we study 2287 scans from 1433 de-identified patients from the Vanderbilt Lung Screening Program (VLSP) and Molecular Characterization Laboratories (MCL) cohorts. Using five-fold cross-validation, we train a 3D attention-based network under two scenarios: (1) single-task learning with only classification, and (2) multi-task learning with both classification and regression. The single-task learning leads to a higher AUC compared with the Kaggle challenge winner pre-trained model (0.878 v. 0.856), and multi-task learning significantly improves the single-task one (AUC 0.895, p<0.01, McNemar test). In summary, the image-based predicted CFPT can be used in follow-up year lung cancer prediction and data assessment.

This document is an invited chapter covering the specificities of ABC model choice, intended for the incoming Handbook of ABC by Sisson, Fan, and Beaumont (2017). Beyond exposing the potential pitfalls of ABC based posterior probabilities, the review emphasizes mostly the solution proposed by Pudlo et al. (2016) on the use of random forests for aggregating summary statistics and and for estimating the posterior probability of the most likely model via a secondary random fores.

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian inference for models associated with intractable likelihood functions. Most ABC implementations require the preliminary selection of a vector of informative statistics summarizing raw data. Furthermore, in almost all existing implementations, the tolerance level that separates acceptance from rejection of simulated parameter values needs to be calibrated. We propose to conduct likelihood-free Bayesian inferences about parameters with no prior selection of the relevant components of the summary statistics and bypassing the derivation of the associated tolerance level. The approach relies on the random forest methodology of Breiman (2001) applied in a (non parametric) regression setting. We advocate the derivation of a new random forest for each component of the parameter vector of interest. When compared with earlier ABC solutions, this method offers significant gains in terms of robustness to the choice of the summary statistics, does not depend on any type of tolerance level, and is a good trade-off in term of quality of point estimator precision and credible interval estimations for a given computing time. We illustrate the performance of our methodological proposal and compare it with earlier ABC methods on a Normal toy example and a population genetics example dealing with human population evolution. All methods designed here have been incorporated in the R package abcrf (version 1.7) available on CRAN.

Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques. We propose a novel approach based on a machine learning tool named random forests to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with random forests and postponing the approximation of the posterior probability of the predicted MAP for a second stage also relying on random forests. Compared with earlier implementations of ABC model choice, the ABC random forest approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least fifty), and (iv) it includes an approximation of the posterior probability of the selected model. The call to random forests will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets. The proposed methodologies are implemented in the R package abcrf available on the CRAN.

Collaboration between human supervisors and remote teams of robots is highly challenging, particularly in high-stakes, distant, hazardous locations, such as off-shore energy platforms. In order for these teams of robots to truly be beneficial, they need to be trusted to operate autonomously, performing tasks such as inspection and emergency response, thus reducing the number of personnel placed in harm's way. As remote robots are generally trusted less than robots in close-proximity, we present a solution to instil trust in the operator through a `mediator robot' that can exhibit social skills, alongside sophisticated visualisation techniques. In this position paper, we present general challenges and then take a closer look at one challenge in particular, discussing an initial study, which investigates the relationship between the level of control the supervisor hands over to the mediator robot and how this affects their trust. We show that the supervisor is more likely to have higher trust overall if their initial experience involves handing over control of the emergency situation to the robotic assistant. We discuss this result, here, as well as other challenges and interaction techniques for human-robot collaboration.

Early detection of lung cancer is essential in reducing mortality. Recent studies have demonstrated the clinical utility of low-dose computed tomography (CT) to detect lung cancer among individuals selected based on very limited clinical information. However, this strategy yields high false positive rates, which can lead to unnecessary and potentially harmful procedures. To address such challenges, we established a pipeline that co-learns from detailed clinical demographics and 3D CT images. Toward this end, we leveraged data from the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL), which focuses on early detection of lung cancer. A 3D attention-based deep convolutional neural net (DCNN) is proposed to identify lung cancer from the chest CT scan without prior anatomical location of the suspicious nodule. To improve upon the non-invasive discrimination between benign and malignant, we applied a random forest classifier to a dataset integrating clinical information to imaging data. The results show that the AUC obtained from clinical demographics alone was 0.635 while the attention network alone reached an accuracy of 0.687. In contrast when applying our proposed pipeline integrating clinical and imaging variables, we reached an AUC of 0.787 on the testing dataset. The proposed network both efficiently captures anatomical information for classification and also generates attention maps that explain the features that drive performance.

The field of lung nodule detection and cancer prediction has been rapidly developing with the support of large public data archives. Previous studies have largely focused on cross-sectional (single) CT data. Herein, we consider longitudinal data. The Long Short-Term Memory (LSTM) model addresses learning with regularly spaced time points (i.e., equal temporal intervals). However, clinical imaging follows patient needs with often heterogeneous, irregular acquisitions. To model both regular and irregular longitudinal samples, we generalize the LSTM model with the Distanced LSTM (DLSTM) for temporally varied acquisitions. The DLSTM includes a Temporal Emphasis Model (TEM) that enables learning across regularly and irregularly sampled intervals. Briefly, (1) the time intervals between longitudinal scans are modeled explicitly, (2) temporally adjustable forget and input gates are introduced for irregular temporal sampling; and (3) the latest longitudinal scan has an additional emphasis term. We evaluate the DLSTM framework in three datasets including simulated data, 1794 National Lung Screening Trial (NLST) scans, and 1420 clinically acquired data with heterogeneous and irregular temporal accession. The experiments on the first two datasets demonstrate that our method achieves competitive performance on both simulated and regularly sampled datasets (e.g. improve LSTM from 0.6785 to 0.7085 on F1 score in NLST). In external validation of clinically and irregularly acquired data, the benchmarks achieved 0.8350 (CNN feature) and 0.8380 (LSTM) on the area under the ROC curve (AUC) score, while the proposed DLSTM achieves 0.8905.

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.

This article introduces a reflexion about behavioural specification for interactive and participative agent-based simulation in virtual reality. Within this context, it is neces sary to reach a high level of expressivness in order to enforce interactions between the designer and the behavioural model during the in-line prototyping. This requires to consider the need of semantic very early in the design process. The Intentional agent model is here exposed as a possible answer. It relies on a mixed imperative and declarative approach which focuses on the link between decision and action. The design of a tool able to simulate virtual environment implying agents based on this model is discuss

We present a Bayesian model selection approach to estimate the intrinsic dimensionality of a high-dimensional dataset. To this end, we introduce a novel formulation of the probabilisitic principal component analysis model based on a normal-gamma prior distribution. In this context, we exhibit a closed-form expression of the marginal likelihood which allows to infer an optimal number of components. We also propose a heuristic based on the expected shape of the marginal likelihood curve in order to choose the hyperparameters. In non-asymptotic frameworks, we show on simulated data that this exact dimensionality selection approach is competitive with both Bayesian and frequentist state-of-the-art methods.

Sparse versions of principal component analysis (PCA) have imposed themselves as simple, yet powerful ways of selecting relevant features of high-dimensional data in an unsupervised manner. However, when several sparse principal components are computed, the interpretation of the selected variables is difficult since each axis has its own sparsity pattern and has to be interpreted separately. To overcome this drawback, we propose a Bayesian procedure called globally sparse probabilistic PCA (GSPPCA) that allows to obtain several sparse components with the same sparsity pattern. This allows the practitioner to identify the original variables which are relevant to describe the data. To this end, using Roweis' probabilistic interpretation of PCA and a Gaussian prior on the loading matrix, we provide the first exact computation of the marginal likelihood of a Bayesian PCA model. To avoid the drawbacks of discrete model selection, a simple relaxation of this framework is presented. It allows to find a path of models using a variational expectation-maximization algorithm. The exact marginal likelihood is then maximized over this path. This approach is illustrated on real and synthetic data sets. In particular, using unlabeled microarray data, GSPPCA infers much more relevant gene subsets than traditional sparse PCA algorithms.

In open-ended and changing environments, agents face a wide range of potential tasks that may or may not come with associated reward functions. Such autonomous learning agents must be able to generate their own tasks through a process of intrinsically motivated exploration, some of which might prove easy, others impossible. For this reason, they should be able to actively select which task to practice at any given moment, to maximize their overall mastery on the set of learnable tasks. This paper proposes CURIOUS, an extension of Universal Value Function Approximators that enables intrinsically motivated agents to learn to achieve both multiple tasks and multiple goals within a unique policy, leveraging hindsight learning. Agents focus on achievable tasks first, using an automated curriculum learning mechanism that biases their attention towards tasks maximizing the absolute learning progress. This mechanism provides robustness to catastrophic forgetting (by refocusing on tasks where performance decreases) and distracting tasks (by avoiding tasks with no absolute learning progress). Furthermore, we show that having two levels of parameterization (tasks and goals within tasks) enables more efficient learning of skills in an environment with a modular physical structure (e.g. multiple objects) as compared to flat, goal-parameterized RL with hindsight experience replay.

In this paper, we investigate a new form of automated curriculum learning based on adaptive selection of accuracy requirements, called accuracy-based curriculum learning. Using a reinforcement learning agent based on the Deep Deterministic Policy Gradient algorithm and addressing the Reacher environment, we first show that an agent trained with various accuracy requirements sampled randomly learns more efficiently than when asked to be very accurate at all times. Then we show that adaptive selection of accuracy requirements, based on a local measure of competence progress, automatically generates a curriculum where difficulty progressively increases, resulting in a better learning efficiency than sampling randomly.

The Random Walks (RW) algorithm is one of the most e - cient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner. However, one of the main drawbacks of using the RW algorithm is that its parameters have to be hand-tuned. we propose a novel discriminative learning framework that estimates the parameters using a training dataset. The main challenge we face is that the training samples are not fully supervised. Speci cally, they provide a hard segmentation of the images, instead of a proba- bilistic segmentation. We overcome this challenge by treating the opti- mal probabilistic segmentation that is compatible with the given hard segmentation as a latent variable. This allows us to employ the latent support vector machine formulation for parameter estimation. We show that our approach signi cantly outperforms the baseline methods on a challenging dataset consisting of real clinical 3D MRI volumes of skeletal muscles.

The Random Walks (RW) algorithm is one of the most e - cient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner. However, one of the main drawbacks of using the RW algorithm is that its parameters have to be hand-tuned. we propose a novel discriminative learning framework that estimates the parameters using a training dataset. The main challenge we face is that the training samples are not fully supervised. Speci cally, they provide a hard segmentation of the images, instead of a proba-bilistic segmentation. We overcome this challenge by treating the optimal probabilistic segmentation that is compatible with the given hard segmentation as a latent variable. This allows us to employ the latent support vector machine formulation for parameter estimation. We show that our approach signi cantly outperforms the baseline methods on a challenging dataset consisting of real clinical 3D MRI volumes of skeletal muscles.

Pressure ulcers are recognized as a major health issue in individuals with spinal cord injuries and new approaches to prevent this pathology are necessary. An innovative health strategy is being developed through the use of computer and sensory substitution via the tongue in order to compensate for the sensory loss in the buttock area for individuals with paraplegia. This sensory compensation will enable individuals with spinal cord injuries to be aware of a localized excess of pressure at the skin/seat interface and, consequently, will enable them to prevent the formation of pressure ulcers by relieving the cutaneous area of suffering. This work reports an initial evaluation of this approach and the feasibility of creating an adapted behavior, with a change in pressure as a response to electro-stimulated information on the tongue. Obtained during a clinical study in 10 healthy seated subjects, the first results are encouraging, with 92% success in 100 performed tests. These results, which have to be completed and validated in the paraplegic population, may lead to a new approach to education in health to prevent the formation of pressure ulcers within this population. Keywords: Spinal Cord Injuries, Pressure Ulcer, Sensory Substitution, Health Education, Biomedical Informatics.

We introduce a novel framework for an approxi- mate recovery of data matrices which are low-rank on graphs, from sampled measurements. The rows and columns of such matrices belong to the span of the first few eigenvectors of the graphs constructed between their rows and columns. We leverage this property to recover the non-linear low-rank structures efficiently from sampled data measurements, with a low cost (linear in n). First, a Resrtricted Isometry Property (RIP) condition is introduced for efficient uniform sampling of the rows and columns of such matrices based on the cumulative coherence of graph eigenvectors. Secondly, a state-of-the-art fast low-rank recovery method is suggested for the sampled data. Finally, several efficient, parallel and parameter-free decoders are presented along with their theoretical analysis for decoding the low-rank and cluster indicators for the full data matrix. Thus, we overcome the computational limitations of the standard linear low-rank recovery methods for big datasets. Our method can also be seen as a major step towards efficient recovery of non- linear low-rank structures. For a matrix of size n X p, on a single core machine, our method gains a speed up of $p^2/k$ over Robust Principal Component Analysis (RPCA), where k << p is the subspace dimension. Numerically, we can recover a low-rank matrix of size 10304 X 1000, 100 times faster than Robust PCA.

Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude 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.

This paper studies schemes to de-bias the Lasso in sparse linear regression where the goal is to estimate and construct confidence intervals for a low-dimensional projection of the unknown coefficient vector in a preconceived direction $a_0$. We assume that the design matrix has iid Gaussian rows with known covariance matrix $\Sigma$. Our analysis reveals that previous propositions to de-bias the Lasso require a modification in order to enjoy asymptotic efficiency in a full range of the level of sparsity. This modification takes the form of a degrees-of-freedom adjustment that accounts for the dimension of the model selected by the Lasso. Let $s_0$ denote the number of nonzero coefficients of the true coefficient vector. The unadjusted de-biasing schemes proposed in previous studies enjoys efficiency if $s_0\lll n^{2/3}$, up to logarithmic factors. However, if $s_0\ggg n^{2/3}$, the unadjusted scheme cannot be efficient in certain directions $a_0$. In the latter regime, it it necessary to modify existing procedures by an adjustment that accounts for the degrees-of-freedom of the Lasso. The proposed degrees-of-freedom adjustment grants asymptotic efficiency for any direction $a_0$. This holds under a Sparse Riecz Condition on the covariance matrix $\Sigma$ and the sample size requirement $s_0/p\to0$ and $s_0\log(p/s_0)/n\to0$. Our analysis also highlights that the degrees-of-freedom adjustment is not necessary when the initial bias of the Lasso in the direction $a_0$ is small, which is granted under more stringent conditions on $\Sigma^{-1}$. This explains why the necessity of degrees-of-freedom adjustment did not appear in some previous studies. The main proof argument involves a Gaussian interpolation path similar to that used to derive Slepian's lemma. It yields a sharp $\ell_\infty$ error bound for the Lasso under Gaussian design which is of independent interest.