arXiv subjects

Alexandre Drouin

Publications and source records attributed to Alexandre Drouin.

46 records · Page 3Linked to original sources

arXiv2021

In Search of Robust Measures of Generalization

One of the principal scientific challenges in deep learning is explaining generalization, i.e., why the particular way the community now trains networks to achieve small training error also leads to small error on held-out data from the same population. It is widely appreciated that some worst-case theories -- such as those based on the VC dimension of the class of predictors induced by modern neural network architectures -- are unable to explain empirical performance. A large volume of work aims to close this gap, primarily by developing bounds on generalization error, optimization error, and excess risk. When evaluated empirically, however, most of these bounds are numerically vacuous. Focusing on generalization bounds, this work addresses the question of how to evaluate such bounds empirically. Jiang et al. (2020) recently described a large-scale empirical study aimed at uncovering potential causal relationships between bounds/measures and generalization. Building on their study, we highlight where their proposed methods can obscure failures and successes of generalization measures in explaining generalization. We argue that generalization measures should instead be evaluated within the framework of distributional robustness.

cs.LG↗

arXiv2020

Synbols: Probing Learning Algorithms with Synthetic Datasets

Progress in the field of machine learning has been fueled by the introduction of benchmark datasets pushing the limits of existing algorithms. Enabling the design of datasets to test specific properties and failure modes of learning algorithms is thus a problem of high interest, as it has a direct impact on innovation in the field. In this sense, we introduce Synbols -- Synthetic Symbols -- a tool for rapidly generating new datasets with a rich composition of latent features rendered in low resolution images. Synbols leverages the large amount of symbols available in the Unicode standard and the wide range of artistic font provided by the open font community. Our tool's high-level interface provides a language for rapidly generating new distributions on the latent features, including various types of textures and occlusions. To showcase the versatility of Synbols, we use it to dissect the limitations and flaws in standard learning algorithms in various learning setups including supervised learning, active learning, out of distribution generalization, unsupervised representation learning, and object counting.

cs.CV↗

arXiv2020

Differentiable Causal Discovery from Interventional Data

Learning a causal directed acyclic graph from data is a challenging task that involves solving a combinatorial problem for which the solution is not always identifiable. A new line of work reformulates this problem as a continuous constrained optimization one, which is solved via the augmented Lagrangian method. However, most methods based on this idea do not make use of interventional data, which can significantly alleviate identifiability issues. This work constitutes a new step in this direction by proposing a theoretically-grounded method based on neural networks that can leverage interventional data. We illustrate the flexibility of the continuous-constrained framework by taking advantage of expressive neural architectures such as normalizing flows. We show that our approach compares favorably to the state of the art in a variety of settings, including perfect and imperfect interventions for which the targeted nodes may even be unknown.

cs.LG↗

arXiv2020

Embedding Propagation: Smoother Manifold for Few-Shot Classification

Few-shot classification is challenging because the data distribution of the training set can be widely different to the test set as their classes are disjoint. This distribution shift often results in poor generalization. Manifold smoothing has been shown to address the distribution shift problem by extending the decision boundaries and reducing the noise of the class representations. Moreover, manifold smoothness is a key factor for semi-supervised learning and transductive learning algorithms. In this work, we propose to use embedding propagation as an unsupervised non-parametric regularizer for manifold smoothing in few-shot classification. Embedding propagation leverages interpolations between the extracted features of a neural network based on a similarity graph. We empirically show that embedding propagation yields a smoother embedding manifold. We also show that applying embedding propagation to a transductive classifier achieves new state-of-the-art results in mini-Imagenet, tiered-Imagenet, Imagenet-FS, and CUB. Furthermore, we show that embedding propagation consistently improves the accuracy of the models in multiple semi-supervised learning scenarios by up to 16\% points. The proposed embedding propagation operation can be easily integrated as a non-parametric layer into a neural network. We provide the training code and usage examples at https://github.com/ElementAI/embedding-propagation.

cs.CV↗

arXiv2019

Deep Learning for Electromyographic Hand Gesture Signal Classification Using Transfer Learning

In recent years, deep learning algorithms have become increasingly more prominent for their unparalleled ability to automatically learn discriminant features from large amounts of data. However, within the field of electromyography-based gesture recognition, deep learning algorithms are seldom employed as they require an unreasonable amount of effort from a single person, to generate tens of thousands of examples. This work's hypothesis is that general, informative features can be learned from the large amounts of data generated by aggregating the signals of multiple users, thus reducing the recording burden while enhancing gesture recognition. Consequently, this paper proposes applying transfer learning on aggregated data from multiple users, while leveraging the capacity of deep learning algorithms to learn discriminant features from large datasets. Two datasets comprised of 19 and 17 able-bodied participants respectively (the first one is employed for pre-training) were recorded for this work, using the Myo Armband. A third Myo Armband dataset was taken from the NinaPro database and is comprised of 10 able-bodied participants. Three different deep learning networks employing three different modalities as input (raw EMG, Spectrograms and Continuous Wavelet Transform (CWT)) are tested on the second and third dataset. The proposed transfer learning scheme is shown to systematically and significantly enhance the performance for all three networks on the two datasets, achieving an offline accuracy of 98.31% for 7 gestures over 17 participants for the CWT-based ConvNet and 68.98% for 18 gestures over 10 participants for the raw EMG-based ConvNet. Finally, a use-case study employing eight able-bodied participants suggests that real-time feedback allows users to adapt their muscle activation strategy which reduces the degradation in accuracy normally experienced over time.

cs.LG↗

arXiv2017

Maximum Margin Interval Trees

Learning a regression function using censored or interval-valued output data is an important problem in fields such as genomics and medicine. The goal is to learn a real-valued prediction function, and the training output labels indicate an interval of possible values. Whereas most existing algorithms for this task are linear models, in this paper we investigate learning nonlinear tree models. We propose to learn a tree by minimizing a margin-based discriminative objective function, and we provide a dynamic programming algorithm for computing the optimal solution in log-linear time. We show empirically that this algorithm achieves state-of-the-art speed and prediction accuracy in a benchmark of several data sets.

stat.ML↗

arXiv2016

Large scale modeling of antimicrobial resistance with interpretable classifiers

Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of antimicrobial agents, by determining which antibiotics are likely to be effective in specific clinical cases. In healthcare, this would allow for the design of treatment plans tailored for specific individuals, likely resulting in better clinical outcomes for patients with bacterial infections. In this work, we present the recent work of Drouin et al. (2016) on using Set Covering Machines to learn highly interpretable models of antibiotic resistance and complement it by providing a large scale application of their method to the entire PATRIC database. We report prediction results for 36 new datasets and present the Kover AMR platform, a new web-based tool allowing the visualization and interpretation of the generated models.

q-bio.GN↗

arXiv2015

Greedy Biomarker Discovery in the Genome with Applications to Antimicrobial Resistance

The Set Covering Machine (SCM) is a greedy learning algorithm that produces sparse classifiers. We extend the SCM for datasets that contain a huge number of features. The whole genetic material of living organisms is an example of such a case, where the number of feature exceeds 10^7. Three human pathogens were used to evaluate the performance of the SCM at predicting antimicrobial resistance. Our results show that the SCM compares favorably in terms of sparsity and accuracy against L1 and L2 regularized Support Vector Machines and CART decision trees. Moreover, the SCM was the only algorithm that could consider the full feature space. For all other algorithms, the latter had to be filtered as a preprocessing step.

q-bio.GN↗

arXiv2014

Learning interpretable models of phenotypes from whole genome sequences with the Set Covering Machine

The increased affordability of whole genome sequencing has motivated its use for phenotypic studies. We address the problem of learning interpretable models for discrete phenotypes from whole genomes. We propose a general approach that relies on the Set Covering Machine and a k-mer representation of the genomes. We show results for the problem of predicting the resistance of Pseudomonas Aeruginosa, an important human pathogen, against 4 antibiotics. Our results demonstrate that extremely sparse models which are biologically relevant can be learnt using this approach.

q-bio.GN↗

arXiv2012

Learning a peptide-protein binding affinity predictor with kernel ridge regression

We propose a specialized string kernel for small bio-molecules, peptides and pseudo-sequences of binding interfaces. The kernel incorporates physico-chemical properties of amino acids and elegantly generalize eight kernels, such as the Oligo, the Weighted Degree, the Blended Spectrum, and the Radial Basis Function. We provide a low complexity dynamic programming algorithm for the exact computation of the kernel and a linear time algorithm for it's approximation. Combined with kernel ridge regression and SupCK, a novel binding pocket kernel, the proposed kernel yields biologically relevant and good prediction accuracy on the PepX database. For the first time, a machine learning predictor is capable of accurately predicting the binding affinity of any peptide to any protein. The method was also applied to both single-target and pan-specific Major Histocompatibility Complex class II benchmark datasets and three Quantitative Structure Affinity Model benchmark datasets. On all benchmarks, our method significantly (p-value < 0.057) outperforms the current state-of-the-art methods at predicting peptide-protein binding affinities. The proposed approach is flexible and can be applied to predict any quantitative biological activity. The method should be of value to a large segment of the research community with the potential to accelerate peptide-based drug and vaccine development.

q-bio.QM↗