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Publications
Two types of human TCR differentially regulate reactivity to self and non-self antigens
Discovering what is learned by neural networks remains a challenge. In self-supervised learning, classification is the most common task used… (see more) to evaluate how good a representation is. However, relying only on such downstream task can limit our understanding of what information is retained in the representation of a given input. In this work, we showcase the use of a Representation Conditional Diffusion Model (RCDM) to visualize in data space the representations learned by self-supervised models. The use of RCDM is motivated by its ability to generate high-quality samples -- on par with state-of-the-art generative models -- while ensuring that the representations of those samples are faithful i.e. close to the one used for conditioning. By using RCDM to analyze self-supervised models, we are able to clearly show visually that i) SSL (backbone) representation are not invariant to the data augmentations they were trained with -- thus debunking an often restated but mistaken belief; ii) SSL post-projector embeddings appear indeed invariant to these data augmentation, along with many other data symmetries; iii) SSL representations appear more robust to small adversarial perturbation of their inputs than representations trained in a supervised manner; and iv) that SSL-trained representations exhibit an inherent structure that can be explored thanks to RCDM visualization and enables image manipulation.
Electronic health records (EHRs) provide rich clinical information and the opportunities to extract epidemiological patterns to understand a… (see more)nd predict patient disease risks with suitable machine learning methods such as topic models. However, existing topic models do not generate identifiable topics each predicting a unique phenotype. One promising direction is to use known phenotype concepts to guide topic inference. We present a seed-guided Bayesian topic model called MixEHR-Seed with 3 contributions: (1) for each phenotype, we infer a dual-form of topic distribution: a seed-topic distribution over a small set of key EHR codes and a regular topic distribution over the entire EHR vocabulary; (2) we model age-dependent disease progression as Markovian dynamic topic priors; (3) we infer seed-guided multi-modal topics over distinct EHR data types. For inference, we developed a variational inference algorithm. Using MixEHR-Seed, we inferred 1569 PheCode-guided phenotype topics from an EHR database in Quebec, Canada covering 1.3 million patients for up to 20-year follow-up with 122 million records for 8539 and 1126 unique diagnostic and drug codes, respectively. We observed (1) accurate phenotype prediction by the guided topics, (2) clinically relevant PheCode-guided disease topics, (3) meaningful age-dependent disease prevalence. Source code is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-Seed.
In many clinical contexts, detecting all lesions is imperative for evaluating disease activity. Standard approaches pose lesion detection as… (see more) a segmentation problem despite the time-consuming nature of acquiring segmentation labels. In this paper, we present a lesion detection method which relies only on point labels. Our model, which is trained via heatmap regression, can detect a variable number of lesions in a probabilistic manner. In fact, our proposed post-processing method offers a reliable way of directly estimating the lesion existence uncertainty. Experimental results on Gad lesion detection show our point-based method performs competitively compared to training on expensive segmentation labels. Finally, our detection model provides a suitable pre-training for segmentation. When fine-tuning on only 17 segmentation samples, we achieve comparable performance to training with the full dataset.
Background: Understanding the relationship between the Omics and the phenotype is a central problem in precision medicine. The high dimensio… (see more)nality of metabolomics data challenges learning algorithms in terms of scalability and generalization. Most learning algorithms do not produce interpretable models -- Method: We propose an ensemble learning algorithm based on conjunctions or disjunctions of decision rules. -- Results : Applications on metabolomics data shows that it produces models that achieves high predictive performances. The interpretability of the models makes them useful for biomarker discovery and patterns discovery in high dimensional data.
