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Publications
A cry for help: Early detection of brain injury in newborns
Over the past years, foundation models have caused a paradigm shift in machine learning due to their unprecedented capabilities for zero-sho… (see more)t and few-shot generalization. However, despite the success of foundation models in modalities such as natural language processing and computer vision, the development of foundation models for time series forecasting has lagged behind. We present Lag-Llama, a general-purpose foundation model for univariate probabilistic time series forecasting based on a decoder-only transformer architecture that uses lags as covariates. Lag-Llama is pretrained on a large corpus of diverse time series data from several domains, and demonstrates strong zero-shot generalization capabilities compared to a wide range of forecasting models on downstream datasets across domains. Moreover, when fine-tuned on relatively small fractions of such previously unseen datasets, Lag-Llama achieves state-of-the-art performance, outperforming prior deep learning approaches, emerging as the best general-purpose model on average. Lag-Llama serves as a strong contender to the current state-of-art in time series forecasting and paves the way for future advancements in foundation models tailored to time series data.
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history a… (see more)nd numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.
Attention mechanisms have demonstrated significant potential in enhancing learning models by identifying key portions of input data, particu… (see more)larly in scenarios with limited training samples. Inspired by human perception, we propose that focusing on essential data segments, rather than the entire dataset, can improve the accuracy and reliability of the learning models. However, identifying these critical data segments, or"hard attention finding,"is challenging, especially in few-shot learning, due to the scarcity of training data and the complexity of model parameters. To address this, we introduce LaHA, a novel framework that leverages language-guided deep reinforcement learning to identify and utilize informative data regions, thereby improving both interpretability and performance. Extensive experiments on benchmark datasets validate the effectiveness of LaHA.
Deep Learning Benchmark for First Break Detection from Hardrock Seismic Reflection Data
Pierre-Luc St-Charles
Bruno Rousseau
Joumana Ghosn
Gilles Bellefleur
E. Schetselaar
Deep learning techniques are used to tackle a variety of tasks related to seismic data processing and interpretation. While many works have … (see more)shown the benefits of deep learning, assessing the generalization capabilities of proposed methods to data acquired in different conditions and geological environments remains challenging. This is especially true for applications in hardrock environments where seismic surveys are still relatively rare. The primary factors that impede the adoption of machine learning in geosciences include the lack of publicly available and labeled datasets, and the use of inadequate evaluation methodologies. Since machine learning models are prone to overfit and underperform when the data used to train them is site-specific, the applicability of these models on new survey data that could be considered “out-of-distribution” is rarely addressed. This is unfortunate, as evaluating predictive models in out-of-distribution settings can provide a good insight into their usefulness in real-world use cases. To tackle these issues, we propose a simple benchmarking methodology for first break picking to evaluate the transferability of deep learning models that are trained across different environments and acquisition conditions. For this, we consider a reflection seismic survey dataset acquired at five distinct hardrock mining sites combined with annotations for first break picking. We train and evaluate a baseline deep learning solution based on a U-Net for future comparisons, and discuss potential improvements to this approach.
Deep learning models can perform well in complex medical imaging classification tasks, even when basing their conclusions on spurious correl… (see more)ations (i.e. confounders), should they be prevalent in the training dataset, rather than on the causal image markers of interest. This would thereby limit their ability to generalize across the population. Explainability based on counterfactual image generation can be used to expose the confounders but does not provide a strategy to mitigate the bias. In this work, we introduce the first end-to-end training framework that integrates both (i) popular debiasing classifiers (e.g. distributionally robust optimization (DRO)) to avoid latching onto the spurious correlations and (ii) counterfactual image generation to unveil generalizable imaging markers of relevance to the task. Additionally, we propose a novel metric, Spurious Correlation Latching Score (SCLS), to quantify the extent of the classifier reliance on the spurious correlation as exposed by the counterfactual images. Through comprehensive experiments on two public datasets (with the simulated and real visual artifacts), we demonstrate that the debiasing method: (i) learns generalizable markers across the population, and (ii) successfully ignores spurious correlations and focuses on the underlying disease pathology.
2023-10-09
Clinical Image-Based Procedures, Fairness of AI in Medical Imaging, and Ethical and Philosophical Issues in Medical Imaging (published)
