Domain generalization is a popular machine learning technique that enables models to perform well on the unseen target domain, by learning from multiple source domains. Domain generalization is useful in cases where data is limited, difficult, or expensive to collect, such as in object recognition and biomedicine. In this paper, we propose a novel domain generalization algorithm called "meta-forests", which builds upon the basic random forests model by incorporating the meta-learning strategy and maximum mean discrepancy measure. The aim of meta-forests is to enhance the generalization ability of classifiers by reducing the correlation among trees and increasing their strength. More specifically, meta-forests conducts meta-learning optimization during each meta-task, while also utilizing the maximum mean discrepancy as a regularization term to penalize poor generalization performance in the meta-test process. To evaluate the effectiveness of our algorithm, we test it on two publicly object recognition datasets and a glucose monitoring dataset that we have used in a previous study. Our results show that meta-forests outperforms state-of-the-art approaches in terms of generalization performance on both object recognition and glucose monitoring datasets.
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The use of deep learning models in computational biology has increased massively in recent years, and is expected to do so further with the current advances in fields like Natural Language Processing. These models, although able to draw complex relations between input and target, are also largely inclined to learn noisy deviations from the pool of data used during their development. In order to assess their performance on unseen data (their capacity to generalize), it is common to randomly split the available data in development (train/validation) and test sets. This procedure, although standard, has lately been shown to produce dubious assessments of generalization due to the existing similarity between samples in the databases used. In this work, we present SpanSeq, a database partition method for machine learning that can scale to most biological sequences (genes, proteins and genomes) in order to avoid data leakage between sets. We also explore the effect of not restraining similarity between sets by reproducing the development of the state-of-the-art model DeepLoc, not only confirming the consequences of randomly splitting databases on the model assessment, but expanding those repercussions to the model development. SpanSeq is available for downloading and installing at //github.com/genomicepidemiology/SpanSeq.
Valid statistical inference is crucial for decision-making but difficult to obtain in supervised learning with multimodal data, e.g., combinations of clinical features, genomic data, and medical images. Multimodal data often warrants the use of black-box algorithms, for instance, random forests or neural networks, which impede the use of traditional variable significance tests. We address this problem by proposing the use of COvariance Measure Tests (COMETs), which are calibrated and powerful tests that can be combined with any sufficiently predictive supervised learning algorithm. We apply COMETs to several high-dimensional, multimodal data sets to illustrate (i) variable significance testing for finding relevant mutations modulating drug-activity, (ii) modality selection for predicting survival in liver cancer patients with multiomics data, and (iii) modality selection with clinical features and medical imaging data. In all applications, COMETs yield results consistent with domain knowledge without requiring data-driven pre-processing which may invalidate type I error control. These novel applications with high-dimensional multimodal data corroborate prior results on the power and robustness of COMETs for significance testing. The comets R package and source code for reproducing all results is available at //github.com/LucasKook/comets. All data sets used in this work are openly available.
Replicability in machine learning (ML) research is increasingly concerning due to the utilization of complex non-deterministic algorithms and the dependence on numerous hyper-parameter choices, such as model architecture and training datasets. Ensuring reproducible and replicable results is crucial for advancing the field, yet often requires significant technical effort to conduct systematic and well-organized experiments that yield robust conclusions. Several tools have been developed to facilitate experiment management and enhance reproducibility; however, they often introduce complexity that hinders adoption within the research community, despite being well-handled in industrial settings. To address the challenge of low adoption, we propose MLXP, an open-source, simple, and lightweight experiment management tool based on Python, available at //github.com/inria-thoth/mlxp . MLXP streamlines the experimental process with minimal practitioner overhead while ensuring a high level of reproducibility.
The objective of this study is to investigate the application of various channel attention mechanisms within the domain of brain-computer interface (BCI) for motor imagery decoding. Channel attention mechanisms can be seen as a powerful evolution of spatial filters traditionally used for motor imagery decoding. This study systematically compares such mechanisms by integrating them into a lightweight architecture framework to evaluate their impact. We carefully construct a straightforward and lightweight baseline architecture designed to seamlessly integrate different channel attention mechanisms. This approach is contrary to previous works which only investigate one attention mechanism and usually build a very complex, sometimes nested architecture. Our framework allows us to evaluate and compare the impact of different attention mechanisms under the same circumstances. The easy integration of different channel attention mechanisms as well as the low computational complexity enables us to conduct a wide range of experiments on four datasets to thoroughly assess the effectiveness of the baseline model and the attention mechanisms. Our experiments demonstrate the strength and generalizability of our architecture framework as well as how channel attention mechanisms can improve the performance while maintaining the small memory footprint and low computational complexity of our baseline architecture. Our architecture emphasizes simplicity, offering easy integration of channel attention mechanisms, while maintaining a high degree of generalizability across datasets, making it a versatile and efficient solution for EEG motor imagery decoding within brain-computer interfaces.
We extend generalized functional linear models under independence to a situation in which a functional covariate is related to a scalar response variable that exhibits spatial dependence. For estimation, we apply basis expansion and truncation for dimension reduction of the covariate process followed by a composite likelihood estimating equation to handle the spatial dependency. We develop asymptotic results for the proposed model under a repeating lattice asymptotic context, allowing us to construct a confidence interval for the spatial dependence parameter and a confidence band for the parameter function. A binary conditionals model is presented as a concrete illustration and is used in simulation studies to verify the applicability of the asymptotic inferential results.
The number of sampling methods could be daunting for a practitioner looking to cast powerful machine learning methods to their specific problem. This paper takes a theoretical stance to review and organize many sampling approaches in the ``generative modeling'' setting, where one wants to generate new data that are similar to some training examples. By revealing links between existing methods, it might prove useful to overcome some of the current challenges in sampling with diffusion models, such as long inference time due to diffusion simulation, or the lack of diversity in generated samples.
Most state-of-the-art machine learning techniques revolve around the optimisation of loss functions. Defining appropriate loss functions is therefore critical to successfully solving problems in this field. We present a survey of the most commonly used loss functions for a wide range of different applications, divided into classification, regression, ranking, sample generation and energy based modelling. Overall, we introduce 33 different loss functions and we organise them into an intuitive taxonomy. Each loss function is given a theoretical backing and we describe where it is best used. This survey aims to provide a reference of the most essential loss functions for both beginner and advanced machine learning practitioners.
Meta-learning, or learning to learn, has gained renewed interest in recent years within the artificial intelligence community. However, meta-learning is incredibly prevalent within nature, has deep roots in cognitive science and psychology, and is currently studied in various forms within neuroscience. The aim of this review is to recast previous lines of research in the study of biological intelligence within the lens of meta-learning, placing these works into a common framework. More recent points of interaction between AI and neuroscience will be discussed, as well as interesting new directions that arise under this perspective.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques.
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