Context. Machine-learning methods for predicting solar flares typically employ physics-based features that have been carefully cho- sen by experts in order to capture the salient features of the photospheric magnetic fields of the Sun.
Aims. Though the sophistication and complexity of these models have grown over time, there has been little evolution in the choice of feature sets, or any systematic study of whether the additional model complexity leads to higher predictive skill.
Methods. This study compares the relative prediction performance of four different machine-learning based flare prediction models with increasing degrees of complexity. It evaluates three different feature sets as input to each model: a “traditional” physics-based feature set, a novel “shape-based” feature set derived from topological data analysis (TDA) of the solar magnetic field, and a com- bination of these two sets. A systematic hyperparameter tuning framework is employed in order to assure fair comparisons of the models across different feature sets. Finally, principal component analysis is used to study the effects of dimensionality reduction on these feature sets.
Results. It is shown that simpler models with fewer free parameters perform better than the more complicated models on the canonical 24-h flare forecasting problem. In other words, more complex machine-learning architectures do not necessarily guarantee better prediction performance. In addition, it is found that shape-based feature sets contain just as much useful information as physics-based feature sets for the purpose of flare prediction, and that the dimension of these feature sets – particularly the shape-based one – can be greatly reduced without impacting predictive accuracy.
more »
« less
This content will become publicly available on November 17, 2024
Topological structure of complex predictions
Current complex prediction models are the result of fitting deep neural networks, graph convolutional networks or transducers to a set of training data. A key challenge with these models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into a simplified topological view of the prediction landscape. The result is a map of the predictions that enables inspection of the model results with more specificity than dimensionality-reduction methods such as tSNE and UMAP. The methods scale up to large datasets across different domains. We present a case study of a transformer-based model previously designed to predict expression levels of a piece of DNA in thousands of genomic tracks. When the model is used to study mutations in the
- NSF-PAR ID:
- 10477224
- Publisher / Repository:
- Nature
- Date Published:
- Journal Name:
- Nature Machine Intelligence
- ISSN:
- 2522-5839
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Deep neural networks can learn powerful prior probability models for images, as evidenced by the high-quality generations obtained with recent score-based diffusion methods. But the means by which these networks capture complex global statistical structure, apparently without suffering from the curse of dimensionality, remain a mystery. To study this, we incorporate diffusion methods into a multi-scale decomposition, reducing dimensionality by assuming a stationary local Markov model for wavelet coefficients conditioned on coarser-scale coefficients. We instantiate this model using convolutional neural networks (CNNs) with local receptive fields, which enforce both the stationarity and Markov properties. Global structures are captured using a CNN with receptive fields covering the entire (but small) low-pass image. We test this model on a dataset of face images, which are highly non-stationary and contain large-scale geometric structures. Remarkably, denoising, super-resolution, and image synthesis results all demonstrate that these structures can be captured with significantly smaller conditioning neighborhoods than required by a Markov model implemented in the pixel domain. Our results show that score estimation for large complex images can be reduced to low-dimensional Markov conditional models across scales, alleviating the curse of dimensionality.more » « less
-
more » « less
Abstract A key problem in social network analysis is to identify nonhuman interactions. State‐of‐the‐art bot‐detection systems like Botometer train machine‐learning models on user‐specific data. Unfortunately, these methods do not work on data sets in which only topological information is available. In this paper, we propose a new, purely topological approach. Our method removes edges that connect nodes exhibiting strong evidence of non‐human activity from publicly available electronic‐social‐network datasets, including, for example, those in the Stanford Network Analysis Project repository (SNAP). Our methodology is inspired by classic work in evolutionary psychology by Dunbar that posits upper bounds on the total strength of the set of social connections in which a single human can be engaged. We model edge strength with Easley and Kleinberg's topological estimate; label nodes as “violators” if the sum of these edge strengths exceeds a Dunbar‐inspired bound; and then remove the violator‐to‐violator edges. We run our algorithm on multiple social networks and show that our Dunbar‐inspired bound appears to hold for social networks, but not for nonsocial networks. Our cleaning process classifies 0.04% of the nodes of the Twitter‐2010 followers graph as violators, and we find that more than 80% of these violator nodes have Botometer scores of 0.5 or greater. Furthermore, after we remove the roughly 15 million violator‐violator edges from the 1.2‐billion‐edge Twitter‐2010 follower graph, 34% of the violator nodes experience a factor‐of‐two decrease in PageRank. PageRank is a key component of many graph algorithms such as node/edge ranking and graph sparsification. Thus, this artificial inflation would bias algorithmic output, and result in some incorrect decisions based on this output.
-
more » « less
Abstract The interaction between T-cell receptors (TCRs) and peptides (epitopes) presented by major histocompatibility complex molecules (MHC) is fundamental to the immune response. Accurate prediction of TCR–epitope interactions is crucial for advancing the understanding of various diseases and their prevention and treatment. Existing methods primarily rely on sequence-based approaches, overlooking the inherent topology structure of TCR–epitope interaction networks. In this study, we present $GTE$, a novel heterogeneous Graph neural network model based on inductive learning to capture the topological structure between TCRs and Epitopes. Furthermore, we address the challenge of constructing negative samples within the graph by proposing a dynamic edge update strategy, enhancing model learning with the nonbinding TCR–epitope pairs. Additionally, to overcome data imbalance, we adapt the Deep AUC Maximization strategy to the graph domain. Extensive experiments are conducted on four public datasets to demonstrate the superiority of exploring underlying topological structures in predicting TCR–epitope interactions, illustrating the benefits of delving into complex molecular networks. The implementation code and data are available at https://github.com/uta-smile/GTE.
-
Machine learning with missing data has been approached in two different ways, including feature imputation where missing feature values are estimated based on observed values and label prediction where downstream labels are learned directly from incomplete data. However, existing imputation models tend to have strong prior assumptions and cannot learn from downstream tasks, while models targeting label prediction often involve heuristics and can encounter scalability issues. Here we propose GRAPE, a graph-based framework for feature imputation as well as label prediction. GRAPE tackles the missing data problem using a graph representation, where the observations and features are viewed as two types of nodes in a bipartite graph, and the observed feature values as edges. Under the GRAPE framework, the feature imputation is formulated as an edge-level prediction task and the label prediction as a node-level prediction task. These tasks are then solved with Graph Neural Networks. Experimental results on nine benchmark datasets show that GRAPE yields 20% lower mean absolute error for imputation tasks and 10% lower for label prediction tasks, compared with existing state-of-the-art methods.more » « less
