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Current machine learning has made great progress on computer vision and many other fields attributed to the large amount of high-quality training samples, while it does not work very well on genomic data analysis, since they are notoriously known as small data. In our work, we focus on few-shot disease subtype prediction problem, identifying subgroups of similar patients that can guide treatment decisions for a specific individual through training on small data. In fact, doctors and clinicians always address this problem by studying several interrelated clinical variables simultaneously. We attempt to simulate such clinical perspective, and introduce meta learning techniques to develop a new model, which can extract the common experience or knowledge from interrelated clinical tasks and transfer it to help address new tasks. Our new model is built upon a carefully designed meta-learner, called Prototypical Network, that is a simple yet effective meta learning machine for few-shot image classification. Observing that gene expression data have specifically high dimensionality and high noise properties compared with image data, we proposed a new extension of it by appending two modules to address these issues. Concretely, we append a feature selection layer to automatically filter out the disease-irrelated genes and incorporate a sample reweighting strategy to adaptively remove noisy data, and meanwhile the extended model is capable of learning from a limited number of training examples and generalize well. Simulations and real gene expression data experiments substantiate the superiority of the proposed method for predicting the subtypes of disease and identifying potential disease-related genes.
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The recent success of graph neural networks has significantly boosted molecular property prediction, advancing activities such as drug discovery. The existing deep neural network methods usually require large training dataset for each property, impairing their performances in cases (especially for new molecular properties) with a limited amount of experimental data, which are common in real situations. To this end, we propose Meta-MGNN, a novel model for few-shot molecular property prediction. Meta-MGNN applies molecular graph neural network to learn molecular representation and builds a meta-learning framework for model optimization. To exploit unlabeled molecular information and address task heterogeneity of different molecular properties, Meta-MGNN further incorporates molecular structure, attribute based self-supervised modules and self-attentive task weights into the former framework, strengthening the whole learning model. Extensive experiments on two public multi-property datasets demonstrate that Meta-MGNN outperforms a variety of state-of-the-art methods.
In this paper we present the first baseline results for the task of few-shot learning of discrete embedding vectors for image recognition. Few-shot learning is a highly researched task, commonly leveraged by recognition systems that are resource constrained to train on a small number of images per class. Few-shot systems typically store a continuous embedding vector of each class, posing a risk to privacy where system breaches or insider threats are a concern. Using discrete embedding vectors, we devise a simple cryptographic protocol, which uses one-way hash functions in order to build recognition systems that do not store their users embedding vectors directly, thus providing the guarantee of computational pan privacy in a practical and wide-spread setting.
Domain similarity measures can be used to gauge adaptability and select suitable data for transfer learning, but existing approaches define ad hoc measures that are deemed suitable for respective tasks. Inspired by work on curriculum learning, we propose to emph{learn} data selection measures using Bayesian Optimization and evaluate them across models, domains and tasks. Our learned measures outperform existing domain similarity measures significantly on three tasks: sentiment analysis, part-of-speech tagging, and parsing. We show the importance of complementing similarity with diversity, and that learned measures are -- to some degree -- transferable across models, domains, and even tasks.
Zero-shot and few-shot learning aim to improve generalization to unseen concepts, which are promising in many realistic scenarios. Due to the lack of data in unseen domain, relation modeling between seen and unseen domains is vital for knowledge transfer in these tasks. Most existing methods capture seen-unseen relation implicitly via semantic embedding or feature generation, resulting in inadequate use of relation and some issues remain (e.g. domain shift). To tackle these challenges, we propose a Transferable Graph Generation (TGG) approach, in which the relation is modeled and utilized explicitly via graph generation. Specifically, our proposed TGG contains two main components: (1) Graph generation for relation modeling. An attention-based aggregate network and a relation kernel are proposed, which generate instance-level graph based on a class-level prototype graph and visual features. Proximity information aggregating is guided by a multi-head graph attention mechanism, where seen and unseen features synthesized by GAN are revised as node embeddings. The relation kernel further generates edges with GCN and graph kernel method, to capture instance-level topological structure while tackling data imbalance and noise. (2) Relation propagation for relation utilization. A dual relation propagation approach is proposed, where relations captured by the generated graph are separately propagated from the seen and unseen subgraphs. The two propagations learn from each other in a dual learning fashion, which performs as an adaptation way for mitigating domain shift. All components are jointly optimized with a meta-learning strategy, and our TGG acts as an end-to-end framework unifying conventional zero-shot, generalized zero-shot and few-shot learning. Extensive experiments demonstrate that it consistently surpasses existing methods of the above three fields by a significant margin.
Cutting plane methods play a significant role in modern solvers for tackling mixed-integer programming (MIP) problems. Proper selection of cuts would remove infeasible solutions in the early stage, thus largely reducing the computational burden without hurting the solution accuracy. However, the major cut selection approaches heavily rely on heuristics, which strongly depend on the specific problem at hand and thus limit their generalization capability. In this paper, we propose a data-driven and generalizable cut selection approach, named Cut Ranking, in the settings of multiple instance learning. To measure the quality of the candidate cuts, a scoring function, which takes the instance-specific cut features as inputs, is trained and applied in cut ranking and selection. In order to evaluate our method, we conduct extensive experiments on both synthetic datasets and real-world datasets. Compared with commonly used heuristics for cut selection, the learning-based policy has shown to be more effective, and is capable of generalizing over multiple problems with different properties. Cut Ranking has been deployed in an industrial solver for large-scale MIPs. In the online A/B testing of the product planning problems with more than $10^7$ variables and constraints daily, Cut Ranking has achieved the average speedup ratio of 12.42% over the production solver without any accuracy loss of solution.
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