scholarly journals Learning Eligibility in Cancer Clinical Trials Using Deep Neural Networks

2018 ◽  
Vol 8 (7) ◽  
pp. 1206 ◽  
Author(s):  
Aurelia Bustos ◽  
Antonio Pertusa
Keyword(s):  
Neural Networks ◽  
Clinical Trials ◽  
Deep Neural Networks ◽  
Medical Knowledge ◽  
Clinical Information ◽  
Representation Learning ◽  
Free Text ◽  
Cancer Clinical Trials ◽  
Word Embeddings ◽  
New Treatments

Interventional cancer clinical trials are generally too restrictive, and some patients are often excluded on the basis of comorbidity, past or concomitant treatments, or the fact that they are over a certain age. The efficacy and safety of new treatments for patients with these characteristics are, therefore, not defined. In this work, we built a model to automatically predict whether short clinical statements were considered inclusion or exclusion criteria. We used protocols from cancer clinical trials that were available in public registries from the last 18 years to train word-embeddings, and we constructed a dataset of 6M short free-texts labeled as eligible or not eligible. A text classifier was trained using deep neural networks, with pre-trained word-embeddings as inputs, to predict whether or not short free-text statements describing clinical information were considered eligible. We additionally analyzed the semantic reasoning of the word-embedding representations obtained and were able to identify equivalent treatments for a type of tumor analogous with the drugs used to treat other tumors. We show that representation learning using deep neural networks can be successfully leveraged to extract the medical knowledge from clinical trial protocols for potentially assisting practitioners when prescribing treatments.

scholarly journals Every Local Minimum Value Is the Global Minimum Value of Induced Model in Nonconvex Machine Learning

2019 ◽  
Vol 31 (12) ◽  
pp. 2293-2323 ◽  
Author(s):  
Kenji Kawaguchi ◽  
Jiaoyang Huang ◽  
Leslie Pack Kaelbling
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Local Minimum ◽  
Deep Neural Networks ◽  
Representation Learning ◽  
Minimum Value ◽  
Special Cases ◽  
Optimal Value ◽  
Special Case ◽  
Theoretical Results

For nonconvex optimization in machine learning, this article proves that every local minimum achieves the globally optimal value of the perturbable gradient basis model at any differentiable point. As a result, nonconvex machine learning is theoretically as supported as convex machine learning with a handcrafted basis in terms of the loss at differentiable local minima, except in the case when a preference is given to the handcrafted basis over the perturbable gradient basis. The proofs of these results are derived under mild assumptions. Accordingly, the proven results are directly applicable to many machine learning models, including practical deep neural networks, without any modification of practical methods. Furthermore, as special cases of our general results, this article improves or complements several state-of-the-art theoretical results on deep neural networks, deep residual networks, and overparameterized deep neural networks with a unified proof technique and novel geometric insights. A special case of our results also contributes to the theoretical foundation of representation learning.

scholarly journals Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations

2021 ◽  
Author(s):  
Yingheng Wang ◽  
Yaosen Min ◽  
Erzhuo Shao ◽  
Ji Wu
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Structural Information ◽  
Molecular Graph ◽  
Representation Learning ◽  
Graph Representation ◽  
Input Graph ◽  
Recent Success ◽  
Real World Datasets ◽  
Comparative Results

ABSTRACTLearning generalizable, transferable, and robust representations for molecule data has always been a challenge. The recent success of contrastive learning (CL) for self-supervised graph representation learning provides a novel perspective to learn molecule representations. The most prevailing graph CL framework is to maximize the agreement of representations in different augmented graph views. However, existing graph CL frameworks usually adopt stochastic augmentations or schemes according to pre-defined rules on the input graph to obtain different graph views in various scales (e.g. node, edge, and subgraph), which may destroy topological semantemes and domain prior in molecule data, leading to suboptimal performance. Therefore, designing parameterized, learnable, and explainable augmentation is quite necessary for molecular graph contrastive learning. A well-designed parameterized augmentation scheme can preserve chemically meaningful structural information and intrinsically essential attributes for molecule graphs, which helps to learn representations that are insensitive to perturbation on unimportant atoms and bonds. In this paper, we propose a novel Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations, MolCLE for brevity, that self-adaptively incorporates chemically significative information from both topological and semantic aspects of molecular graphs. Specifically, we apply deep neural networks to parameterize the augmentation process for both the molecular graph topology and atom attributes, to highlight contributive molecular substructures and recognize underlying chemical semantemes. Comprehensive experiments on a variety of real-world datasets demonstrate that our proposed method consistently outperforms compared baselines, which verifies the effectiveness of the proposed framework. Detailedly, our self-supervised MolCLE model surpasses many supervised counterparts, and meanwhile only uses hundreds of thousands of parameters to achieve comparative results against the state-of-the-art baseline, which has tens of millions of parameters. We also provide detailed case studies to validate the explainability of augmented graph views.CCS CONCEPTS• Mathematics of computing → Graph algorithms; • Applied computing → Bioinformatics; • Computing methodologies → Neural networks; Unsupervised learning.

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