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Register a new userLearning Genomic Representations to Predict Clinical Outcomes in Cancer
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Added by
Safoora Yousefi
Publication date
2016
fields
Informatics Engineering
and research's language is
English
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Genomics are rapidly transforming medical practice and basic biomedical research, providing insights into disease mechanisms and improving therapeutic strategies, particularly in cancer. The ability to predict the future course of a patients disease from high-dimensional genomic profiling will be essential in realizing the promise of genomic medicine, but presents significant challenges for state-of-the-art survival analysis methods. In this abstract we present an investigation in learning genomic representations with neural networks to predict patient survival in cancer. We demonstrate the advantages of this approach over existing survival analysis methods using brain tumor data.
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Much of model-based reinforcement learning involves learning a model of an agents world, and training an agent to leverage this model to perform a task more efficiently. While these models are demonstrably useful for agents, every naturally occurring model of the world of which we are aware---e.g., a brain---arose as the byproduct of competing evolutionary pressures for survival, not minimization of a supervised forward-predictive loss via gradient descent. That useful models can arise out of the messy and slow optimization process of evolution suggests that forward-predictive modeling can arise as a side-effect of optimization under the right circumstances. Crucially, this optimization process need not explicitly be a forward-predictive loss. In this work, we introduce a modification to traditional reinforcement learning which we call observational dropout, whereby we limit the agents ability to observe the real environment at each timestep. In doing so, we can coerce an agent into learning a world model to fill in the observation gaps during reinforcement learning. We show that the emerged world model, while not explicitly trained to predict the future, can help the agent learn key skills required to perform well in its environment. Videos of our results available at https://learningtopredict.github.io/
Many research fields codify their findings in standard formats, often by reporting correlations between quantities of interest. But the space of all testable correlates is far larger than scientific resources can currently address, so the ability to accurately predict correlations would be useful to plan research and allocate resources. Using a dataset of approximately 170,000 correlational findings extracted from leading social science journals, we show that a trained neural network can accurately predict the reported correlations using only the text descriptions of the correlates. Accurate predictive models such as these can guide scientists towards promising untested correlates, better quantify the information gained from new findings, and has implications for moving artificial intelligence systems from predicting structures to predicting relationships in the real world.
Clinical prediction models (CPMs) are used to predict clinically relevant outcomes or events. Typically, prognostic CPMs are derived to predict the risk of a single future outcome. However, with rising emphasis on the prediction of multi-morbidity, there is growing need for CPMs to simultaneously predict risks for each of multiple future outcomes. A common approach to multi-outcome risk prediction is to derive a CPM for each outcome separately, then multiply the predicted risks. This approach is only valid if the outcomes are conditionally independent given the covariates, and it fails to exploit the potential relationships between the outcomes. This paper outlines several approaches that could be used to develop prognostic CPMs for multiple outcomes. We consider four methods, ranging in complexity and assumed conditional independence assumptions: namely, probabilistic classifier chain, multinomial logistic regression, multivariate logistic regression, and a Bayesian probit model. These are compared with methods that rely on conditional independence: separate univariate CPMs and stacked regression. Employing a simulation study and real-world example via the MIMIC-III database, we illustrate that CPMs for joint risk prediction of multiple outcomes should only be derived using methods that model the residual correlation between outcomes. In such a situation, our results suggest that probabilistic classification chains, multinomial logistic regression or the Bayesian probit model are all appropriate choices. We call into question the development of CPMs for each outcome in isolation when multiple correlated or structurally related outcomes are of interest and recommend more holistic risk prediction.
In this paper, we propose SwarmNet -- a neural network architecture that can learn to predict and imitate the behavior of an observed swarm of agents in a centralized manner. Tested on artificially generated swarm motion data, the network achieves high levels of prediction accuracy and imitation authenticity. We compare our model to previous approaches for modelling interaction systems and show how modifying components of other models gradually approaches the performance of ours. Finally, we also discuss an extension of SwarmNet that can deal with nondeterministic, noisy, and uncertain environments, as often found in robotics applications.
Among the most impressive recent applications of neural decoding is the visual representation decoding, where the category of an object that a subject either sees or imagines is inferred by observing his/her brain activity. Even though there is an increasing interest in the aforementioned visual representation decoding task, there is no extensive study of the effect of using different machine learning models on the decoding accuracy. In this paper we provide an extensive evaluation of several machine learning models, along with different similarity metrics, for the aforementioned task, drawing many interesting conclusions. That way, this paper a) paves the way for developing more advanced and accurate methods and b) provides an extensive and easily reproducible baseline for the aforementioned decoding task.
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