Goto

Collaborating Authors

 drug activity prediction



Meta-learning with an Adaptive Task Scheduler

Neural Information Processing Systems

To benefit the learning of a new task, meta-learning has been proposed to transfer a well-generalized meta-model learned from various meta-training tasks. Existing meta-learning algorithms randomly sample meta-training tasks with a uniform probability, under the assumption that tasks are of equal importance. However, it is likely that tasks are detrimental with noise or imbalanced given a limited number of meta-training tasks. To prevent the meta-model from being corrupted by such detrimental tasks or dominated by tasks in the majority, in this paper, we propose an adaptive task scheduler (ATS) for the meta-training process. In ATS, for the first time, we design a neural scheduler to decide which meta-training tasks to use next by predicting the probability being sampled for each candidate task, and train the scheduler to optimize the generalization capacity of the metamodel to unseen tasks. We identify two meta-model-related factors as the input of the neural scheduler, which characterize the difficulty of a candidate task to the meta-model. Theoretically, we show that a scheduler taking the two factors into account improves the meta-training loss and also the optimization landscape. Under the setting of meta-learning with noise and limited budgets, ATS improves the performance on both miniImageNet and a real-world drug discovery benchmark by up to 13%and 18%, respectively, compared to state-of-the-art task schedulers.





A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction

Neural Information Processing Systems

In drug activity prediction (as in handwritten character recogni(cid:173) tion), the features extracted to describe a training example depend on the pose (location, orientation, etc.) of the example. In hand(cid:173) written character recognition, one of the best techniques for ad(cid:173) dressing this problem is the tangent distance method of Simard, LeCun and Denker (1993). Jain, et al. (1993a; 1993b) introduce a new technique-dynamic reposing-that also addresses this prob(cid:173) lem. Dynamic reposing iteratively learns a neural network and then reposes the examples in an effort to maximize the predicted out(cid:173) put values. New models are trained and new poses computed until models and poses converge.


Don't Overlook the Support Set: Towards Improving Generalization in Meta-learning

arXiv.org Machine Learning

Meta-learning has proven to be a powerful paradigm for transferring the knowledge from previously tasks to facilitate the learning of a novel task. Current dominant algorithms train a well-generalized model initialization which is adapted to each task via the support set. The crux, obviously, lies in optimizing the generalization capability of the initialization, which is measured by the performance of the adapted model on the query set of each task. Unfortunately, this generalization measure, evidenced by empirical results, pushes the initialization to overfit the query but fail the support set, which significantly impairs the generalization and adaptation to novel tasks. To address this issue, we include the support set when evaluating the generalization to produce a new meta-training strategy, MetaMix, that linearly combines the input and hidden representations of samples from both the support and query sets. Theoretical studies on classification and regression tasks show how MetaMix can improve the generalization of meta-learning. More remarkably, MetaMix obtains state-of-the-art results by a large margin across many datasets and remains compatible with existing meta-learning algorithms.


A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction

Neural Information Processing Systems

The task of drug activity prediction is to predict the activity of proposed drug compounds by learning from the observed activity of previously-synthesized drug compounds. Accurate drug activity prediction can save substantial time and money by focusing the efforts of chemists and biologists on the synthesis and testing of compounds whose predicted activity is high. If the requirements for highly active binding can be displayed in three dimensions, chemists can work from such displays to design new compounds having high predicted activity. Drug molecules usually act by binding to localized sites on large receptor molecules or large enyzme molecules. One reasonable way to represent drug molecules is to capture the location of their surface in the (fixed) frame of reference of the (hypothesized) binding site.


A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction

Neural Information Processing Systems

The task of drug activity prediction is to predict the activity of proposed drug compounds by learning from the observed activity of previously-synthesized drug compounds. Accurate drug activity prediction can save substantial time and money by focusing the efforts of chemists and biologists on the synthesis and testing of compounds whose predicted activity is high. If the requirements for highly active binding can be displayed in three dimensions, chemists can work from such displays to design new compounds having high predicted activity. Drug molecules usually act by binding to localized sites on large receptor molecules or large enyzme molecules. One reasonable way to represent drug molecules is to capture the location of their surface in the (fixed) frame of reference of the (hypothesized) binding site.


A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction

Neural Information Processing Systems

Thomas G. Dietterich Arris Pharmaceutical Corporation and Oregon State University Corvallis, OR 97331-3202 Ajay N. Jain Arris Pharmaceutical Corporation 385 Oyster Point Blvd., Suite 3 South San Francisco, CA 94080 Richard H. Lathrop and Tomas Lozano-Perez Arris Pharmaceutical Corporation and MIT Artificial Intelligence Laboratory 545 Technology Square Cambridge, MA 02139 Abstract In drug activity prediction (as in handwritten character recognition), thefeatures extracted to describe a training example depend on the pose (location, orientation, etc.) of the example. In handwritten characterrecognition, one of the best techniques for addressing thisproblem is the tangent distance method of Simard, LeCun and Denker (1993). Jain, et al. (1993a; 1993b) introduce a new technique-dynamic reposing-that also addresses this problem. Dynamicreposing iteratively learns a neural network and then reposes the examples in an effort to maximize the predicted output values.New models are trained and new poses computed until models and poses converge. This paper compares dynamic reposing to the tangent distance method on the task of predicting the biological activityof musk compounds.