Incremental Kernel Mapping Algorithms for Scalable Recommender Systems

Recommender systems apply machine learning techniques for filtering unseen information and can predict whether a user would like a given item. Kernel Mapping Recommender (KMR)system algorithms have been proposed, which offer state-of-the-art performance. One potential drawback of the KMR algorithms is that the training is done in one step and hence they cannot accommodate the incremental update with the arrival of new data making them unsuitable for the dynamic environments. From this line of research, we propose a new heuristic, which can build the model incrementally without retraining the whole model from scratch when new data (item or user) are added to the recommender system dataset. Furthermore, we proposed a novel perceptron type algorithm, which is a fast incremental algorithm for building the model that maintains a good level of accuracy and scales well with the data. We show empirically over two datasets that the proposed algorithms give quite accurate results while providing significant computation savings

Ranking algorithms for implicit feedback

This report presents novel algorithms to use eye movements as an implicit relevance feedback in order to improve the performance of the searches. The algorithms are evaluated on "Transport Rank Five" Dataset which were previously collected in Task 8.3. We demonstrated that simple linear combination or tensor product of eye movement and image features can improve the retrieval accuracy

Modeling drug combination effects via latent tensor reconstruction

Motivation: Combination therapies have emerged as a powerful treatment modality to overcome drug resistance and improve treatment efficacy. However, the number of possible drug combinations increases very rapidly with the number of individual drugs in consideration, which makes the comprehensive experimental screening infeasible in practice. Machine-learning models offer time- and cost-efficient means to aid this process by prioritizing the most effective drug combinations for further pre-clinical and clinical validation. However, the complexity of the underlying interaction patterns across multiple drug doses and in different cellular contexts poses challenges to the predictive modeling of drug combination effects. Results: We introduce comboLTR, highly time-efficient method for learning complex, non-linear target functions for describing the responses of therapeutic agent combinations in various doses and cancer cell-contexts. The method is based on a polynomial regression via powerful latent tensor reconstruction. It uses a combination of recommender system-style features indexing the data tensor of response values in different contexts, and chemical and multi-omics features as inputs. We demonstrate that comboLTR outperforms state-of-the-art methods in terms of predictive performance and running time, and produces highly accurate results even in the challenging and practical inference scenario where full dose-response matrices are predicted for completely new drug combinations with no available combination and monotherapy response measurements in any training cell line.Peer reviewe

Initial state prediction in planning

While recent advances in offline reasoning techniques and online execution strategies have made planning under uncertainty more robust, the application of plans in partially-known environments is still a difficult and important topic. In this paper we present an approach for predicting new information about a partially-known initial state, represented as a multi- graph utilizing Maximum-Margin Multi-Valued Regression. We evaluate this approach in four different domains, demonstrating high recall and accuracy

Modeling drug combination effects via latent tensor reconstruction

AB Combination therapies have emerged as a powerful treatment modality to overcome drug resistance and improve treatment efficacy. However, the number of possible drug combinations increases very rapidly with the number of individual drugs in consideration, which makes the comprehensive experimental screening infeasible in practice. Machine-learning models offer time- and cost-efficient means to aid this process by prioritizing the most effective drug combinations for further pre-clinical and clinical validation. However, the complexity of the underlying interaction patterns across multiple drug doses and in different cellular contexts poses challenges to the predictive modeling of drug combination effects.We introduce comboLTR, highly time-efficient method for learning complex, non-linear target functions for describing the responses of therapeutic agent combinations in various doses and cancer cell-contexts. The method is based on a polynomial regression via powerful latent tensor reconstruction. It uses a combination of recommender system-style features indexing the data tensor of response values in different contexts, and chemical and multi-omics features as inputs. We demonstrate that comboLTR outperforms state-of-the-art methods in terms of predictive performance and running time, and produces highly accurate results even in the challenging and practical inference scenario where full dose–response matrices are predicted for completely new drug combinations with no available combination and monotherapy response measurements in any training cell line</p

Learning with multiple pairwise kernels for drug bioactivity prediction

Motivation: Many inference problems in bioinformatics, including drug bioactivity prediction, can be formulated as pairwise learning problems, in which one is interested in making predictions for pairs of objects, e.g. drugs and their targets. Kernel-based approaches have emerged as powerful tools for solving problems of that kind, and especially multiple kernel learning (MKL) offers promising benefits as it enables integrating various types of complex biomedical information sources in the form of kernels, along with learning their importance for the prediction task. However, the immense size of pairwise kernel spaces remains a major bottleneck, making the existing MKL algorithms computationally infeasible even for small number of input pairs. Results: We introduce pairwiseMKL, the first method for time- and memory-efficient learning with multiple pairwise kernels. pairwiseMKL first determines the mixture weights of the input pairwise kernels, and then learns the pairwise prediction function. Both steps are performed efficiently without explicit computation of the massive pairwise matrices, therefore making the method applicable to solving large pairwise learning problems. We demonstrate the performance of pairwiseMKL in two related tasks of quantitative drug bioactivity prediction using up to 167 995 bioactivity measurements and 3120 pairwise kernels: (i) prediction of anticancer efficacy of drug compounds across a large panel of cancer cell lines; and (ii) prediction of target profiles of anticancer compounds across their kinome-wide target spaces. We show that pairwiseMKL provides accurate predictions using sparse solutions in terms of selected kernels, and therefore it automatically identifies also data sources relevant for the prediction problem.Peer reviewe

Multiclass Learning at One-class Complexity

We show in this paper the multiclass classification problem can be implemented in the maximum margin framework with the complexity of one binary Support Vector Machine. We show reducing the complexity does not involve diminishing performance but in some cases this approach can improve the classification accuracy. The multiclass classification is realized in the framework where the output labels are vector valued

Canonical correlation analysis; An overview with application to learning methods

We present a general method using kernel Canonical Correlation Analysis to learn a semantic representation to web images and their associated text. The semantic space provides a common representation and enables a comparison between the text and images. In the experiments we look at two approaches of retrieving images based only on their content from a text query. We compare the approaches against a standard cross-representation retrieval technique known as the Generalised Vector Space Model