1,785 research outputs found
Multi-Target Prediction: A Unifying View on Problems and Methods
Multi-target prediction (MTP) is concerned with the simultaneous prediction
of multiple target variables of diverse type. Due to its enormous application
potential, it has developed into an active and rapidly expanding research field
that combines several subfields of machine learning, including multivariate
regression, multi-label classification, multi-task learning, dyadic prediction,
zero-shot learning, network inference, and matrix completion. In this paper, we
present a unifying view on MTP problems and methods. First, we formally discuss
commonalities and differences between existing MTP problems. To this end, we
introduce a general framework that covers the above subfields as special cases.
As a second contribution, we provide a structured overview of MTP methods. This
is accomplished by identifying a number of key properties, which distinguish
such methods and determine their suitability for different types of problems.
Finally, we also discuss a few challenges for future research
A Comparative Study of Pairwise Learning Methods based on Kernel Ridge Regression
Many machine learning problems can be formulated as predicting labels for a
pair of objects. Problems of that kind are often referred to as pairwise
learning, dyadic prediction or network inference problems. During the last
decade kernel methods have played a dominant role in pairwise learning. They
still obtain a state-of-the-art predictive performance, but a theoretical
analysis of their behavior has been underexplored in the machine learning
literature.
In this work we review and unify existing kernel-based algorithms that are
commonly used in different pairwise learning settings, ranging from matrix
filtering to zero-shot learning. To this end, we focus on closed-form efficient
instantiations of Kronecker kernel ridge regression. We show that independent
task kernel ridge regression, two-step kernel ridge regression and a linear
matrix filter arise naturally as a special case of Kronecker kernel ridge
regression, implying that all these methods implicitly minimize a squared loss.
In addition, we analyze universality, consistency and spectral filtering
properties. Our theoretical results provide valuable insights in assessing the
advantages and limitations of existing pairwise learning methods.Comment: arXiv admin note: text overlap with arXiv:1606.0427
VB-MK-LMF: Fusion of drugs, targets and interactions using Variational Bayesian Multiple Kernel Logistic Matrix Factorization
Background
Computational fusion approaches to drug-target interaction (DTI) prediction, capable of utilizing multiple sources of background knowledge, were reported to achieve superior predictive performance in multiple studies. Other studies showed that specificities of the DTI task, such as weighting the observations and focusing the side information are also vital for reaching top performance.
Method
We present Variational Bayesian Multiple Kernel Logistic Matrix Factorization (VB-MK-LMF), which unifies the advantages of (1) multiple kernel learning, (2) weighted observations, (3) graph Laplacian regularization, and (4) explicit modeling of probabilities of binary drug-target interactions.
Results
VB-MK-LMF achieves significantly better predictive performance in standard benchmarks compared to state-of-the-art methods, which can be traced back to multiple factors. The systematic evaluation of the effect of multiple kernels confirm their benefits, but also highlights the limitations of linear kernel combinations, already recognized in other fields. The analysis of the effect of prior kernels using varying sample sizes sheds light on the balance of data and knowledge in DTI tasks and on the rate at which the effect of priors vanishes. This also shows the existence of ``small sample size'' regions where using side information offers significant gains. Alongside favorable predictive performance, a notable property of MF methods is that they provide a unified space for drugs and targets using latent representations. Compared to earlier studies, the dimensionality of this space proved to be surprisingly low, which makes the latent representations constructed by VB-ML-LMF especially well-suited for visual analytics. The probabilistic nature of the predictions allows the calculation of the expected values of hits in functionally relevant sets, which we demonstrate by predicting drug promiscuity. The variational Bayesian approximation is also implemented for general purpose graphics processing units yielding significantly improved computational time.
Conclusion
In standard benchmarks, VB-MK-LMF shows significantly improved predictive performance in a wide range of settings. Beyond these benchmarks, another contribution of our work is highlighting and providing estimates for further pharmaceutically relevant quantities, such as promiscuity, druggability and total number of interactions.
Availability
Data and code are available at http://bioinformatics.mit.bme.hu
A two-step learning approach for solving full and almost full cold start problems in dyadic prediction
Dyadic prediction methods operate on pairs of objects (dyads), aiming to
infer labels for out-of-sample dyads. We consider the full and almost full cold
start problem in dyadic prediction, a setting that occurs when both objects in
an out-of-sample dyad have not been observed during training, or if one of them
has been observed, but very few times. A popular approach for addressing this
problem is to train a model that makes predictions based on a pairwise feature
representation of the dyads, or, in case of kernel methods, based on a tensor
product pairwise kernel. As an alternative to such a kernel approach, we
introduce a novel two-step learning algorithm that borrows ideas from the
fields of pairwise learning and spectral filtering. We show theoretically that
the two-step method is very closely related to the tensor product kernel
approach, and experimentally that it yields a slightly better predictive
performance. Moreover, unlike existing tensor product kernel methods, the
two-step method allows closed-form solutions for training and parameter
selection via cross-validation estimates both in the full and almost full cold
start settings, making the approach much more efficient and straightforward to
implement
Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models
Many complex multi-target prediction problems that concern large target
spaces are characterised by a need for efficient prediction strategies that
avoid the computation of predictions for all targets explicitly. Examples of
such problems emerge in several subfields of machine learning, such as
collaborative filtering, multi-label classification, dyadic prediction and
biological network inference. In this article we analyse efficient and exact
algorithms for computing the top- predictions in the above problem settings,
using a general class of models that we refer to as separable linear relational
models. We show how to use those inference algorithms, which are modifications
of well-known information retrieval methods, in a variety of machine learning
settings. Furthermore, we study the possibility of scoring items incompletely,
while still retaining an exact top-K retrieval. Experimental results in several
application domains reveal that the so-called threshold algorithm is very
scalable, performing often many orders of magnitude more efficiently than the
naive approach
- …