25 research outputs found
Conditional Ranking on Relational Data
In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. Conditional ranking from symmetric or reciprocal relations can in this framework be treated as two important special cases. Furthermore, we propose an efficient algorithm for conditional ranking by optimizing a squared ranking loss function. Experiments on synthetic and real-world data illustrate that such an approach delivers state-of-the-art performance in terms of predictive power and computational complexity. Moreover, we also show empirically that incorporating domain knowledge in the model about the underlying relations can improve the generalization performance
Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data
In domains like bioinformatics, information retrieval and social network
analysis, one can find learning tasks where the goal consists of inferring a
ranking of objects, conditioned on a particular target object. We present a
general kernel framework for learning conditional rankings from various types
of relational data, where rankings can be conditioned on unseen data objects.
We propose efficient algorithms for conditional ranking by optimizing squared
regression and ranking loss functions. We show theoretically, that learning
with the ranking loss is likely to generalize better than with the regression
loss. Further, we prove that symmetry or reciprocity properties of relations
can be efficiently enforced in the learned models. Experiments on synthetic and
real-world data illustrate that the proposed methods deliver state-of-the-art
performance in terms of predictive power and computational efficiency.
Moreover, we also show empirically that incorporating symmetry or reciprocity
properties can improve the generalization performance
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
Identification of functionally related enzymes by learning-to-rank methods
Enzyme sequences and structures are routinely used in the biological sciences
as queries to search for functionally related enzymes in online databases. To
this end, one usually departs from some notion of similarity, comparing two
enzymes by looking for correspondences in their sequences, structures or
surfaces. For a given query, the search operation results in a ranking of the
enzymes in the database, from very similar to dissimilar enzymes, while
information about the biological function of annotated database enzymes is
ignored.
In this work we show that rankings of that kind can be substantially improved
by applying kernel-based learning algorithms. This approach enables the
detection of statistical dependencies between similarities of the active cleft
and the biological function of annotated enzymes. This is in contrast to
search-based approaches, which do not take annotated training data into
account. Similarity measures based on the active cleft are known to outperform
sequence-based or structure-based measures under certain conditions. We
consider the Enzyme Commission (EC) classification hierarchy for obtaining
annotated enzymes during the training phase. The results of a set of sizeable
experiments indicate a consistent and significant improvement for a set of
similarity measures that exploit information about small cavities in the
surface of enzymes
A kernel-based framework for learning graded relations from data
Driven by a large number of potential applications in areas like
bioinformatics, information retrieval and social network analysis, the problem
setting of inferring relations between pairs of data objects has recently been
investigated quite intensively in the machine learning community. To this end,
current approaches typically consider datasets containing crisp relations, so
that standard classification methods can be adopted. However, relations between
objects like similarities and preferences are often expressed in a graded
manner in real-world applications. A general kernel-based framework for
learning relations from data is introduced here. It extends existing approaches
because both crisp and graded relations are considered, and it unifies existing
approaches because different types of graded relations can be modeled,
including symmetric and reciprocal relations. This framework establishes
important links between recent developments in fuzzy set theory and machine
learning. Its usefulness is demonstrated through various experiments on
synthetic and real-world data.Comment: This work has been submitted to the IEEE for possible publication.
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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
Learning valued relations from data
Driven by a large number of potential applications in areas like bioinformatics, information retrieval and social network analysis, the problem setting of inferring relations between pairs of data objects has recently been investigated quite intensively in the machine learning community. To this end, current approaches typically consider datasets containing crisp relations, so that standard classification methods can be adopted. However, relations between objects like similarities and preferences are in many real-world applications often expressed in a graded manner. A general kernel-based framework for learning relations from data is introduced here. It extends existing approaches because both crisp and valued relations are considered, and it unifies existing approaches because different types of valued relations can be modeled, including symmetric and reciprocal relations. This framework establishes in this way important links between recent developments in fuzzy set theory and machine learning. Its usefulness is demonstrated on a case study in document retrieval
Changes in connectivity patterns in the kainate model of epilepsy
Epilepsy is a neurological disorder characterized by seizures, i.e. excessive and hyper synchronous activity of neurons in the brain. ElectroEncephaloGram (EEG) is the recording of brain activity in time through electrodes placed on the scalp and is one of the most used techniques to monitor brain activity. In order to identify pattern of propagation across brain areas that are specific to epilepsy, connectivity measures such as the Directed Transfer Function (DTF) and the Partial Directed Coherence (PDC) have been developed. These measures reveal connections between different areas by exploiting statistical dependencies within multichannel EEG recordings. This work proposes a framework to identify and compare interdependencies between EEG signals in different brain states. We considered an animal model of epilepsy characterized by spontaneous recurrent seizures. In three rats we identified a normal healthy baseline state and an epileptic state for which we estimated interdependencies between EEG channels using DTF and PDC and extracted significant differences between both states. We showed the feasibility of detection of connectivity patterns in a simple animal model of epilepsy. We found common patterns of propagation in the brain of the three rats during the baseline state. After the kainic acid injection, the connectivity pattern of interictal period is significantly altered compared to the baseline situation. Inter-rat variations are observed, but the intra-rat pattern alterations are consistent in time, revealing that the kainic acid permanently changes the brain connectivity
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