7,584 research outputs found
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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A Survey on Metric Learning for Feature Vectors and Structured Data
The need for appropriate ways to measure the distance or similarity between
data is ubiquitous in machine learning, pattern recognition and data mining,
but handcrafting such good metrics for specific problems is generally
difficult. This has led to the emergence of metric learning, which aims at
automatically learning a metric from data and has attracted a lot of interest
in machine learning and related fields for the past ten years. This survey
paper proposes a systematic review of the metric learning literature,
highlighting the pros and cons of each approach. We pay particular attention to
Mahalanobis distance metric learning, a well-studied and successful framework,
but additionally present a wide range of methods that have recently emerged as
powerful alternatives, including nonlinear metric learning, similarity learning
and local metric learning. Recent trends and extensions, such as
semi-supervised metric learning, metric learning for histogram data and the
derivation of generalization guarantees, are also covered. Finally, this survey
addresses metric learning for structured data, in particular edit distance
learning, and attempts to give an overview of the remaining challenges in
metric learning for the years to come.Comment: Technical report, 59 pages. Changes in v2: fixed typos and improved
presentation. Changes in v3: fixed typos. Changes in v4: fixed typos and new
method
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
This work introduces a number of algebraic topology approaches, such as
multicomponent persistent homology, multi-level persistent homology and
electrostatic persistence for the representation, characterization, and
description of small molecules and biomolecular complexes. Multicomponent
persistent homology retains critical chemical and biological information during
the topological simplification of biomolecular geometric complexity.
Multi-level persistent homology enables a tailored topological description of
inter- and/or intra-molecular interactions of interest. Electrostatic
persistence incorporates partial charge information into topological
invariants. These topological methods are paired with Wasserstein distance to
characterize similarities between molecules and are further integrated with a
variety of machine learning algorithms, including k-nearest neighbors, ensemble
of trees, and deep convolutional neural networks, to manifest their descriptive
and predictive powers for chemical and biological problems. Extensive numerical
experiments involving more than 4,000 protein-ligand complexes from the PDBBind
database and near 100,000 ligands and decoys in the DUD database are performed
to test respectively the scoring power and the virtual screening power of the
proposed topological approaches. It is demonstrated that the present approaches
outperform the modern machine learning based methods in protein-ligand binding
affinity predictions and ligand-decoy discrimination
Hyperbolic Interaction Model For Hierarchical Multi-Label Classification
Different from the traditional classification tasks which assume mutual
exclusion of labels, hierarchical multi-label classification (HMLC) aims to
assign multiple labels to every instance with the labels organized under
hierarchical relations. Besides the labels, since linguistic ontologies are
intrinsic hierarchies, the conceptual relations between words can also form
hierarchical structures. Thus it can be a challenge to learn mappings from word
hierarchies to label hierarchies. We propose to model the word and label
hierarchies by embedding them jointly in the hyperbolic space. The main reason
is that the tree-likeness of the hyperbolic space matches the complexity of
symbolic data with hierarchical structures. A new Hyperbolic Interaction Model
(HyperIM) is designed to learn the label-aware document representations and
make predictions for HMLC. Extensive experiments are conducted on three
benchmark datasets. The results have demonstrated that the new model can
realistically capture the complex data structures and further improve the
performance for HMLC comparing with the state-of-the-art methods. To facilitate
future research, our code is publicly available
Pathway-Based Genomics Prediction using Generalized Elastic Net.
We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach
Generative Adversarial Networks (GANs): Challenges, Solutions, and Future Directions
Generative Adversarial Networks (GANs) is a novel class of deep generative
models which has recently gained significant attention. GANs learns complex and
high-dimensional distributions implicitly over images, audio, and data.
However, there exists major challenges in training of GANs, i.e., mode
collapse, non-convergence and instability, due to inappropriate design of
network architecture, use of objective function and selection of optimization
algorithm. Recently, to address these challenges, several solutions for better
design and optimization of GANs have been investigated based on techniques of
re-engineered network architectures, new objective functions and alternative
optimization algorithms. To the best of our knowledge, there is no existing
survey that has particularly focused on broad and systematic developments of
these solutions. In this study, we perform a comprehensive survey of the
advancements in GANs design and optimization solutions proposed to handle GANs
challenges. We first identify key research issues within each design and
optimization technique and then propose a new taxonomy to structure solutions
by key research issues. In accordance with the taxonomy, we provide a detailed
discussion on different GANs variants proposed within each solution and their
relationships. Finally, based on the insights gained, we present the promising
research directions in this rapidly growing field.Comment: 42 pages, Figure 13, Table
Identifying networks with common organizational principles
Many complex systems can be represented as networks, and the problem of
network comparison is becoming increasingly relevant. There are many techniques
for network comparison, from simply comparing network summary statistics to
sophisticated but computationally costly alignment-based approaches. Yet it
remains challenging to accurately cluster networks that are of a different size
and density, but hypothesized to be structurally similar. In this paper, we
address this problem by introducing a new network comparison methodology that
is aimed at identifying common organizational principles in networks. The
methodology is simple, intuitive and applicable in a wide variety of settings
ranging from the functional classification of proteins to tracking the
evolution of a world trade network.Comment: 26 pages, 7 figure
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