1,322 research outputs found
TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions
Although deep learning approaches have had tremendous success in image, video
and audio processing, computer vision, and speech recognition, their
applications to three-dimensional (3D) biomolecular structural data sets have
been hindered by the entangled geometric complexity and biological complexity.
We introduce topology, i.e., element specific persistent homology (ESPH), to
untangle geometric complexity and biological complexity. ESPH represents 3D
complex geometry by one-dimensional (1D) topological invariants and retains
crucial biological information via a multichannel image representation. It is
able to reveal hidden structure-function relationships in biomolecules. We
further integrate ESPH and convolutional neural networks to construct a
multichannel topological neural network (TopologyNet) for the predictions of
protein-ligand binding affinities and protein stability changes upon mutation.
To overcome the limitations to deep learning arising from small and noisy
training sets, we present a multitask topological convolutional neural network
(MT-TCNN). We demonstrate that the present TopologyNet architectures outperform
other state-of-the-art methods in the predictions of protein-ligand binding
affinities, globular protein mutation impacts, and membrane protein mutation
impacts.Comment: 20 pages, 8 figures, 5 table
Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions
Graph representation learning (GRL) has emerged as a pivotal field that has
contributed significantly to breakthroughs in various fields, including
biomedicine. The objective of this survey is to review the latest advancements
in GRL methods and their applications in the biomedical field. We also
highlight key challenges currently faced by GRL and outline potential
directions for future research.Comment: Accepted by 2023 IMIA Yearbook of Medical Informatic
Building Machines That Learn and Think Like People
Recent progress in artificial intelligence (AI) has renewed interest in
building systems that learn and think like people. Many advances have come from
using deep neural networks trained end-to-end in tasks such as object
recognition, video games, and board games, achieving performance that equals or
even beats humans in some respects. Despite their biological inspiration and
performance achievements, these systems differ from human intelligence in
crucial ways. We review progress in cognitive science suggesting that truly
human-like learning and thinking machines will have to reach beyond current
engineering trends in both what they learn, and how they learn it.
Specifically, we argue that these machines should (a) build causal models of
the world that support explanation and understanding, rather than merely
solving pattern recognition problems; (b) ground learning in intuitive theories
of physics and psychology, to support and enrich the knowledge that is learned;
and (c) harness compositionality and learning-to-learn to rapidly acquire and
generalize knowledge to new tasks and situations. We suggest concrete
challenges and promising routes towards these goals that can combine the
strengths of recent neural network advances with more structured cognitive
models.Comment: In press at Behavioral and Brain Sciences. Open call for commentary
proposals (until Nov. 22, 2016).
https://www.cambridge.org/core/journals/behavioral-and-brain-sciences/information/calls-for-commentary/open-calls-for-commentar
Discovering core terms for effective short text clustering
This thesis aims to address the current limitations in short texts clustering and provides a systematic framework that includes three novel methods to effectively measure similarity of two short texts, efficiently group short texts, and dynamically cluster short text streams
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