25,743 research outputs found
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
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
ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural Network
With the development of next generation sequencing techniques, it is fast and
cheap to determine protein sequences but relatively slow and expensive to
extract useful information from protein sequences because of limitations of
traditional biological experimental techniques. Protein function prediction has
been a long standing challenge to fill the gap between the huge amount of
protein sequences and the known function. In this paper, we propose a novel
method to convert the protein function problem into a language translation
problem by the new proposed protein sequence language "ProLan" to the protein
function language "GOLan", and build a neural machine translation model based
on recurrent neural networks to translate "ProLan" language to "GOLan"
language. We blindly tested our method by attending the latest third Critical
Assessment of Function Annotation (CAFA 3) in 2016, and also evaluate the
performance of our methods on selected proteins whose function was released
after CAFA competition. The good performance on the training and testing
datasets demonstrates that our new proposed method is a promising direction for
protein function prediction. In summary, we first time propose a method which
converts the protein function prediction problem to a language translation
problem and applies a neural machine translation model for protein function
prediction.Comment: 13 pages, 5 figure
Thirty Years of Machine Learning: The Road to Pareto-Optimal Wireless Networks
Future wireless networks have a substantial potential in terms of supporting
a broad range of complex compelling applications both in military and civilian
fields, where the users are able to enjoy high-rate, low-latency, low-cost and
reliable information services. Achieving this ambitious goal requires new radio
techniques for adaptive learning and intelligent decision making because of the
complex heterogeneous nature of the network structures and wireless services.
Machine learning (ML) algorithms have great success in supporting big data
analytics, efficient parameter estimation and interactive decision making.
Hence, in this article, we review the thirty-year history of ML by elaborating
on supervised learning, unsupervised learning, reinforcement learning and deep
learning. Furthermore, we investigate their employment in the compelling
applications of wireless networks, including heterogeneous networks (HetNets),
cognitive radios (CR), Internet of things (IoT), machine to machine networks
(M2M), and so on. This article aims for assisting the readers in clarifying the
motivation and methodology of the various ML algorithms, so as to invoke them
for hitherto unexplored services as well as scenarios of future wireless
networks.Comment: 46 pages, 22 fig
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
Backwards is the way forward: feedback in the cortical hierarchy predicts the expected future
Clark offers a powerful description of the brain as a prediction machine, which offers progress on two distinct levels. First, on an abstract conceptual level, it provides a unifying framework for perception, action, and cognition (including subdivisions such as attention, expectation, and imagination). Second, hierarchical prediction offers progress on a concrete descriptive level for testing and constraining conceptual elements and mechanisms of predictive coding models (estimation of predictions, prediction errors, and internal models)
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