63,743 research outputs found
Unsupervised decoding of long-term, naturalistic human neural recordings with automated video and audio annotations
Fully automated decoding of human activities and intentions from direct
neural recordings is a tantalizing challenge in brain-computer interfacing.
Most ongoing efforts have focused on training decoders on specific, stereotyped
tasks in laboratory settings. Implementing brain-computer interfaces (BCIs) in
natural settings requires adaptive strategies and scalable algorithms that
require minimal supervision. Here we propose an unsupervised approach to
decoding neural states from human brain recordings acquired in a naturalistic
context. We demonstrate our approach on continuous long-term
electrocorticographic (ECoG) data recorded over many days from the brain
surface of subjects in a hospital room, with simultaneous audio and video
recordings. We first discovered clusters in high-dimensional ECoG recordings
and then annotated coherent clusters using speech and movement labels extracted
automatically from audio and video recordings. To our knowledge, this
represents the first time techniques from computer vision and speech processing
have been used for natural ECoG decoding. Our results show that our
unsupervised approach can discover distinct behaviors from ECoG data, including
moving, speaking and resting. We verify the accuracy of our approach by
comparing to manual annotations. Projecting the discovered cluster centers back
onto the brain, this technique opens the door to automated functional brain
mapping in natural settings
BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments
Advances in sequencing techniques have led to exponential growth in
biological data, demanding the development of large-scale bioinformatics
experiments. Because these experiments are computation- and data-intensive,
they require high-performance computing (HPC) techniques and can benefit from
specialized technologies such as Scientific Workflow Management Systems (SWfMS)
and databases. In this work, we present BioWorkbench, a framework for managing
and analyzing bioinformatics experiments. This framework automatically collects
provenance data, including both performance data from workflow execution and
data from the scientific domain of the workflow application. Provenance data
can be analyzed through a web application that abstracts a set of queries to
the provenance database, simplifying access to provenance information. We
evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree
assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a
RASopathy analysis workflow. We analyze each workflow from both computational
and scientific domain perspectives, by using queries to a provenance and
annotation database. Some of these queries are available as a pre-built feature
of the BioWorkbench web application. Through the provenance data, we show that
the framework is scalable and achieves high-performance, reducing up to 98% of
the case studies execution time. We also show how the application of machine
learning techniques can enrich the analysis process
Cooperation between expert knowledge and data mining discovered knowledge: Lessons learned
Expert systems are built from knowledge traditionally elicited from the human expert. It is precisely knowledge elicitation from the expert that is the bottleneck in expert system construction. On the other hand, a data mining system, which automatically extracts knowledge, needs expert guidance on the successive decisions to be made in each of the system phases. In this context, expert knowledge and data mining discovered knowledge can cooperate, maximizing their individual capabilities: data mining discovered knowledge can be used as a complementary source of knowledge for the expert system, whereas expert knowledge can be used to guide the data mining process. This article summarizes different examples of systems where there is cooperation between expert knowledge and data mining discovered knowledge and reports our experience of such cooperation gathered from a medical diagnosis project called Intelligent Interpretation of Isokinetics Data, which we developed. From that experience, a series of lessons were learned throughout project development. Some of these lessons are generally applicable and others pertain exclusively to certain project types
Data Science and Ebola
Data Science---Today, everybody and everything produces data. People produce
large amounts of data in social networks and in commercial transactions.
Medical, corporate, and government databases continue to grow. Sensors continue
to get cheaper and are increasingly connected, creating an Internet of Things,
and generating even more data. In every discipline, large, diverse, and rich
data sets are emerging, from astrophysics, to the life sciences, to the
behavioral sciences, to finance and commerce, to the humanities and to the
arts. In every discipline people want to organize, analyze, optimize and
understand their data to answer questions and to deepen insights. The science
that is transforming this ocean of data into a sea of knowledge is called data
science. This lecture will discuss how data science has changed the way in
which one of the most visible challenges to public health is handled, the 2014
Ebola outbreak in West Africa.Comment: Inaugural lecture Leiden Universit
Classification of Humans into Ayurvedic Prakruti Types using Computer Vision
Ayurveda, a 5000 years old Indian medical science, believes that the universe and hence humans are made up of five elements namely ether, fire, water, earth, and air. The three Doshas (Tridosha) Vata, Pitta, and Kapha originated from the combinations of these elements. Every person has a unique combination of Tridosha elements contributing to a person’s ‘Prakruti’. Prakruti governs the physiological and psychological tendencies in all living beings as well as the way they interact with the environment. This balance influences their physiological features like the texture and colour of skin, hair, eyes, length of fingers, the shape of the palm, body frame, strength of digestion and many more as well as the psychological features like their nature (introverted, extroverted, calm, excitable, intense, laidback), and their reaction to stress and diseases. All these features are coded in the constituents at the time of a person’s creation and do not change throughout their lifetime. Ayurvedic doctors analyze the Prakruti of a person either by assessing the physical features manually and/or by examining the nature of their heartbeat (pulse). Based on this analysis, they diagnose, prevent and cure the disease in patients by prescribing precision medicine.
This project focuses on identifying Prakruti of a person by analysing his facial features like hair, eyes, nose, lips and skin colour using facial recognition techniques in computer vision. This is the first of its kind research in this problem area that attempts to bring image processing into the domain of Ayurveda
Properties of Healthcare Teaming Networks as a Function of Network Construction Algorithms
Network models of healthcare systems can be used to examine how providers
collaborate, communicate, refer patients to each other. Most healthcare service
network models have been constructed from patient claims data, using billing
claims to link patients with providers. The data sets can be quite large,
making standard methods for network construction computationally challenging
and thus requiring the use of alternate construction algorithms. While these
alternate methods have seen increasing use in generating healthcare networks,
there is little to no literature comparing the differences in the structural
properties of the generated networks. To address this issue, we compared the
properties of healthcare networks constructed using different algorithms and
the 2013 Medicare Part B outpatient claims data. Three different algorithms
were compared: binning, sliding frame, and trace-route. Unipartite networks
linking either providers or healthcare organizations by shared patients were
built using each method. We found that each algorithm produced networks with
substantially different topological properties. Provider networks adhered to a
power law, and organization networks to a power law with exponential cutoff.
Censoring networks to exclude edges with less than 11 shared patients, a common
de-identification practice for healthcare network data, markedly reduced edge
numbers and greatly altered measures of vertex prominence such as the
betweenness centrality. We identified patterns in the distance patients travel
between network providers, and most strikingly between providers in the
Northeast United States and Florida. We conclude that the choice of network
construction algorithm is critical for healthcare network analysis, and discuss
the implications for selecting the algorithm best suited to the type of
analysis to be performed.Comment: With links to comprehensive, high resolution figures and networks via
figshare.co
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