Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Фев. 14, 2023
Stunting
affects
one-in-five
children
globally
and
is
associated
with
greater
infectious
morbidity,
mortality
neurodevelopmental
deficits.
Recent
evidence
suggests
that
the
early-life
gut
microbiome
child
growth
through
immune,
metabolic
endocrine
pathways.
Using
whole
metagenomic
sequencing,
we
map
assembly
of
in
335
from
rural
Zimbabwe
1-18
months
age
who
were
enrolled
Sanitation,
Hygiene,
Infant
Nutrition
Efficacy
Trial
(SHINE;
NCT01824940),
a
randomized
trial
improved
water,
sanitation
hygiene
(WASH)
infant
young
feeding
(IYCF).
Here,
show
undergoes
programmed
unresponsive
to
interventions
intended
improve
linear
growth.
However,
maternal
HIV
infection
over-diversification
over-maturity
their
uninfected
children,
addition
reduced
abundance
Bifidobacterium
species.
machine
learning
models
(XGBoost),
taxonomic
features
are
poorly
predictive
growth,
however
functional
features,
particularly
B-vitamin
nucleotide
biosynthesis
pathways,
moderately
predict
both
attained
ponderal
velocity.
New
approaches
targeting
early
childhood
may
complement
efforts
combat
undernutrition.
Methods in Ecology and Evolution,
Год журнала:
2023,
Номер
14(4), С. 994 - 1016
Опубликована: Фев. 13, 2023
Abstract
The
popularity
of
machine
learning
(ML),
deep
(DL)
and
artificial
intelligence
(AI)
has
risen
sharply
in
recent
years.
Despite
this
spike
popularity,
the
inner
workings
ML
DL
algorithms
are
often
perceived
as
opaque,
their
relationship
to
classical
data
analysis
tools
remains
debated.
Although
it
is
assumed
that
excel
primarily
at
making
predictions,
can
also
be
used
for
analytical
tasks
traditionally
addressed
with
statistical
models.
Moreover,
most
discussions
reviews
on
focus
mainly
DL,
failing
synthesise
wealth
different
advantages
general
principles.
Here,
we
provide
a
comprehensive
overview
field
starting
by
summarizing
its
historical
developments,
existing
algorithm
families,
differences
traditional
tools,
universal
We
then
discuss
why
when
models
prediction
where
they
could
offer
alternatives
methods
inference,
highlighting
current
emerging
applications
ecological
problems.
Finally,
summarize
trends
such
scientific
causal
ML,
explainable
AI,
responsible
AI
may
significantly
impact
future.
conclude
powerful
new
predictive
modelling
analysis.
superior
performance
compared
explained
higher
flexibility
automatic
data‐dependent
complexity
optimization.
However,
use
inference
still
disputed
predictions
creates
challenges
interpretation
these
Nevertheless,
expect
become
an
indispensable
tool
ecology
evolution,
comparable
other
tools.
ACM SIGKDD Explorations Newsletter,
Год журнала:
2020,
Номер
22(1), С. 18 - 33
Опубликована: Май 13, 2020
Machine
learning
models
have
had
discernible
achievements
in
a
myriad
of
applications.
However,
most
these
are
black-boxes,
and
it
is
obscure
how
the
decisions
made
by
them.
This
makes
unreliable
untrustworthy.
To
provide
insights
into
decision
making
processes
models,
variety
traditional
interpretable
been
proposed.
Moreover,
to
generate
more
humanfriendly
explanations,
recent
work
on
interpretability
tries
answer
questions
related
causality
such
as
"Why
does
this
model
decisions?"
or
"Was
specific
feature
that
caused
model?".
In
work,
aim
causal
referred
models.
The
existing
surveys
covered
concepts
methodologies
interpretability.
we
present
comprehensive
survey
from
aspects
problems
methods.
addition,
provides
in-depth
evaluation
metrics
for
measuring
interpretability,
which
can
help
practitioners
understand
what
scenarios
each
metric
suitable.
Computational and Structural Biotechnology Journal,
Год журнала:
2021,
Номер
19, С. 1092 - 1107
Опубликована: Янв. 1, 2021
Advances
in
nucleic
acid
sequencing
technology
have
enabled
expansion
of
our
ability
to
profile
microbial
diversity.
These
large
datasets
taxonomic
and
functional
diversity
are
key
better
understanding
ecology.
Machine
learning
has
proven
be
a
useful
approach
for
analyzing
community
data
making
predictions
about
outcomes
including
human
environmental
health.
applied
profiles
been
used
predict
disease
states
health,
quality
presence
contamination
the
environment,
as
trace
evidence
forensics.
appeal
powerful
tool
that
can
provide
deep
insights
into
communities
identify
patterns
data.
However,
often
machine
models
black
boxes
specific
outcome,
with
little
how
arrived
at
predictions.
Complex
algorithms
may
value
higher
accuracy
performance
sacrifice
interpretability.
In
order
leverage
more
translational
research
related
microbiome
strengthen
extract
meaningful
biological
information,
it
is
important
interpretable.
Here
we
review
current
trends
applications
ecology
well
some
challenges
opportunities
broad
application
communities.
Ageing Research Reviews,
Год журнала:
2020,
Номер
60, С. 101050 - 101050
Опубликована: Апрель 6, 2020
The
aging
process
results
in
multiple
traceable
footprints,
which
can
be
quantified
and
used
to
estimate
an
organism's
age.
Examples
of
such
biomarkers
include
epigenetic
changes,
telomere
attrition,
alterations
gene
expression
metabolite
concentrations.
More
than
a
dozen
clocks
use
molecular
features
predict
age,
each
them
utilizing
different
data
types
training
procedures.
Here,
we
offer
detailed
comparison
existing
mouse
human
clocks,
discuss
their
technological
limitations
the
underlying
machine
learning
algorithms.
We
also
promising
future
directions
research
biohorology
-
science
measuring
passage
time
living
systems.
Overall,
expect
deep
learning,
neural
networks
generative
approaches
next
power
tools
this
timely
actively
developing
field.
Water Resources Research,
Год журнала:
2021,
Номер
57(4)
Опубликована: Фев. 10, 2021
Abstract
Hydrometeorological
flood
generating
processes
(excess
rain,
short
long
snowmelt,
and
rain‐on‐snow)
underpin
our
understanding
of
behavior.
Knowledge
about
improves
hydrological
models,
frequency
analysis,
estimation
climate
change
impact
on
floods,
etc.
Yet,
not
much
is
known
how
catchment
attributes
influence
the
spatial
distribution
processes.
This
study
aims
to
offer
a
comprehensive
structured
approach
close
this
knowledge
gap.
We
employ
large
sample
(671
catchments
across
contiguous
United
States)
evaluate
use
two
complementary
approaches:
A
statistics‐based
which
compares
attribute
distributions
different
processes;
random
forest
model
in
combination
with
an
interpretable
machine
learning
(accumulated
local
effects
[ALE]).
The
ALE
method
has
been
used
often
hydrology,
it
overcomes
significant
obstacle
many
statistical
methods,
confounding
effect
correlated
attributes.
As
expected,
we
find
(fraction
snow,
aridity,
precipitation
seasonality,
mean
precipitation)
be
most
influential
process
distribution.
However,
varies
both
type.
also
can
predicted
for
ungauged
relatively
high
accuracy
(
R
2
between
0.45
0.9).
implication
these
findings
should
considered
future
studies,
as
changes
characteristics