Improving entity recognition using ensembles of deep learning and fine-tuned large language models: A case study on adverse event extraction from VAERS and social media
Yiming Li,
Deepthi Viswaroopan,
William He
и другие.
Journal of Biomedical Informatics,
Год журнала:
2025,
Номер
unknown, С. 104789 - 104789
Опубликована: Фев. 1, 2025
Язык: Английский
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models
Journal of Biomedical Semantics,
Год журнала:
2024,
Номер
15(1)
Опубликована: Авг. 9, 2024
Vaccines
have
revolutionized
public
health
by
providing
protection
against
infectious
diseases.
They
stimulate
the
immune
system
and
generate
memory
cells
to
defend
targeted
Clinical
trials
evaluate
vaccine
performance,
including
dosage,
administration
routes,
potential
side
effects.
Язык: Английский
Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase
Frontiers in Cellular and Infection Microbiology,
Год журнала:
2025,
Номер
15
Опубликована: Фев. 7, 2025
Viral
vaccines
have
been
proven
significant
in
protecting
us
against
viral
diseases
such
as
COVID-19.
To
better
understand
and
design
vaccines,
it
is
critical
to
systematically
collect,
annotate,
analyse
various
identify
enriched
patterns
from
these
vaccines.
We
collected
experimentally
verified
the
literature,
manually
annotated,
stored
information
VIOLIN
vaccine
database.
The
annotated
included
basic
names,
pathogens
diseases,
components,
formulations,
their
induced
host
responses.
Enriched
were
identified
our
systematical
analysis
of
antigens.
A
total
2,847
95
species
(including
72
RNA
23
DNA
species)
collected,
These
used
542
taxonomical
found
viruses
covered
by
target
different
life
cycle
stages
(e.g.,
entry,
assembly,
exit,
immune
evasion)
top
ranked
human,
animal
HPV
antigen
proteins
also
show
up
virion
locations
HRSV
Both
structural
non-structural
for
development.
Protective
antigens
tend
a
protegenicity
score
>85%
based
on
Vaxign-ML
calculation,
which
measures
predicted
suitability
use.
While
adhesins
still
significantly
higher
chances
being
protective
antigens,
only
21.42%
be
adhesins.
Furthermore,
Gene
Ontology
(GO)
enrichment
using
customized
Fisher's
exact
test
many
entry
into
cell,
DNA/RNA/ATP/ion
binding,
suppression
type
1
interferon-mediated
signaling
pathway.
associated
entities
relations
are
ontologically
modeled
represented
Vaccine
(VO).
web
interface
was
developed
support
user
friendly
queries
knowledgebase,
insightful
patterns.
Язык: Английский
Impact of climate change on vaccine responses and inequity
Nature Climate Change,
Год журнала:
2024,
Номер
14(12), С. 1216 - 1218
Опубликована: Ноя. 15, 2024
Язык: Английский
VaxBot-HPV: a GPT-based chatbot for answering HPV vaccine-related questions
JAMIA Open,
Год журнала:
2024,
Номер
8(1)
Опубликована: Дек. 26, 2024
Abstract
Objective
Human
Papillomavirus
(HPV)
vaccine
is
an
effective
measure
to
prevent
and
control
the
diseases
caused
by
HPV.
However,
widespread
misinformation
hesitancy
remain
significant
barriers
its
uptake.
This
study
focuses
on
development
of
VaxBot-HPV,
a
chatbot
aimed
at
improving
health
literacy
promoting
vaccination
uptake
providing
information
answering
questions
about
HPV
vaccine.
Methods
We
constructed
knowledge
base
(KB)
for
which
consists
451
documents
from
biomedical
literature
web
sources
extracted
202
question-answer
pairs
KB
39
generated
GPT-4
training
testing
purposes.
To
comprehensively
understand
capabilities
potential
GPT-based
chatbots,
3
models
were
involved
in
this
study:
GPT-3.5,
GPT-4.
The
evaluation
criteria
included
answer
relevancy
faithfulness.
Results
VaxBot-HPV
demonstrated
superior
performance
faithfulness
compared
baselines.
For
test
KB,
it
achieved
score
0.85
0.97.
Similarly,
attained
scores
0.96
GPT-generated
questions.
Discussion
demonstrates
effectiveness
fine-tuned
large
language
healthcare,
outperforming
generic
GPT
accuracy
relevance.
Fine-tuning
mitigates
hallucinations
misinformation,
ensuring
reliable
while
allowing
dynamic
tailored
responses.
specific
fine-tuning,
includes
context
addition
pairs,
enables
provide
explanations
reasoning
behind
answers,
enhancing
transparency
user
trust.
Conclusions
underscores
importance
leveraging
fine-tuning
techniques
chatbots
healthcare
applications,
with
implications
medical
education
public
communication.
Язык: Английский
Exploring Temporal and Spatial Characteristics of Serious Adverse Event Reports Following COVID-19 Bivalent Vaccines
Research Square (Research Square),
Год журнала:
2025,
Номер
unknown
Опубликована: Март 3, 2025
Abstract
Background
To
mitigate
the
spread
of
variants
such
as
Omicron
in
COVID-19
pandemic,
development
and
utilization
bivalent
vaccines
have
become
essential.
However,
an
expected
subset
individuals
may
experience
serious
adverse
events
(AE)
after
receiving
vaccine.
Methods
In
this
research,
we
conducted
in-depth
analysis
data
obtained
from
Centers
for
Disease
Control
Prevention
(CDC)
Vaccine
Adverse
Event
Reporting
System
(VAERS)
to
evaluate
safety
administered
between
9/15/2022
9/1/2023.
The
Standard
Federal
Regions
were
used
region
partitions.
broaden
our
understanding
post-vaccination
AE,
performed
temporal
investigate
trends
Top
10
reported
AE
all
event
reports.
We
also
examined
similarity
across
diverse
regions
within
United
States.
Results
Our
findings
indicated
that
a
relatively
stably
decreasing
trend
was
observed
over
time,
with
four
peaks
December
2022,
February
2023,
Mar
2023
April
2023.
terms
spatial
analysis,
middle
northern
exhibited
higher
rates
AEs
associated
An
obvious
similar
pattern
is
(III,
IV,
V,
VI,
VII).
Conclusion
Overall,
research
underscores
ongoing
need
vigilant
post-licensure
vaccine
monitoring,
emphasizing
continuous
surveillance
essential
upholding
effectiveness
vaccines.
Язык: Английский
Exploring Associations Between COVID-19 Bivalent Vaccines and Their Related Adverse Events: A Correlational Study
Research Square (Research Square),
Год журнала:
2025,
Номер
unknown
Опубликована: Март 10, 2025
Abstract
Introduction
COVID-19,
a
global
health
crisis,
prompted
rapid
vaccine
development.
Bivalent
vaccines
by
Pfizer-BioNTech
and
Moderna
target
both
original
Omicron
strains.
Despite
vaccination
efforts,
the
persistence
of
adverse
events
underscores
importance
ongoing
safety
monitoring.
Method
We
collected
COVID-19
bivalent
event
reports
from
Vaccine
Adverse
Event
Reporting
System
(VAERS)
(September
15,
2022,
to
September
1,
2023).
The
Medical
Dictionary
for
Regulatory
Activities
(MedDRA)
categorized
reported
symptoms
into
corresponding
concepts.
Statistical
analyses
included
zero-truncated
Poisson
regression
estimating
symptom
rates,
logistic
identifying
risk
factors,
Spearman
correlation
assessing
non-parametric
relationships
between
in
different
Organ
Classes
(SOCs).
Results
Our
analysis
identified
significant
correlations
SOCs.
Notably,
positive
(ρ
=
0.3)
linked
Infections
(SOC
1)
with
Respiratory
disorders
13),
while
negative
(ρ=-0.3)
connected
Investigations
23)
Injury
24).
Zero-truncated
modeling
estimated
an
average
6.179
per
individual,
varying
age,
gender,
vaccine.
Gender
age
significantly
influence
associated
vaccines.
Females
generally
experienced
higher
odds
most
SOCs
compared
males,
except
cardiac
product-related
issues.
Older
adults
showed
likelihood
across
various
SOCs,
children
adolescents
had
distinct
susceptibility
patterns.
Additionally,
Pfizer
were
mainly
immune
skin
primarily
metabolic
Conclusion
In
conclusion,
our
study
aligned
self-reported
items
widely-accepted
medical
terminology
rigorously
analyzed
following
using
advanced
statistical
methods.
findings
provide
crucial
insights,
guiding
evidence-based
strategies
interventions
safety.
Язык: Английский
Enhancing Relation Extraction for COVID-19 Vaccine Shot-Adverse Event Associations with Large Language Models
Yiming Li,
Deepthi Viswaroopan,
William He
и другие.
Research Square (Research Square),
Год журнала:
2025,
Номер
unknown
Опубликована: Март 17, 2025
Objective
The
rapid
evolution
of
the
COVID-19
virus
has
led
to
development
different
vaccine
shots,
each
designed
combat
specific
variants
and
enhance
overall
efficacy.
While
vaccines
have
been
crucial
in
controlling
spread
virus,
they
can
also
cause
adverse
events
(AEs).
Understanding
these
relationships
is
vital
for
safety
monitoring
surveillance.
Methods
In
our
study,
we
collected
data
from
Vaccine
Adverse
Event
Reporting
System
(VAERS)
social
media
platforms
(Twitter
Reddit)
extract
between
shots
events.
dataset
comprised
771
relation
pairs,
enabling
a
comprehensive
analysis
event
patterns.
We
employed
state-of-the-art
GPT
models,
including
GPT-3.5
GPT-4,
alongside
traditional
models
such
as
Recurrent
Neural
Networks
(RNNs)
BioBERT,
relationships.
Additionally,
used
two
sets
post-processing
rules
further
refine
extracted
relations.
Evaluation
metrics
precision,
recall,
F1-score
were
assess
performance
extracting
accurately.
Results
most
commonly
reported
AEs
following
primary
series
include
arm
soreness,
fatigue,
headache,
while
spectrum
boosters
more
diverse.
extraction,
fine-tuned
with
Sentence-based
Relation
Identification
achieved
highest
precision
0.94
perfect
recall
1,
resulting
an
impressive
F1
score
0.97.
Conclusion
This
study
advances
biomedical
informatics
by
showing
how
large
language
deep
learning
VAERS
media.
These
findings
improve
clinical
practice
enhancing
understanding
post-vaccination
symptoms.
precedent
future
research
natural
processing
informatics,
potential
applications
pharmacovigilance
decision-making.
Язык: Английский
A case of autosomal dominant polycystic kidney disease with systemic lupus erythematosus developing after SARS-CoV-2 vaccination
CEN Case Reports,
Год журнала:
2025,
Номер
unknown
Опубликована: Май 20, 2025
Язык: Английский
Post-COVID-19 Vaccination and Long COVID: Insights from Patient-Reported Data
Vaccines,
Год журнала:
2024,
Номер
12(12), С. 1427 - 1427
Опубликована: Дек. 18, 2024
COVID-19
vaccinations
reduce
the
severity
and
number
of
symptoms
for
acute
SARS-CoV-2
infections
may
risk
developing
Long
COVID,
also
known
as
post-acute
sequelae
(PASC).
Limited
heterogenous
data
exist
on
how
these
received
after
infection
might
impact
trajectory
PASC,
once
persistent
have
developed.
We
investigated
association
post-COVID-19
vaccination
with
any
vaccine(s)
PASC
in
two
independent
cohorts:
a
retrospective
chart
review
self-reported
from
patients
(n
=
128)
seen
Stanford
Clinic
between
May
2021
2022
2023
multinational
survey
assessment
individuals
484).
Within
patient
cohort
128),
58.6%
75)
were
female,
41.4%
53)
male;
50%
64)
white,
38.3%
49)
non-white.
A
total
60.2%
77)
reported
no
change
their
vaccination,
17.2%
22)
improved
symptoms,
22.7%
29)
worsened
symptoms.
In
484),
380
U.S.,
104
outside
U.S.;
88.4%
428)
11.6%
56)
88.8%
430)
11.2%
54)
The
distribution
vaccine
effects
was
20.2%
98),
60.5%
effect
293),
19.2%
93).
both
cohorts,
demographic
features,
including
age,
sex,
race/ethnicity,
not
significantly
associated
post-vaccination
symptom
changes.
There
non-significant
difference
median
dates
among
different
outcomes.
BMI
significant
improvement
(p
0.026)
cohort,
while
history
booster
doses
<
0.001)
cohort.
Most
did
report
changes
overall
following
onset.
Further
research
is
needed
to
better
understand
relationship
PASC.
Язык: Английский