Bayesian networks to estimate prognosis in vascular cognitive impairment and small vessel disease: integrated analyses of interdependent contributors to multiple outcomes

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[1] § Material and Methods › BN training › Variable discretization and algorithm ↔ layerbn/bn_utils.py, lines 161–224 · score 0.64 · DiscreteTypeProcessor, pyAgrum, enforce, K2, Bayesian, bins

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The authors' code

Python · 648 lines · 26 KB · MIT · 1 match

"""Bayesian network structure learning, bootstrapping, and scenarios.
Everything cohort-specific is a parameter: which layers to exclude, which
layer names mark the outcome and dropout roles, the score, the seed. No
cohort's conventions are assumed.
These functions take the layer map, the discretisation and the layer role
patterns as separate arguments, which means a caller has to keep them
consistent with the spec at every call site. `layerbn.analysis.Analysis`
does that for you and is the recommended entry point; use these directly
when you need control it does not expose.
"""
from __future__ import annotations
import random
from collections import defaultdict
from collections.abc import Callable, Iterable, Mapping, Sequence
from itertools import product
from typing import Any
import numpy as np
import pandas as pd
from layerbn.discretisation import state_for_value
# Layer-name substrings that identify semantic roles. Override when your
# cohort names its layers differently.
DEFAULT_OUTCOME_LAYER_PATTERNS: tuple[str, ...] = ("Outcomes",)
DEFAULT_DROPOUT_LAYER_PATTERNS: tuple[str, ...] = ("Dropout",)
def _match_any(layer_name: str, patterns: Sequence[str]) -> bool:
return any(p in layer_name for p in patterns)
def collect_outcome_vars(
layer_map: Mapping[str, Sequence[str]],
*,
outcome_patterns: Sequence[str] = DEFAULT_OUTCOME_LAYER_PATTERNS,
dropout_patterns: Sequence[str] = DEFAULT_DROPOUT_LAYER_PATTERNS,
) -> tuple[list[str], list[str]]:
"""Return `(outcome_vars, dropout_vars)` inferred from layer names."""
outcome_vars: list[str] = []
dropout_vars: list[str] = []
for layer, variables in layer_map.items():
if _match_any(layer, dropout_patterns):
dropout_vars.extend(variables)
elif _match_any(layer, outcome_patterns):
outcome_vars.extend(variables)
return outcome_vars, dropout_vars
def configure_guided_structure(
learner: Any,
layer_map_filtered: Mapping[str, Sequence[str]],
variables_to_keep: Sequence[str],
outcomes: Sequence[str],
*,
dropout_patterns: Sequence[str] = DEFAULT_DROPOUT_LAYER_PATTERNS,
within_layers: bool = True,
arcs_between_outcomes: bool = False,
selection_parents: str = "outcomes",
forbidden_pairs: Iterable[tuple[str, str]] = (),
mandatory_pairs: Iterable[tuple[str, str]] = (),
no_parents: Iterable[str] = (),
no_children: Iterable[str] = (),
) -> tuple[list[str], list[str]]:
"""Restrict the learner to arcs that go downward through the layers.
Rules always encoded:
* Arcs may only go from an earlier layer to the same or a later layer.
Rules that the keyword arguments control, whose defaults reproduce the
behaviour this function had before they existed:
* `within_layers` — whether two variables in the same layer may be
connected. False makes each layer internally independent.
* `arcs_between_outcomes` — whether one outcome may point at another.
* `selection_parents` — `"outcomes"` allows arcs into a dropout-layer
variable only from an outcome, on the grounds that dropout follows
the outcomes rather than the covariates. `"any"` drops that
restriction and lets the layer order alone decide.
Additional structural knowledge:
* `forbidden_pairs` — `(parent, child)` arcs to rule out even though
the layer order permits them.
* `mandatory_pairs` — arcs the learner must include. These must be
consistent with everything above; a pair that is both mandatory and
forbidden raises `ValueError` rather than reaching pyAgrum, whose own
message does not say which pair was at fault.
* `no_parents` / `no_children` — variables pinned as roots or sinks.
Returns `(dropout_vars, true_outcomes)` for the caller to reuse when
adding hard outcome→dropout arcs after learning.
"""
if selection_parents not in ("outcomes", "any"):
raise ValueError(
f"selection_parents must be 'outcomes' or 'any', got {selection_parents!r}")
layer_keys = list(layer_map_filtered.keys())
dropout_vars = [v for k in layer_keys if _match_any(k, dropout_patterns)
for v in layer_map_filtered[k]]
true_outcomes = [v for v in outcomes if v not in dropout_vars]
keep = set(variables_to_keep)
forbidden_pairs = set(forbidden_pairs)
mandatory_pairs = set(mandatory_pairs)
no_parents = set(no_parents)
no_children = set(no_children)
conflict = forbidden_pairs & mandatory_pairs
if conflict:
raise ValueError(
f"these arcs are both mandatory and forbidden: {sorted(conflict)}")
allowed_arcs: list[tuple[str, str]] = []
for i, from_key in enumerate(layer_keys):
for j, to_key in enumerate(layer_keys[i:], start=i):
if i == j and not within_layers:
continue
for parent, child in product(layer_map_filtered[from_key],
layer_map_filtered[to_key]):
if child in dropout_vars and selection_parents == "outcomes":
if parent in outcomes:
allowed_arcs.append((parent, child))
continue
if parent in keep and child in keep:
allowed_arcs.append((parent, child))
allowed_set = set(allowed_arcs) - forbidden_pairs
for parent in variables_to_keep:
for child in variables_to_keep:
if parent != child and (parent, child) not in allowed_set:
learner.addForbiddenArc(parent, child)
if not arcs_between_outcomes:
for parent in true_outcomes:
for child in true_outcomes:
if parent != child:
learner.addForbiddenArc(parent, child)
# Node-level constraints are applied after the pairwise ones so that a
# variable pinned as a root or a sink stays that way regardless of what
# the layer order allowed.
for variable in sorted(no_parents & keep):
learner.addNoParentNode(variable)
for variable in sorted(no_children & keep):
learner.addNoChildrenNode(variable)
# Mandatory arcs come last: pyAgrum resolves them against the
# constraints already registered.
for parent, child in sorted(mandatory_pairs):
if parent in keep and child in keep:
learner.addMandatoryArc(parent, child)
return dropout_vars, true_outcomes
def build_bn(
df: pd.DataFrame,
outcomes: Sequence[str],
layer_map: Mapping[str, Sequence[str]],
type_processor: Any,
*,
score: str = "K2",
use_tabu: bool = True,
random_seed: int = 42,
enforce_structure: bool = True,
fixed_template: Any = None,
use_smoothing: bool = False,
exclude_layers: Iterable[str] = (),
max_indegree: int = 5,
outcome_patterns: Sequence[str] = DEFAULT_OUTCOME_LAYER_PATTERNS,
dropout_patterns: Sequence[str] = DEFAULT_DROPOUT_LAYER_PATTERNS,
within_layers: bool = True,
arcs_between_outcomes: bool = False,
selection_parents: str = "outcomes",
forbidden_pairs: Iterable[tuple[str, str]] = (),
mandatory_pairs: Iterable[tuple[str, str]] = (),
no_parents: Iterable[str] = (),
no_children: Iterable[str] = (),
) -> Any:
"""Learn a layered Bayesian network with pyAgrum.
Parameters
----------
df : DataFrame
Fully-imputed input data. Columns not needed as outcomes and not
listed in `exclude_layers` become learnable nodes.
outcomes : sequence of str
Outcome variable names to keep in the network. Any *other* variable
that belongs to an outcome/dropout layer is dropped before learning.
layer_map : mapping
`{layer_name: [variable, ...]}` defining the expert layering.
type_processor : DiscreteTypeProcessor
Constructed via `layerbn.discretisation.make_type_processor`.
score : {"K2", "BIC", "BDeu"}
Structure-learning score.
fixed_template : optional
Use a pre-computed discretisation template so bootstrap resamples
share bin edges. Build once with `type_processor.discretizedTemplate(df)`.
exclude_layers : iterable of str
Layer names whose variables should be dropped before learning, for
instance to leave out a layer measured on only part of the cohort.
use_smoothing : bool
Add a Laplace prior, so that a parent configuration nobody in the
sample happens to occupy gets a small probability rather than zero.
Always on for BIC, which carries no prior of its own and whose
zero cells otherwise break inference on bootstrap resamples.
Ignored for K2 and BDeu: both already contain an implicit prior,
and adding a second one double-counts it. aGrUM reports that as
"the K2 score already contains a different 'implicit' prior ...
the learning will probably be biased", which is exactly what would
happen, so the request is dropped rather than honoured.
within_layers, arcs_between_outcomes, selection_parents
The three structural conventions. See `configure_guided_structure`;
the defaults reproduce the behaviour that used to be fixed in code.
forbidden_pairs, mandatory_pairs, no_parents, no_children
Extra structural knowledge, as `(parent, child)` pairs and variable
names. `layerbn.spec` builds these from a spec's `constraints`
block, and `layerbn.analysis.Analysis` passes them in for you.
Notes
-----
* When `enforce_structure=True`, `configure_guided_structure` restricts
arcs to obey the layer order and any constraints given.
* When `enforce_structure=False` every constraint is skipped, including
the layer order. That is a genuinely unconstrained search, useful as a
comparison but not as the analysis.
* After learning, hard outcome→dropout arcs are added if not already
present, so scenario inference always sees the dropout mechanism.
"""
import pyagrum as gum
random.seed(random_seed)
np.random.seed(random_seed)
exclude_layers = set(exclude_layers)
layer_map_filtered = {k: v for k, v in layer_map.items() if k not in exclude_layers}
excluded_vars = [v for k in exclude_layers for v in layer_map.get(k, [])]
outcome_vars_all, dropout_vars_all = collect_outcome_vars(
layer_map, outcome_patterns=outcome_patterns, dropout_patterns=dropout_patterns,
)
outcome_layer_vars = outcome_vars_all + dropout_vars_all
drop_outcomes = [v for v in outcome_layer_vars if v not in outcomes]
df_reduced = df.drop(columns=drop_outcomes + excluded_vars, errors="ignore")
variables_to_keep = df_reduced.columns.tolist()
template = fixed_template if fixed_template is not None \
else type_processor.discretizedTemplate(df_reduced)
learner = gum.BNLearner(df_reduced, template)
score = score.upper()
if score == "K2":
learner.useScoreK2()
elif score == "BIC":
learner.useScoreBIC()
elif score == "BDEU":
learner.useScoreBDeu(ess=1)
else:
raise ValueError(f"Unsupported score {score!r}: choose K2, BIC, or BDeu")
# Only BIC has no prior of its own. K2 and BDeu each carry an implicit
# one, and stacking a smoothing prior on top of it biases the score --
# aGrUM emits a notification saying so for every fit, which under a
# bootstrap means hundreds of them. See `use_smoothing` above.
if score == "BIC":
learner.useSmoothingPrior()
if use_tabu:
learner.useLocalSearchWithTabuList()
else:
learner.useGreedyHillClimbing()
if enforce_structure:
dropout_vars, true_outcomes = configure_guided_structure(
learner, layer_map_filtered, variables_to_keep, outcomes,
dropout_patterns=dropout_patterns,
within_layers=within_layers,
arcs_between_outcomes=arcs_between_outcomes,
selection_parents=selection_parents,
forbidden_pairs=forbidden_pairs,
mandatory_pairs=mandatory_pairs,
no_parents=no_parents,
no_children=no_children,
)
else:
# Same pair `configure_guided_structure` would have returned, without
# touching the learner. NB: `collect_outcome_vars` returns
# (outcome_vars, dropout_vars) — the opposite order — so it must not be
# unpacked into (dropout_vars, true_outcomes) directly.
dropout_vars = [v for k in layer_map_filtered
if _match_any(k, dropout_patterns)
for v in layer_map_filtered[k]]
true_outcomes = [v for v in outcomes if v not in dropout_vars]
learner.setMaxIndegree(max_indegree)
bn = learner.learnBN()
if enforce_structure:
# Connect every outcome to the selection layer, so scenario inference
# always sees the dropout mechanism even when the score did not pick
# the arc up. An arc the caller forbade explicitly is left out: the
# spec's promise is that constraints narrow what the layer order
# allows, and silently reinstating one here would break it.
forbidden = set(forbidden_pairs)
try:
names = set(bn.names())
for dropout in (n for n in dropout_vars if n in names):
for outcome in (n for n in true_outcomes if n in names):
if (outcome, dropout) in forbidden:
continue
out_id, drop_id = bn.idFromName(outcome), bn.idFromName(dropout)
if not bn.existsArc(out_id, drop_id):
bn.addArc(out_id, drop_id)
except Exception:
pass # gum.InvalidArgument etc. — arc already exists / var missing
return bn
def bootstrap_edge_frequencies(
df: pd.DataFrame,
*,
outcomes: Sequence[str],
layer_map: Mapping[str, Sequence[str]],
type_processor: Any,
build_bn_func: Callable[..., Any] = build_bn,
n_bootstraps: int = 100,
random_seed: int = 42,
**build_kwargs: Any,
) -> dict[tuple[str, str], float]:
"""Fit `build_bn_func` on `n_bootstraps` resamples; return per-arc frequencies.
Extra keyword arguments are forwarded to `build_bn_func` unchanged so
callers can pin `score`, `use_smoothing`, `fixed_template`, etc.
Notes
-----
The denominator is `n_bootstraps`, **not** the number of resamples that
fitted successfully. A failed fit therefore lowers every frequency rather
than being excluded from the calculation. These frequencies are reported
as the `f=NN%` arc labels in published figures, so changing the
denominator would silently restate them.
"""
counts: dict[tuple[str, str], int] = defaultdict(int)
successes = 0
for i in range(n_bootstraps):
seed = random_seed + i
boot = df.sample(frac=1.0, replace=True, random_state=seed)
try:
bn = build_bn_func(
boot, outcomes=outcomes, layer_map=layer_map,
type_processor=type_processor, random_seed=seed, **build_kwargs,
)
except Exception as exc:
print(f"Bootstrap {i} failed: {exc}")
continue
successes += 1
for parent_id, child_id in bn.arcs():
counts[(bn.variable(parent_id).name(), bn.variable(child_id).name())] += 1
if successes < n_bootstraps:
print(f"Note: {n_bootstraps - successes}/{n_bootstraps} bootstrap fits "
"failed; frequencies are still divided by n_bootstraps.")
return {edge: count / n_bootstraps for edge, count in counts.items()}
def bootstrap_scenario_risks(
df: pd.DataFrame,
*,
scenario_profiles: Sequence[tuple[str, Mapping[str, Any]]],
target_outcomes: Sequence[tuple[str, str]],
build_bn_func: Callable[..., Any] = build_bn,
layer_map: Mapping[str, Sequence[str]],
type_processor: Any,
outcomes_for_learning: Sequence[str],
n_bootstraps: int = 200,
random_seed: int = 42,
**build_kwargs: Any,
) -> pd.DataFrame:
"""Compute posterior probabilities under a set of patient profiles.
Parameters
----------
scenario_profiles : sequence of (label, evidence_dict)
Each dict maps a variable name to the evidence for it, passed to
`LazyPropagation.setEvidence` unchanged. Prefer **state indices**:
pyAgrum reads a bare integer as a state index, a numeric *string*
as a value to place in a bin, and rejects an interval label such as
`'(45;64.6['` outright. `layerbn.analysis.Analysis.resolve_profile`
converts any of these to indices and reports what it could not
match; using it avoids the failure mode below.
target_outcomes : sequence of (var_name, display_label)
outcomes_for_learning : sequence of str
Passed to `build_bn_func` as the fixed set of outcomes so bootstrap
networks are structurally comparable across resamples.
Notes
-----
Evidence that pyAgrum rejects raises `gum.InvalidArgument`, which this
function catches and skips. The affected scenario then produces no rows
at all rather than an error, so check that every profile you passed
appears in the result.
Pass `fixed_template` (via `**build_kwargs`) when the profiles refer to
discretised variables. Without it every resample recomputes its own bin
edges, and a fixed profile silently refers to a different group of
people in each resample.
"""
import pyagrum as gum
samples: dict[tuple[str, str, str], list[float]] = defaultdict(list)
label_cache: dict[str, list[str]] = {}
failed = 0
for i in range(n_bootstraps):
seed = random_seed + i
boot = df.sample(frac=1.0, replace=True, random_state=seed)
try:
bn = build_bn_func(
boot, outcomes=list(outcomes_for_learning), layer_map=layer_map,
type_processor=type_processor, random_seed=seed, **build_kwargs,
)
except Exception:
failed += 1
continue
for scenario_name, evidence in scenario_profiles:
ie = gum.LazyPropagation(bn)
try:
ie.setEvidence(dict(evidence))
except gum.InvalidArgument:
continue
for outcome_name, _ in target_outcomes:
if outcome_name not in label_cache:
label_cache[outcome_name] = list(
bn.variable(bn.idFromName(outcome_name)).labels()
)
posterior = ie.posterior(outcome_name)
for idx, state in enumerate(label_cache[outcome_name]):
samples[(scenario_name, outcome_name, state)].append(float(posterior[idx]))
outcome_labels = dict(target_outcomes)
rows = []
for (scenario_name, outcome_name, state), values in samples.items():
arr = np.asarray(values, float)
arr = arr[np.isfinite(arr)]
if arr.size == 0:
continue
rows.append({
"Scenario": scenario_name,
"Outcome": outcome_labels.get(outcome_name, outcome_name),
"Category": state,
"Mean probability": arr.mean(),
"Std": arr.std(ddof=1) if arr.size > 1 else 0.0,
"CI 2.5%": np.quantile(arr, 0.025),
"CI 97.5%": np.quantile(arr, 0.975),
"Bootstraps": int(arr.size),
})
if failed:
print(f"Warning: {failed}/{n_bootstraps} bootstrap fits failed and were skipped.")
return (pd.DataFrame(rows)
.sort_values(["Scenario", "Outcome", "Category"])
.reset_index(drop=True))
def descendants(bn: Any, start_id: int) -> set[int]:
"""All nodes reachable from `start_id` by following directed arcs."""
seen: set[int] = set()
stack = [start_id]
while stack:
for child in bn.children(stack.pop()):
if child not in seen:
seen.add(child)
stack.append(child)
return seen
def bootstrap_knob_sweep(
df: pd.DataFrame,
*,
base_profile: Mapping[str, Any],
knob: str,
outcomes: Sequence[str],
outcomes_for_learning: Sequence[str],
layer_map: Mapping[str, Sequence[str]],
type_processor: Any,
build_bn_func: Callable[..., Any] = build_bn,
n_bootstraps: int = 200,
random_seed: int = 42,
verbose: bool = True,
**build_kwargs: Any,
) -> tuple[pd.DataFrame, dict[str, Any]]:
"""Sensitivity sweep: fix a patient, vary one variable across its states.
Returns `(sweep_df, meta)` where `sweep_df` has one row per
(outcome, knob state, outcome state) with bootstrap mean and 95% CI.
`meta` carries the resolved knob states and outcome states.
Notes
-----
Warns if any variable in `base_profile` lies on a directed path from
`knob` to an outcome (overadjustment / blocked mediator). Uses a fixed
discretisation template so knob states mean the same thing across
resamples.
"""
import pyagrum as gum
fixed_template = type_processor.discretizedTemplate(
_reduced_for_template(
df, layer_map, outcomes_for_learning,
build_kwargs.get("exclude_layers", ()),
outcome_patterns=build_kwargs.get(
"outcome_patterns", DEFAULT_OUTCOME_LAYER_PATTERNS),
dropout_patterns=build_kwargs.get(
"dropout_patterns", DEFAULT_DROPOUT_LAYER_PATTERNS),
)
)
# `use_smoothing` is deliberately NOT forced on here. It only takes
# effect under BIC (see `build_bn`), and forcing it meant every sweep
# resample was learned under a different prior from the network being
# reported -- so the interval described a procedure nobody ran.
build_kwargs = {**build_kwargs, "fixed_template": fixed_template}
ref_bn = build_bn_func(
df, outcomes=list(outcomes_for_learning), layer_map=layer_map,
type_processor=type_processor, random_seed=random_seed, **build_kwargs,
)
def labels_of(name: str) -> list[str]:
return list(ref_bn.variable(ref_bn.idFromName(name)).labels())
if knob in base_profile:
raise ValueError("base_profile must not contain the knob variable.")
applied, rejected, snapped = {}, {}, {}
for var, val in base_profile.items():
if var not in ref_bn.names():
rejected[var] = val
continue
state = state_for_value(labels_of(var), val)
if state is None:
rejected[var] = val
else:
applied[var] = state
if str(val) != state:
snapped[var] = f"{val} -> {state!r}"
if verbose:
print("Fixed patient — evidence applied:", applied or "(none)")
if snapped:
print("Fixed patient — snapped to bin:", snapped)
if rejected:
print("Fixed patient — REJECTED:", rejected,
"(unknown variable or value not matchable — check the discretised template).")
knob_descendants = {
ref_bn.variable(i).name()
for i in descendants(ref_bn, ref_bn.idFromName(knob))
}
blocked = [v for v in applied if v in knob_descendants]
if blocked and verbose:
print(f"WARNING: base_profile fixes {blocked}, which lie downstream of "
f"{knob!r}. Holding a mediator constant blocks part of the knob's "
"effect on the outcomes.")
applied_idx = {v: labels_of(v).index(s) for v, s in applied.items()}
knob_states = labels_of(knob)
outcome_states = {o: labels_of(o) for o in outcomes}
samples: dict[tuple[str, str, str], list[float]] = defaultdict(list)
failed = 0
for i in range(n_bootstraps):
seed = random_seed + i
boot = df.sample(frac=1.0, replace=True, random_state=seed)
try:
bn = build_bn_func(
boot, outcomes=list(outcomes_for_learning), layer_map=layer_map,
type_processor=type_processor, random_seed=seed, **build_kwargs,
)
except Exception:
failed += 1
continue
for k_idx, k_state in enumerate(knob_states):
try:
ie = gum.LazyPropagation(bn)
ie.setEvidence({**applied_idx, knob: k_idx})
post = {o: ie.posterior(o) for o in outcomes}
except Exception:
continue
for outcome in outcomes:
for s_idx, s_label in enumerate(outcome_states[outcome]):
samples[(outcome, k_state, s_label)].append(float(post[outcome][s_idx]))
rows = []
for (outcome, k_state, s_label), values in samples.items():
arr = np.asarray(values, float)
arr = arr[np.isfinite(arr)]
if arr.size == 0:
continue
rows.append({
"Outcome": outcome,
knob: k_state,
"Outcome state": s_label,
"P": arr.mean(),
"CI_low": np.quantile(arr, 0.025),
"CI_high": np.quantile(arr, 0.975),
"Bootstraps": int(arr.size),
})
if verbose and failed:
print(f"Note: {failed}/{n_bootstraps} bootstrap fits failed and were skipped.")
if not rows:
raise RuntimeError("No valid scenarios were produced — check base_profile.")
return pd.DataFrame(rows), {
"knob": knob, "knob_states": knob_states,
"outcomes": list(outcomes), "outcome_states": outcome_states,
}
def _reduced_for_template(
df: pd.DataFrame,
layer_map: Mapping[str, Sequence[str]],
outcomes_for_learning: Sequence[str],
exclude_layers: Iterable[str],
*,
outcome_patterns: Sequence[str] = DEFAULT_OUTCOME_LAYER_PATTERNS,
dropout_patterns: Sequence[str] = DEFAULT_DROPOUT_LAYER_PATTERNS,
) -> pd.DataFrame:
"""Reproduce `build_bn`'s column reduction so one template covers all bootstraps.
The patterns must be the same ones `build_bn` will be called with. If they
are not, this function and `build_bn` disagree about which columns are
outcomes, the template ends up describing a different set of variables
than the learner is given, and `BNLearner` raises.
"""
excluded = [v for k in exclude_layers for v in layer_map.get(k, [])]
outcome_all, dropout_all = collect_outcome_vars(
layer_map, outcome_patterns=outcome_patterns, dropout_patterns=dropout_patterns,
)
drop_outcomes = [v for v in outcome_all + dropout_all if v not in outcomes_for_learning]
return df.drop(columns=drop_outcomes + excluded, errors="ignore")

bn_utils.py at commit fd5d083, under MIT · at the source

Overview

Authors: L. Malin Overmars¹, Cor Allaart^2,3, Esther E. Bron⁴, Hans-Peter Brunner La Rocca⁵, Jeroen de Bresser⁶, Majon Muller⁷, Matthias J.P. van Osch⁶, Charlotte Teunissen⁸, Betty M Tijms⁹, Frank J. Wolters^4,10, Geert Jan Biessels¹

ORCID iDs: L. Malin Overmars, Charlotte Teunissen, Betty M Tijms, Frank J. Wolters, Geert Jan Biessels

Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
Department of Cardiology, Institute for Cardiovascular Research, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
Department of Cardiology, Radboud University Medical Center, Radboud University, Nijmegen, The Netherlands
Department of Radiology and Nuclear Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, Maastricht, the Netherlands
Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
Department of Internal Medicine, Section Geriatrics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
Department of Clinical Chemistry, Neurochemistry Laboratory, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
Alzheimer Center Amsterdam, Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, the Netherlands

Institutions: University Medical Center Utrecht (Netherlands); Amsterdam University Medical Centers (Netherlands); Vrije Universiteit Amsterdam (Netherlands); Radboud University Medical Center (Netherlands); Radboud University Nijmegen (Netherlands); Erasmus MC (Netherlands); Maastricht University Medical Centre (Netherlands); Leiden University Medical Center (Netherlands); Amsterdam Neuroscience (Netherlands)

Journal: medRxiv (preprint)

Dates: published online 4 June 2026

Type: Preprint

License: CC BY-NC-ND

Identifiers: DOI 10.64898/2026.06.03.26354793 · OpenAlex W7163507635

Open access: green, a free copy (OpenAlex)

Status: code verified

Categories: human (organism), Alzheimer's / dementia (population), stroke (population), clinical / translational (subfield)

Methods: Connectivity, Machine learning, Statistics

Keywords: Vascular cognitive impairment, Small vessel disease, BN, Prognosis, Explainability

Topic: Dementia and Cognitive Impairment Research (Psychiatry and Mental health, Medicine), according to OpenAlex

Funding: ZonMw (10510032120003)

Citations: not cited yet (Europe PMC); 40 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

umcu/vci-bayes

License: MIT

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: fd5d083d2d20afde79d57d6c88e5c4e1017eece4, 24 August 2026

Languages: Python (19), Jupyter (1)

Size: 32 files, 20 scripts

Software Heritage: not archived

Found in: “Data Availability Statement”

Holds: README, license file, CITATION.cff, environment (pyproject.toml), tests, continuous integration, documentation, 1 notebook

Tools: pandas (8 files), NumPy (4 files), Matplotlib (1 file), scikit-learn (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

22 files

layerbn/__init__.py, Python, 38 lines
layerbn/__main__.py, Python, 139 lines
layerbn/analysis.py, Python, 767 lines
layerbn/bn_utils.py, Python, 648 lines, 1 match
layerbn/config.py, Python, 169 lines
layerbn/demo.py, Python, 186 lines
layerbn/discretisation.py, Python, 98 lines
layerbn/inference.py, Python, 84 lines
layerbn/plotting.py, Python, 157 lines
layerbn/preprocess.py, Python, 112 lines
layerbn/spec.py, Python, 805 lines
layerbn/templates/analysis.ipynb, Jupyter, 341 lines
tests/__init__.py, Python, 1 line
tests/conftest.py, Python, 73 lines
tests/test_cli.py, Python, 93 lines
tests/test_config.py, Python, 69 lines
tests/test_learning.py, Python, 201 lines
tests/test_notebook.py, Python, 94 lines
tests/test_reproducibility.py, Python, 92 lines
tests/test_spec.py, Python, 160 lines
LICENSE, License, 21 lines
README.md, Text, 272 lines

At the source: github.com/umcu/vci-bayes

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
20 scripts, each with its path and the digest of its content;
1 match between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

it points to the authors' code: umcu/vci-bayes
it says that the data are available on request

Read it in the paper: doi.org/10.64898/2026.06.03.26354793.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

Authors: added L. Malin Overmars (0000-0001-7086-0864); Geert Jan Biessels (0000-0001-6862-2496); removed L. Malin Overmars; Geert Jan Biessels

Version 1, 27 September 2026: the first record

Recorded: type, journal, dates, 11 authors, 5 keywords, 1 funder, 36 references.

Cite

This paper

Overmars, L. M., Allaart, C., Bron, E. E., Brunner La Rocca, H.-P., de Bresser, J., Muller, M., van Osch, M. J., Teunissen, C., Tijms, B. M., Wolters, F. J., & Biessels, G. J. (2026). Bayesian networks to estimate prognosis in vascular cognitive impairment and small vessel disease: integrated analyses of interdependent contributors to multiple outcomes. medRxiv (preprint). https://doi.org/10.64898/2026.06.03.26354793

BibTeX

@article{overmars2026bayesian, author = {Overmars, L. Malin and Allaart, Cor and Bron, Esther E. and Brunner La Rocca, Hans-Peter and de Bresser, Jeroen and Muller, Majon and van Osch, Matthias J.P. and Teunissen, Charlotte and Tijms, Betty M and Wolters, Frank J. and Biessels, Geert Jan}, title = {{Bayesian networks to estimate prognosis in vascular cognitive impairment and small vessel disease: integrated analyses of interdependent contributors to multiple outcomes}}, journal = {medRxiv (preprint)}, year = {2026}, month = jun, publisher = {medRxiv}, doi = {10.64898/2026.06.03.26354793}, url = {https://doi.org/10.64898/2026.06.03.26354793} }

RIS

TY - JOUR AU - Overmars, L. Malin AU - Allaart, Cor AU - Bron, Esther E. AU - Brunner La Rocca, Hans-Peter AU - de Bresser, Jeroen AU - Muller, Majon AU - van Osch, Matthias J.P. AU - Teunissen, Charlotte AU - Tijms, Betty M AU - Wolters, Frank J. AU - Biessels, Geert Jan TI - Bayesian networks to estimate prognosis in vascular cognitive impairment and small vessel disease: integrated analyses of interdependent contributors to multiple outcomes T2 - medRxiv (preprint) J2 - medRxiv PY - 2026 DA - 2026/06/04 PB - medRxiv DO - 10.64898/2026.06.03.26354793 UR - https://doi.org/10.64898/2026.06.03.26354793 ER -

CSL-JSON

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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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