Chronological Diagnostic Algorithm Predicting Neuropathology in Parkinsonism.
The 2 matches
- [1] § Results › Progression of the Diseases ↔ chronognosis/chronognosis.py, lines 130–189 · score 0.78 · sleep behavior disorder, upper motor neuron, eye movement, hyposmia, postural, RBD
- [2] § Results › Progression of the Diseases ↔ chronognosis/chronognosis.py, lines 130–189 · score 0.72 · sleep behavior disorder, upper motor neuron, eye movement, UMN, postural, RBD
Paper
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The authors' code
Python · 263 lines · 13 KB · Apache-2.0 · 2 matches
- import os
- import warnings
- import pandas as pd
- import shap
- from catboost import CatBoostClassifier, Pool
- # Suppress warnings
- warnings.simplefilter('ignore')
- def main(root, input_path, yr_th):
- dx_list = [
- 'LBD', 'LBD-AD', 'PSP', 'PSP-AD', 'PSP-LBD', 'MSA', 'CBD', 'AD', 'FTLD'
- ]
- label_dict = {label: idx for idx, label in enumerate(dx_list)}
- int_dict = {value: key for key, value in label_dict.items()}
- rename_dict = {
- 'Age_onset': 'Age at onset (yr)',
- 'EOMI_onset': 'EOM restriction',
- 'hypomimia_onset': 'Hypomimia',
- 'masked_face_onset': 'Masked face',
- 'bradykinesia_onset': 'Bradykinesia',
- 'slow_movement_onset': 'Slow movement',
- 'decreased_arm_swing_onset': 'Decreased arm swing',
- 'micrographia_onset': 'Micrographia',
- 'small_handwrtiting_onset': 'Small handwrtiting',
- 'akinesia_onset': 'Akinesia',
- 'no_spontaneous_movements_onset': 'No spontaneous movements',
- 'gait_freezing_onset': 'Gait freezing',
- 'glued_gait_onset': 'Glued gait',
- 'magnetic_gait_onset': 'Magnetic gait',
- 'rigidity_onset': 'Rigidity',
- 'axial_rigidity_onset': 'Axial rigidity',
- 'nuchal__neck__rigidity_onset': 'Nuchal neck rigidity',
- 'appendicular__limb__rigidity_onset': 'Appendicular limb rigidity',
- 'cogwheel_rigidity_onset': 'Cogwheel rigidity',
- 'stiffness_onset': 'Stiffness',
- 'increased_muscle_tone_onset': 'Increased muscle tone',
- 'the_fact_patient_fell__not_risk_of_fall_onset': 'Fall',
- 'early_falls_onset': 'Early falls',
- 'multiple_frequent_falls_onset': 'Multiple frequent falls',
- 'falling_forwards_onset': 'Falling forwards',
- 'positive_pull_test_onset': 'Positive pull test',
- 'falling_backwards_onset': 'Falling backwards',
- 'imbalance_onset': 'Imbalance',
- 'shuffling_gait_onset': 'Shuffling gait',
- 'festinating_gait_onset': 'Festinating gait',
- 'turning_en_bloc_onset': 'Turning en bloc',
- 'stooped_posture_onset': 'Stooped posture',
- 'pisa_sign_onset': 'Pisa sign',
- 'camptocormia_onset': 'Camptocormia',
- 'scoliosis_onset': 'Scoliosis',
- 'memory_loss__deficit_onset': 'Memory loss deficit',
- 'memory_loss_deficit_benefited_by_cues_onset': 'Memory loss deficit benefited by cues',
- 'amnesia_onset': 'Amnesia',
- 'word_finding_difficulty_onset': 'Word finding difficulty',
- 'dysorientation_onset': 'Disorientation',
- 'lost_date_onset': 'Lost date',
- 'lost_name_onset': 'Lost name',
- 'lost_place_onset': 'Lost place',
- 'impaired_serial_sevens_onset': 'Impaired serial sevens',
- 'abnormal_clock_test_onset': 'Abnormal clock test',
- 'impaired_spelling_WORLD_backwards_onset': 'Impaired spelling world backwards',
- 'wander_onset': 'Wander',
- 'gets_lost_onset': 'Gets lost',
- 'prosopagnosia_onset': 'Prosopagnosia',
- 'unable_to_answer_famous_faces_onset': 'Unable to answer famous faces',
- 'fluctuation_of_neuropsychiatric_symptoms_onset': 'Fluctuation of neuropsychiatric symptoms',
- 'sundowning_onset': 'Sundowning',
- 'hallucinations_onset': 'Hallucinations',
- 'visual_hallucinations_onset': 'Visual hallucinations',
- 'paranoid_delusions_onset': 'Paranoid delusions',
- 'apathy_onset': 'Apathy',
- 'social_withdrawal_onset': 'Social withdrawal',
- 'abulia_onset': 'Abulia',
- 'bradyphrenia_onset': 'Bradyphrenia',
- 'dysececutive_syndrome_onset': 'Dysexecutive syndrome',
- 'change_in_personality_onset': 'Change in personality',
- 'disinhibition_onset': 'Disinhibition',
- 'impulsivity_onset': 'Impulsivity',
- 'obsession_onset': 'Obsession',
- 'compulsivity_onset': 'Compulsivity',
- 'hyperorality_onset': 'Hyperorality',
- 'abnormally_increased_appetite_onset': 'Abnormally increased appetite',
- 'hyperphagia_onset': 'Hyperphagia',
- 'perseveration_onset': 'Perseveration',
- 'echolalia_onset': 'Echolalia',
- 'palilalia_onset': 'Palilalia',
- 'groping_onset': 'Groping',
- 'speaking_out_of_turn_onset': 'Speaking out of turn',
- 'stereotyped_behavior_onset': 'Stereotyped behavior',
- 'joking_jovial_behavior_onset': 'Joking jovial behavior',
- 'kleptomania_stealing_onset': 'Kleptomania stealing',
- 'cussing_behavior_onset': 'Cussing behavior',
- 'hypersexuality_onset': 'Hypersexuality',
- 'caught_in_a_scam_fraud_onset': 'Caught in a scam fraud',
- 'gambling_onset': 'Gambling',
- 'addiction_abuse_onset': 'Addiction abuse',
- 'Baker_acted_onset': 'Baker acted',
- 'suicidal_ideation_onset': 'Suicidal ideation',
- 'criminal_behavior_onset': 'Criminal behavior',
- 'hospitalized_in_psychiatric_ward_asylum_onset': 'Hospitalized in psychiatric ward asylum',
- 'positive_grasping_reflex_onset': 'Positive grasping reflex',
- 'positive_snout_reflex_onset': 'Positive snout reflex',
- 'positive_sucking_reflex_onset': 'Positive sucking reflex',
- 'positive_palmomental_reflex_onset': 'Positive palmomental reflex',
- 'frontal_release_sign_onset': 'Frontal release sign',
- 'gegenhalten_onset': 'Gegenhalten',
- 'paratonia_onset': 'Paratonia',
- 'abnormal_Luria_test_onset': 'Abnormal luria test',
- 'abnormal_fist_edge_palm_test_onset': 'Abnormal fist edge palm test',
- 'applause_sign_onset': 'Applause sign',
- 'abnormal_go_no_go_test_onset': 'Abnormal go no go test',
- 'stopped_driving_onset': 'Stopped driving',
- 'car_accident_onset': 'Car accident',
- 'metamorphosis_onset': 'Metamorphosis',
- 'loss_of_appetite_onset': 'Loss of appetite',
- 'cries_a_lot_onset': 'Cries a lot',
- 'aphasia_primary_progressive_aphasia__PPA__onset': 'Aphasia primary progressive aphasia (PPA)',
- 'agrammatic_aphasia_onset': 'Agrammatic aphasia',
- 'reduced_fluency_onset': 'Reduced fluency',
- 'apraxia_of_speech_onset': 'Apraxia of speech',
- 'abnormal_articulation_pronunciation_onset': 'Abnormal articulation pronunciation',
- 'jumbled_speech_onset': 'Jumbled speech',
- 'spasmodic_speech_dysphornia_onset': 'Spasmodic speech dysphonia',
- 'mutism_onset': 'Mutism',
- 'alien_hand_or_limb_onset': 'Alien hand or limb',
- 'orobuccal_apraxia_onset': 'Orobuccal apraxia',
- 'apraxia_onset': 'Apraxia',
- 'ideomotor_apraxia_onset': 'Ideomotor apraxia',
- 'cannot_pantomime_onset': 'Cannot pantomime',
- 'limb_apraxia_onset': 'Limb apraxia',
- 'unable_to_stick_out_tongue_onset': 'Unable to stick out tongue',
- 'unable_to_lick_lips_onset': 'Unable to lick lips',
- 'unable_to_wristle_onset': 'Unable to whistle',
- 'simultanagnosia_onset': 'Simultanagnosia',
- 'cortical_sensory_deficit_onset': 'Cortical sensory deficit',
- 'REM_sleep_behavior_disorder__RBD__onset': 'RBD',
- 'hyposmia_onset': 'Hyposmia',
- 'loss_of_smell_onset': 'Loss of smell',
- 'restricted_eye_movement_gaze_palsy_onset': 'Restricted eye movement gaze palsy',
- 'vertical_hypometric_saccades_onset': 'Vertical hypometric saccades',
- 'downgaze_palsy_onset': 'Downgaze palsy',
- 'slow_saccades_onset': 'Slow saccades',
- 'eyelid_opening_apraxia_onset': 'Eyelid opening apraxia',
- 'blepharospasm_onset': 'Blepharospasm',
- 'photophobia_onset': 'Photophobia',
- 'ataxia_onset': 'Ataxia',
- 'hypermetric_saccades_onset': 'Hypermetric saccades',
- 'saccadic_hypormetria__onset': 'Saccadic hypometria ',
- 'overshoot_onset': 'Overshoot',
- 'scanned_speech_onset': 'Scanned speech',
- 'dysmetria_onset': 'Dysmetria',
- 'hypermetria_onset': 'Hypermetria',
- 'abnormal_finger_to_nose_onset': 'Abnormal finger to nose',
- 'abnormal_heel_to_shin_onset': 'Abnormal heel to shin',
- 'positive_or_abnormal_Romberg_sign_onset': 'Abnormal Romberg sign',
- 'square_wave_jerks_onset': 'Square wave jerks',
- 'nystagmus_onset': 'Nystagmus',
- 'dysdiadochokinesis_onset': 'Dysdiadochokinesis',
- 'unable_to_walk_a_line_onset': 'Unable to walk a line',
- 'unable_to_perform_tandem_gait_onset': 'Unable to perform tandem gait',
- 'involuntary_movement_onset': 'Involuntary movement',
- 'chorea_writhing_onset': 'Chorea writhing',
- 'athetosis_onset': 'Athetosis',
- 'dyskinesia_onset': 'Dyskinesia',
- 'hemifacial_spasm_onset': 'Hemifacial spasm',
- 'myokimia_onset': 'Myokimia',
- 'shaking_onset': 'Shaking',
- 'tremor_onset': 'Tremor',
- 'tremor_at_rest_onset': 'Tremor at rest',
- 'postural_tremor_onset': 'Postural tremor',
- 'kinetic_tremor_onset': 'Kinetic tremor',
- 'essential_tremor__ET__onset': 'Essential tremor et ',
- 'jaw_chin_tremor_onset': 'Jaw chin tremor',
- 'myoclonus_onset': 'Myoclonus',
- 'cortical_myoclonus_onset': 'Cortical myoclonus',
- 'limb_myoclonus_onset': 'Limb myoclonus',
- 'facial_myoclonus_onset': 'Facial myoclonus',
- 'finger_myoclonus_onset': 'Finger myoclonus',
- 'polyminimyoclonus_onset': 'Polyminimyoclonus',
- 'dystonia_onset': 'Dystonia',
- 'antecollis_onset': 'Antecollis',
- 'retrocollis_onset': 'Retrocollis',
- 'clenched_fist_onset': 'Clenched fist',
- 'hand_dystonia_onset': 'Hand dystonia',
- 'foot_dystonia_onset': 'Foot dystonia',
- 'upper_motor_neuron__UMN__signs_onset': 'Upper motor neuron umn signs',
- 'pseudobulbar_palsy_onset': 'Pseudobulbar palsy',
- 'inappropriate_pathological_laughter_onset': 'Inappropriate pathological laughter',
- 'inappropriate_pathological_crying_onset': 'Inappropriate pathological crying',
- 'hyperreflexia_onset': 'Hyperreflexia',
- 'positive_Hoffmann_sign_reflex_onset': 'Positive hoffmann sign reflex',
- 'positive_extensor_upgoing__not_absent_flexor_downgoing__Babinski_sign_reflex_onset': 'Babinski sign',
- 'positive_extensor_upgoing__not_absent_flexor_downgoing__plantar_reflex_onset': 'Abnormal plantar reflex',
- 'spasticity_onset': 'Spasticity',
- 'lower_motor_neuron__LMN__signs_onset': 'Lower motor neuron lmn signs',
- 'fasciculations_onset': 'Fasciculations',
- 'tongue_atrophy_onset': 'Tongue atrophy',
- 'dysarthria_onset': 'Dysarthria',
- 'dysphasia_onset': 'Dysphasia',
- 'swallowing_difficulty_onset': 'Swallowing difficulty',
- 'aspiration_onset': 'Aspiration',
- 'PEG_feeding_tube_inserstion_onset': 'PEG/feeding tube insertion',
- 'stridor_onset': 'Stridor',
- 'lightheaded_dizziness_onset': 'Lightheadedness dizziness',
- 'orthostatic_hypotension_onset': 'Orthostatic hypotension',
- 'urinary_dysfunction_onset': 'Urinary dysfunction',
- 'urinary_incontinence_onset': 'Urinary incontinence',
- 'urinary_catheter_onset': 'Urinary catheter',
- 'urinary_tract_infection__UTI__onset': 'Urinary tract infection (UTI) ',
- 'erectile_dysfunction__ED__onset': 'Erectile dysfunction (ED)',
- 'abnormal_sweat_onset': 'Abnormal sweat',
- 'cold_discolored_hands_feet_onset': 'Cold discolored hands feet',
- 'improvement_with_l_dopa__levodopa_or_simenet_onset': 'L-dopa responsiveness',
- 'Sex_M': 'Sex (male=1, female=0)',
- 'FHx_Yes': 'FHx (yes=1, no=0)',
- 'FHx_adopted': 'FHx (adopted=1)'
- }
- filename = os.path.basename(input_path).split('.')[0]
- save_dir = f'{root}/results/{filename}'
- os.makedirs(save_dir, exist_ok=True)
- weight_path = f'{root}/weights/catboost_model_{yr_th}_yr.cbm'
- model_loaded = CatBoostClassifier(iterations=1000, learning_rate=0.1, depth=6, verbose=False)
- model_loaded.load_model(weight_path)
- # Load and preprocess input
- input_data = pd.read_excel(input_path, index_col='index').sort_index()
- input_data.index = rename_dict.keys()
- X_case = input_data['onset'].to_frame().T.fillna(50)
- X_pool = Pool(X_case, feature_names=list(X_case.columns))
- # Calculate SHAP values
- shap_values = model_loaded.get_feature_importance(X_pool, type="ShapValues")
- # pred_th = model_loaded.predict_proba(input_data['onset'])
- pred_th = model_loaded.predict_proba(input_data['onset'].fillna(50))
- indices_desc = sorted(range(len(pred_th)), key=lambda i: pred_th[i], reverse=True)
- sample_index = 0
- for class_index in indices_desc:
- print(int_dict[class_index], f'Prob:{pred_th[class_index]:.02f}')
- shap_values_sample = shap_values[sample_index, class_index, :-1]
- base_value = shap_values[sample_index, class_index, -1]
- # Force Plot visualization
- force_plot = shap.force_plot(
- base_value,
- shap_values_sample,
- X_case.iloc[sample_index, :].round(1),
- feature_names=list(rename_dict.values()),
- )
- display(force_plot)
- # Save Force Plot as HTML
- prob_str = f"{pred_th[class_index]:.02f}".replace('.', '')
- shap.save_html(f"{save_dir}/Prob_{prob_str}_{int_dict[class_index]}.html", force_plot)
- if __name__ == '__main__':
- root = "path_to_root" # Replace with the actual root path
- input_path = "path_to_input.xlsx" # Replace with the actual input path
- main(root, input_path, yr_th=3)
chronognosis.py at commit bdac5b4, under Apache-2.0 · at the source
Overview
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
- Department of Neurology and Neurological Science, Institute of Science – Tokyo, Tokyo, Japan
- School of Statistical Thinking, The Institute of Statistical Mathematics, Tokyo, Japan
- Department of Neurology, Mayo Clinic, Jacksonville, FL
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
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onnonuro/chronognosis
bdac5b43a9f05aff514960dab6b12959c7aaddf7, 6 January 2026Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
6 files
- chronognosis/
__init__.py , Python, 3 lines - chronognosis/
chronognosis.py , Python, 263 lines, 2 matches - setup.py, Python, 14 lines
- tutorial.ipynb, Jupyter, 35 lines
- LICENSE, License, 201 lines
- README.md, Text, 73 lines
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Version 1, 30 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 12 MeSH terms, 3 funders, 45 references.
Cite
This paper
Ono, D., Sekiya, H., Maier, A. R., Graff‐Radford, N. R., Wszolek, Z. K., & Dickson, D. W. (2026). Chronological Diagnostic Algorithm Predicting Neuropathology in Parkinsonism. Annals of neurology, 99(6), 1405-1414. https://
BibTeX
@article{ono2026chronolo
author = {Ono, Daisuke and Sekiya, Hiroaki and Maier, Alexia R and Graff‐Radford, Neill R and Wszolek, Zbigniew K and Dickson, Dennis W},
title = {{Chronological Diagnostic Algorithm Predicting Neuropathology in Parkinsonism}},
journal = {Annals of neurology},
year = {2026},
month = mar,
volume = {99},
number = {6},
pages = {1405--1414},
publisher = {Wiley},
issn = {0364-5134},
doi = {10.1002/
url = {https://
pmid = {41830446},
pmcid = {PMC13206486}
}
RIS
TY - JOUR
AU - Ono, Daisuke
AU - Sekiya, Hiroaki
AU - Maier, Alexia R
AU - Graff‐Radford, Neill R
AU - Wszolek, Zbigniew K
AU - Dickson, Dennis W
TI - Chronological Diagnostic Algorithm Predicting Neuropathology in Parkinsonism
T2 - Annals of neurology
J2 - Ann Neurol
PY - 2026
DA - 2026/
VL - 99
IS - 6
SP - 1405
EP - 1414
SN - 0364-5134
PB - Wiley
DO - 10.1002/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1002/
"type": "article-journal",
"title": "Chronological Diagnostic Algorithm Predicting Neuropathology in Parkinsonism",
"container-title": "Annals of neurology",
"author": [
{
"family": "Ono",
"given": "Daisuke"
},
{
"family": "Sekiya",
"given": "Hiroaki"
},
{
"family": "Maier",
"given": "Alexia R"
},
{
"family": "Graff‐Radford",
"given": "Neill R"
},
{
"family": "Wszolek",
"given": "Zbigniew K"
},
{
"family": "Dickson",
"given": "Dennis W"
}
],
"container-title-short":
"volume": "99",
"issue": "6",
"page": "1405-1414",
"DOI": "10.1002/
"PMID": "41830446",
"PMCID": "PMC13206486",
"ISSN": "0364-5134",
"publisher": "Wiley",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
14
]
]
}
}
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