Petkovich

Petkovich#

Index#

  1. Instantiate model class

  2. Define clock metadata

  3. Download clock dependencies

  4. Load features

  5. Load weights into base model

  6. Load reference values

  7. Load preprocess and postprocess objects

  8. Check all clock parameters

  9. Basic test

  10. Save torch model

  11. Clear directory

Let’s first import some packages:

[1]:

import os
import inspect
import shutil
import json
import torch
import pandas as pd
import pyaging as pya

Instantiate model class#

[2]:

def print_entire_class(cls):
    source = inspect.getsource(cls)
    print(source)

print_entire_class(pya.models.Petkovich)

class Petkovich(pyagingModel):
    def __init__(self):
        super().__init__()

    def preprocess(self, x):
        return x

    def postprocess(self, x):
        """
        Applies a convertion from the output of an ElasticNet to mouse age in months.
        """
        a = 0.1666
        b = 0.4185
        c = -1.712
        age = ((x - c) / a) ** (1 / b)
        age = age / 30.5  # days to months
        return age


[3]:

model = pya.models.Petkovich()

Define clock metadata#

[4]:

model.metadata["clock_name"] = 'petkovich'
model.metadata["data_type"] = 'methylation'
model.metadata["species"] = 'Mus musculus'
model.metadata["year"] = 2017
model.metadata["approved_by_author"] = '⌛'
model.metadata["citation"] = "Petkovich, Daniel A., et al. \"Using DNA methylation profiling to evaluate biological age and longevity interventions.\" Cell metabolism 25.4 (2017): 954-960."
model.metadata["doi"] = "https://doi.org/10.1016/j.cmet.2017.03.016"
model.metadata["research_only"] = None
model.metadata["notes"] = None

Download clock dependencies#

Download directly with curl#

[5]:

supplementary_url = "https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNDA2NzUvZWxpZmUtNDA2NzUtc3VwcDMtdjIueGxzeA--/elife-40675-supp3-v2.xlsx?_hash=qzOMc4yUFACfDFG%2FlgxkFTHWt%2BSXSmP9zz1BM3oOTRM%3D"
supplementary_file_name = "coefficients.xlsx"
os.system(f"curl -o {supplementary_file_name} {supplementary_url}")

[5]:

0

Load features#

From Excel file#

[6]:

df = pd.read_excel('coefficients.xlsx', sheet_name='Blood', nrows=90)
df['feature'] = df['Chromosome'].astype(str) + ':' + df['Position'].astype(int).astype(str)
df['coefficient'] = df['Weight']

model.features = df['feature'].tolist()

Load weights into base model#

[7]:

weights = torch.tensor(df['coefficient'].tolist()).unsqueeze(0)
intercept = torch.tensor([0.0])

Linear model#

[8]:

base_model = pya.models.LinearModel(input_dim=len(model.features))

base_model.linear.weight.data = weights.float()
base_model.linear.bias.data = intercept.float()

model.base_model = base_model

Load reference values#

[9]:

model.reference_values = None

Load preprocess and postprocess objects#

[10]:

model.preprocess_name = None
model.preprocess_dependencies = None

[11]:

model.postprocess_name = 'petkovich'
model.postprocess_dependencies = None

Check all clock parameters#

[12]:

pya.utils.print_model_details(model)


%==================================== Model Details ====================================%
Model Attributes:

training: True
metadata: {'approved_by_author': '⌛',
 'citation': 'Petkovich, Daniel A., et al. "Using DNA methylation profiling to '
             'evaluate biological age and longevity interventions." Cell '
             'metabolism 25.4 (2017): 954-960.',
 'clock_name': 'petkovich',
 'data_type': 'methylation',
 'doi': 'https://doi.org/10.1016/j.cmet.2017.03.016',
 'notes': None,
 'research_only': None,
 'species': 'Mus musculus',
 'version': None,
 'year': 2017}
reference_values: None
preprocess_name: None
preprocess_dependencies: None
postprocess_name: 'petkovich'
postprocess_dependencies: None
features: ['chr19:23893237', 'chr19:34746572', 'chr18:45589182', 'chr18:58836611', 'chr16:10502162', 'chr16:10502211', 'chr16:36990110', 'chr16:44812861', 'chr16:44812942', 'chr16:72663969', 'chr15:84756593', 'chr15:98780540', 'chr14:74978494', 'chr13:25850022', 'chr13:60687073', 'chr12:103214578', 'chr12:103214639', 'chr12:17993343', 'chr12:20196778', 'chr12:20196795', 'chr12:24252005', 'chr12:24252044', 'chr12:24252062', 'chr12:24252074', 'chr11:109011767', 'chr11:49978547', 'chr11:57832738', 'chr11:59283095', 'chr11:82930766', 'chr11:82930771']... [Total elements: 90]
base_model_features: None

%==================================== Model Details ====================================%
Model Structure:

base_model: LinearModel(
  (linear): Linear(in_features=90, out_features=1, bias=True)
)

%==================================== Model Details ====================================%
Model Parameters and Weights:

base_model.linear.weight: [0.013973841443657875, -0.208111971616745, -0.052282609045505524, 0.09845656156539917, 0.2287983000278473, 0.041504427790641785, -0.12888140976428986, -0.1270751655101776, -0.11876147240400314, 0.07533302158117294, 0.006506402976810932, 0.02291547879576683, -0.015255635604262352, -0.04044732078909874, -0.028440294787287712, -0.009072709828615189, -0.1302095651626587, 0.13603146374225616, 0.0851239338517189, 0.0067262169905006886, 0.20910842716693878, 0.006870004814118147, 0.06277254968881607, 0.03797502815723419, 0.1745307892560959, -0.09591705352067947, 0.05482637137174606, -0.08698525279760361, 0.016051754355430603, 0.13305535912513733]... [Tensor of shape torch.Size([1, 90])]
base_model.linear.bias: tensor([0.])

%==================================== Model Details ====================================%

Basic test#

[13]:

torch.manual_seed(42)
input = torch.randn(10, len(model.features), dtype=float)
model.eval()
model.to(float)
pred = model(input)
pred

[13]:

tensor([[50.8075],
        [27.5472],
        [ 1.1953],
        [ 6.6927],
        [17.1703],
        [24.9932],
        [15.8308],
        [ 1.1290],
        [ 3.4376],
        [ 0.0714]], dtype=torch.float64, grad_fn=<DivBackward0>)

Save torch model#

[14]:

torch.save(model, f"../weights/{model.metadata['clock_name']}.pt")

Clear directory#

[15]:

# Function to remove a folder and all its contents
def remove_folder(path):
    try:
        shutil.rmtree(path)
        print(f"Deleted folder: {path}")
    except Exception as e:
        print(f"Error deleting folder {path}: {e}")

# Get a list of all files and folders in the current directory
all_items = os.listdir('.')

# Loop through the items
for item in all_items:
    # Check if it's a file and does not end with .ipynb
    if os.path.isfile(item) and not item.endswith('.ipynb'):
        os.remove(item)
        print(f"Deleted file: {item}")
    # Check if it's a folder
    elif os.path.isdir(item):
        remove_folder(item)

Deleted file: coefficients.xlsx
Contents