Exercises · Day 5 (Optional) — Treatment Pathway Analysis
Sample notebook
Run the companion notebook in Colab (synthetic data, no credentials needed): 
or download it.
What you will do
- Define a target cohort (the population to trace) and at least three event cohorts (the treatments to track).
- Configure a Cohort Pathways analysis in ATLAS, including the combination window.
- Generate the analysis and interpret the sunburst plot and its tabular view.
- Adjust one parameter and compare the results.
Setup and extraction are site specific
These steps require a generated cohort in your ATLAS environment and access to a training CDM. ATLAS must be connected to a CDM that has the cohorts you created. The Colab notebook uses fully synthetic data if you need a CDM-free alternative.
Background: the example analysis
This exercise uses ALS medication sequences as the example, because:
- ALS has few medications, so the pathways are short and easy to read
- A second medication may be added to the first or started later, which shows how combinations are handled
- The Day 2 and Day 3 exercises already built the underlying concept sets and cohorts
Adapt to your own disease area by substituting your target condition and the relevant drugs.
Step 1: Assemble your cohorts
You need one target cohort and the event cohorts already created in your ATLAS instance.
Target cohort: - People with a motor neuron disease diagnosis (condition-based entry, using the Day 2 concept set)
Event cohorts (create or reuse from Day 2–3): - Riluzole (ingredient, include descendants) - Edaravone (ingredient, include descendants) - Any other ALS medication your site records, one cohort per ingredient
If you already have some of these concept sets from Day 2, build cohorts from them now. Set the entry to the first exposure and the exit to the end of continuous drug exposure with a persistence window (for example 30 days), because the exit rule is where the allowed gap between fills is set.
Step 2: Configure the pathway analysis
- In ATLAS, choose Cohort Pathways in the left menu, then New.
- Set the name:
TtT Day5 ALS medication pathways. - Add the target cohort you identified in Step 1.
- Add each event cohort and give it a short label (e.g., "Riluzole," "Edaravone").
- Configure analysis settings:
- Combination window (labeled Collapse Days in some ATLAS versions): 30 days (events that start within 30 days of each other are shown as a combination).
- Minimum cell count: 5 (paths with fewer people are not shown).
- Maximum path length: 5 (traces up to 5 steps per person).
- Allow repeats: off for the first run.
- Save and Generate against your training CDM.
Expected wait time
Pathway generation may take several minutes depending on cohort size and CDM complexity. Proceed with the Colab notebook while you wait.
Step 3: Interpret the sunburst plot
Once generation completes, open the Executions tab and choose View reports for that run.
Reading the Sunburst:
- The center circle = your entire target cohort.
- Ring 1 (innermost): the first event cohort each person entered. The size of the arc is proportional to the count, and clicking an arc shows the path with its count and percentage.
- Ring 2: the second step, branching from each first-step arc.
- Grey: the end of a pathway, meaning no further event cohort was observed during follow-up.
Questions to answer: 1. What is the most common first step? Is it what you expected to see? 2. After the most common first-line, what is the most common switch? Is it a switch or an add-on? 3. What fraction of the cohort has only one observable treatment step? 4. Hover over any arc — record the count and percentage.
Step 4: Read the tabular view
Click Tabular to see the same results as a table.
Questions to answer: 1. Which full sequence is followed by the most people, and by what percent of the target cohort? 2. Where do the sequences diverge most, at the first to second step or the second to third? 3. Identify one sequence that you did not expect. What might explain it, including data capture (for example infusions recorded as procedures, or medication supplied outside the health system)?
Step 5: Adjust one parameter and compare
Return to the pathway configuration and change one setting:
- Option A: Change the combination window (for example from 30 days to 1 day). Regenerate and compare: do combinations appear more or less often?
- Option B: Add or remove one event cohort. How do the sequences change?
- Option C: Restrict the target cohort to new users only (if not already done). Does the sequence pattern change?
Write one sentence per change explaining what changed and how it affects interpretation.
Homework
- Identify one real research question from your work that treatment pathway analysis could address.
- Write a brief (3–5 bullet) analysis plan: target cohort, event cohorts, key parameters you would choose, and what you would expect to see.
- Optional: try the Colab notebook and compare the synthetic pathway output to your ATLAS result.