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https://github.com/joseruiz01/mlranking

Listwise Machine Learning model to rank medical documents based on a query
https://github.com/joseruiz01/mlranking

listwise machine-learning-algorithms medical-documents query ranking-algorithm

Last synced: 3 months ago
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Listwise Machine Learning model to rank medical documents based on a query

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README 

        
# **Listwise Learning to Rank (LTR) for Lab Test Ranking**  

Listwise Learning to Rank (LTR) optimizes the **entire ranking order** for a given query, rather than comparing individual items (Pointwise) or pairs (Pairwise). This is particularly useful for ranking **lab tests** based on their relevance to queries like *"glucose in blood"*, *"bilirubin in plasma"*, and *"white blood cells count"*.  



---



## **Step 1: Define the Listwise LTR Model**  

Listwise LTR models learn a *ranking function* that orders a list of items to maximize evaluation metrics like *NDCG (Normalized Discounted Cumulative Gain)*.



1. **Input**: A list of lab test results (documents) for a query.  

2. **Scoring Function**: A machine learning model predicts a *relevance score* for each test result.  

3. **Loss Function**: The model optimizes the ranking order using a loss function such as:

   - **eXtreme NDCG** (variant of the *Normalized Discounted Cumulative Gain (NDCG)* metric, designed to optimize ranking models directly)  

   - **LambdaRank** (optimizes for NDCG directly)  

4. **Output**: A ranked list of test results for the query.  



---



## **Step 2: Data Preparation**  

We implement a method for calculating relevance scores for lab tests based on a given query. The query consists of two main features: the *component* (e.g., "Glucose") and the *system* (e.g., "Blood"). 



### **1. Define Key Query Features**

   The query is parsed into two primary elements:

   - **Component**: The substance being measured (e.g., "Glucose").

   - **System**: The environment where the measurement takes place (e.g., "Blood").



### **2. Preprocess the Data**

   Each lab test in the dataset contains:

   - **Component**: The substance being measured (e.g., "Glucose").

   - **System**: The location or context of the test (e.g., "Blood", "Serum/Plasma").



### **3. Match Criteria**  

   To calculate the relevance score for each test:

   - **Exact Match**: The component or system exactly matches the query term (e.g., "Glucose" matches "Glucose").

   - **Partial Match**: The component or system contains terms closely related or synonymous to the query (e.g., "Glucose in Urine" partially matches "Glucose").

   - **System Match**: The system field matches the query's system (e.g., "Blood" matches "Blood").



### **4. Scoring Scheme**

   Points are awarded based on the match type:

   - **Exact Match on Component**:  weight(component) * weight(component)

   - **Partial Match on Component**: weight(component)/2 * weight(component)

   - **Exact Match on System**: weight(system) * weight(system)

   - **Partial Match on System**: weight(system)/2 * weight(system)

   - **No Match**: 0 points.



### **5. Normalize Scores**

   To standardize the scores across tests, normalize them to a scale (e.g., from 0 to 1). For example, if the highest score in the dataset is 5, the formula to normalize is:  

   - **Normalized Score** = \( score \ max_score \).



   By following this method, each test is assigned a relevance score based on how well it matches the query's component and system. This system can be adjusted by fine-tuning the scoring weights to better suit specific applications and queries.



### **6. Save the new CSV**

   Save into a new *CSV* file the data with the calculated scores and features to train the model.



---



## **Step 3: Implementing the Listwise LTR Model**  



We use *LightGBM*, which is fast, supports listwise ranking, and is easy to implement.



### **1. Dataset Prepraration**  

   Before training, we need to format our dataset appropriately for LightGBM:

   - Read the data from the *CSV* file with scores.

   - Categorical columns (`Query`, `Name`, `Component`, `System`, `Property`, `Measurement`) are encoded numerically.

   - A `Score_label` is created from the `Normalized_Score` to serve as the target variable.

   - Data is split into *train_dataset* and *test_dataset*.



### **2. LightGBM Dataset Setup**   

   - **Features:** Encoded categorical columns.

   - **Grouping:** Rows are grouped by `Query` to support listwise ranking.

   - **Labels:** `Score_label` is the target for learning.



### **3. Train the Model**  

   Since `LightGBM` doesn’t directly support *AdaRank*, we simulate its boosting and reweighting mechanism.

   - **Objective:** `rank_xendcg` (listwise ranking).

   - **Parameters:** We set and modified different parameters of the `LightGBM` base model to reach an optimal solution.\



### **5. Prediction**

   - Predictions are scaled between 0 and 1.

   - Results are sorted by `Query` and `Predicted Score` and saved to `results.csv`.



---



## **Step 4: Enhancing the Dataset**  

To improve the model *NDCG* metric, we enhance the dataset with more *features*, *data* and *expanded queries*.



### **1. Expanding Queries**  

   We extended the dataset with two more queries appart from the first three included in the excel. 



   - Firstly, we introduced the query '`calcium in serum` and continue to do experiments with it and variations of the query.

   - Finally, we extended again including `cells in urine` and variation of the query to add more variety to the dataset.



### **2. Expanding Dataset**

   To cover more search variations, we added *custom queries* into the *LOINC Search* tool and downloaded *CSV* files with the documents retrieved.

   

   We did several experiments, including documents results for the following queries:

   - bilirubin in plasma

   - bilirubin 

   - plasma or serum

   - calcium in serum

   - calcium

   - glucose in blood

   - glucose

   - blood

   - leukocytes

   - white blood cells count

   - cells in urine

   - cells

   - urine



## **3. Evaluating the Model**  

   These are the following **Metrics** performed to evaluate the Model:

   - **MSE** (Mean Squared Error): *Lower* values are better [0, ∞], indicating less error between predictions and actual scores

   - **R²** (R-squared score): *Higher* values are better [-∞, 1], showing how well the model explains the variance in data

   - **Spearman's Correlation**: *Higher* values are better [-1, 1], indicate a strong monotonic relationship between predicted and actual rankings.

   - **NDCG** (Normalized Discounted Cumulative Gain): *Higher* values are better [0, 1], reflecting how well the model ranks items compared to an ideal ranking



   **3.1. Basic Dataset:** Basic excel.

   - Mean Squared Error (MSE): 0.1642

   - R-squared (R²): -2.5187

   - Spearman's Rank Correlation: 0.7265

   - NDCG Mean Score: 0.9086

      - NDCG for 'bilirubin in plasma': 0.8360

      - NDCG for 'glucose in blood': 0.9584

      - NDCG for 'white blood cells count': 0.9313



   **3.2. First Enhanced Dataset:** 4 basic queries.

   - Mean Squared Error (MSE): 0.0479

   - R-squared (R²): -1.9010

   - Spearman's Rank Correlation: 0.4700

   - NDCG Mean Score: 0.8533

      - NDCG for 'bilirubin in plasma': 0.8916

      - NDCG for 'calcium in serum': 0.9431

      - NDCG for 'glucose in blood': 0.6946

      - NDCG for 'white blood cells count': 0.8838



   **3.3. Second Enhanced Dataset:** Included variations `bilirubin`, `calcium`, `glucose` and `leukocytes`.

   - Mean Squared Error (MSE): 0.0461

   - R-squared (R²): -0.8984

   - Spearman's Rank Correlation: 0.6024

   - NDCG Mean Score: 0.9421

      - NDCG for 'bilirubin in plasma': 0.9287

      - NDCG for 'calcium in serum': 0.9338

      - NDCG for 'glucose in blood': 0.9383

      - NDCG for 'white blood cells count': 0.9678



   **3.4. Third Enhanced Dataset:** Included variations `blood` and `serum or plasma`.

   - Mean Squared Error (MSE): 0.0252

   - R-squared (R²): -0.4765

   - Spearman's Rank Correlation: 0.4983

   - NDCG Mean Score: 0.9398

      - NDCG for 'bilirubin in plasma': 0.9326

      - NDCG for 'calcium in serum': 0.9494

      - NDCG for 'glucose in blood': 0.9381

      - NDCG for 'white blood cells count': 0.9391



   **3.5. Fourth Enhanced Dataset:** Included new query `cells in urine`.

   - Mean Squared Error (MSE): 0.0450

   - R-squared (R²): -1.4383

   - Spearman's Rank Correlation: 0.4323

   - NDCG Mean Score: 0.9448

      - NDCG for 'bilirubin in plasma': 0.9483

      - NDCG for 'calcium in serum': 0.9594

      - NDCG for 'cells in urine': 0.9277

      - NDCG for 'glucose in blood': 0.9435

      - NDCG for 'white blood cells count': 0.9451



   **3.6. Fifth Enhanced Dataset:**Included variations `cells` and `urine`.

   - Mean Squared Error (MSE): 0.0191

   - R-squared (R²): -0.6009

   - Spearman's Rank Correlation: 0.4615

   - NDCG Mean Score: 0.9517

      - NDCG for 'bilirubin in plasma': 0.9499

      - NDCG for 'calcium in serum': 0.9637

      - NDCG for 'cells in urine': 0.9448

      - NDCG for 'glucose in blood': 0.9663

      - NDCG for 'white blood cells count': 0.9339