initialize and template new class for interactions between genes

src/dialect/models/interaction.py

@@ -0,0 +1,50 @@
+import logging
+import numpy as np
+from scipy.optimize import minimize
+
+from dialect.models.gene import Gene
+
+
+class Interaction:
+    def __init__(self, gene_a, gene_b):
+        """
+        Initialize an Interaction object to represent the interaction between two genes.
+
+        :param gene_a (Gene): The first gene in the interaction.
+        :param gene_b (Gene): The second gene in the interaction.
+        """
+        if not isinstance(gene_a, Gene) or not isinstance(gene_b, Gene):
+            raise ValueError("Both inputs must be instances of the Gene class.")
+
+        self.gene_a = gene_a
+        self.gene_b = gene_b
+        self.name = f"{gene_a.name}:{gene_b.name}"  # Interaction name
+        self.tau_00 = None  # P(D = 0, D' = 0) for genes A and B
+        self.tau_01 = None  # P(D = 0, D' = 1) for genes A and B
+        self.tau_10 = None  # P(D = 1, D' = 0) for genes A and B
+        self.tau_11 = None  # P(D = 1, D' = 1) for genes A and B
+
+    # ---------------------------------------------------------------------------- #
+    #                        Likelihood & Metric Evaluation                        #
+    # ---------------------------------------------------------------------------- #
+
+    # Placeholder for methods to compute interaction-specific metrics (e.g., likelihood ratio)
+    # def compute_log_likelihood(self):
+    #     pass
+    #
+    # def compute_likelihood_ratio(self):
+    #     pass
+    #
+    # def compute_log_odds_ratio(self):
+    #     pass
+
+    # ---------------------------------------------------------------------------- #
+    #                         Parameter Estimation Methods                         #
+    # ---------------------------------------------------------------------------- #
+
+    # Placeholder for methods to estimate interaction parameters
+    # def estimate_interaction_with_optimization(self):
+    #     pass
+    #
+    # def estimate_interaction_with_em(self):
+    #     pass