First approximation to a DASM: 20 output dimensions but same loss

netam/dasm.py

@@ -0,0 +1,191 @@
+"""Here we define a mutation-selection model that is per-amino-acid."""
+
+import torch
+import torch.nn.functional as F
+
+# Amazingly, using one thread makes things 50x faster for branch length
+# optimization on our server.
+torch.set_num_threads(1)
+
+import numpy as np
+import pandas as pd
+
+from netam.common import (
+    clamp_probability,
+)
+import netam.dnsm as dnsm
+import netam.molevol as molevol
+import netam.sequences as sequences
+from netam.sequences import (
+    translate_sequence,
+)
+
+
+class DASMDataset(dnsm.DNSMDataset):
+
+    def update_neutral_probs(self):
+        neutral_aa_probs_l = []
+
+        for nt_parent, mask, rates, branch_length, subs_probs in zip(
+            self.nt_parents,
+            self.mask,
+            self.all_rates,
+            self._branch_lengths,
+            self.all_subs_probs,
+        ):
+            mask = mask.to("cpu")
+            rates = rates.to("cpu")
+            subs_probs = subs_probs.to("cpu")
+            # Note we are replacing all Ns with As, which means that we need to be careful
+            # with masking out these positions later. We do this below.
+            parent_idxs = sequences.nt_idx_tensor_of_str(nt_parent.replace("N", "A"))
+            parent_len = len(nt_parent)
+
+            mut_probs = 1.0 - torch.exp(-branch_length * rates[:parent_len])
+            normed_subs_probs = molevol.normalize_sub_probs(
+                parent_idxs, subs_probs[:parent_len, :]
+            )
+
+            neutral_aa_probs = molevol.neutral_aa_probs(
+                parent_idxs.reshape(-1, 3),
+                mut_probs.reshape(-1, 3),
+                normed_subs_probs.reshape(-1, 3, 4),
+            )
+
+            if not torch.isfinite(neutral_aa_probs).all():
+                print(f"Found a non-finite neutral_aa_probs")
+                print(f"nt_parent: {nt_parent}")
+                print(f"mask: {mask}")
+                print(f"rates: {rates}")
+                print(f"subs_probs: {subs_probs}")
+                print(f"branch_length: {branch_length}")
+                raise ValueError(f"neutral_aa_probs is not finite: {neutral_aa_probs}")
+
+            # Ensure that all values are positive before taking the log later
+            neutral_aa_probs = clamp_probability(neutral_aa_probs)
+
+            pad_len = self.max_aa_seq_len - neutral_aa_probs.shape[0]
+            if pad_len > 0:
+                neutral_aa_probs = F.pad(
+                    neutral_aa_probs, (0, 0, 0, pad_len), value=1e-8
+                )
+            # Here we zero out masked positions.
+            neutral_aa_probs *= mask[:, None]
+
+            neutral_aa_probs_l.append(neutral_aa_probs)
+
+        # Note that our masked out positions will have a nan log probability,
+        # which will require us to handle them correctly downstream.
+        self.log_neutral_aa_probs = torch.log(torch.stack(neutral_aa_probs_l))
+
+    def __getitem__(self, idx):
+        return {
+            "aa_parents_idxs": self.aa_parents_idxs[idx],
+            "subs_indicator": self.aa_subs_indicator_tensor[idx],
+            "mask": self.mask[idx],
+            "log_neutral_aa_probs": self.log_neutral_aa_probs[idx],
+            "rates": self.all_rates[idx],
+            "subs_probs": self.all_subs_probs[idx],
+        }
+
+    def to(self, device):
+        self.aa_parents_idxs = self.aa_parents_idxs.to(device)
+        self.aa_subs_indicator_tensor = self.aa_subs_indicator_tensor.to(device)
+        self.mask = self.mask.to(device)
+        self.log_neutral_aa_probs = self.log_neutral_aa_probs.to(device)
+        self.all_rates = self.all_rates.to(device)
+        self.all_subs_probs = self.all_subs_probs.to(device)
+
+
+def zero_predictions_along_diagonal(predictions, aa_parents_idxs):
+    """Zero out the diagonal of a batch of predictions.
+
+    We do this so that we can sum then have the same type of predictions as for the
+    DNSM.
+    """
+    # We would like to do
+    # predictions[torch.arange(len(aa_parents_idxs)), aa_parents_idxs] = 0.0
+    # but we have a batch dimension. Thus the following.
+
+    batch_size, L, _ = predictions.shape
+    batch_indices = torch.arange(batch_size, device=predictions.device)
+    predictions[
+        batch_indices[:, None],
+        torch.arange(L, device=predictions.device),
+        aa_parents_idxs,
+    ] = 0.0
+
+    return predictions
+
+
+class DASMBurrito(dnsm.DNSMBurrito):
+
+    def prediction_pair_of_batch(self, batch):
+        """Get log neutral AA probabilities and log selection factors for a batch of
+        data."""
+        aa_parents_idxs = batch["aa_parents_idxs"].to(self.device)
+        mask = batch["mask"].to(self.device)
+        log_neutral_aa_probs = batch["log_neutral_aa_probs"].to(self.device)
+        if not torch.isfinite(log_neutral_aa_probs[mask]).all():
+            raise ValueError(
+                f"log_neutral_aa_probs has non-finite values at relevant positions: {log_neutral_aa_probs[mask]}"
+            )
+        log_selection_factors = self.model(aa_parents_idxs, mask)
+        return log_neutral_aa_probs, log_selection_factors
+
+    def predictions_of_pair(self, log_neutral_aa_probs, log_selection_factors):
+        # Take the product of the neutral mutation probabilities and the
+        # selection factors, namely p_{j, a} * f_{j, a}.
+        # In contrast to a DNSM, each of these now have last dimension of 20.
+        predictions = torch.exp(log_neutral_aa_probs + log_selection_factors)
+        assert torch.isfinite(predictions).all()
+        predictions = clamp_probability(predictions)
+        return predictions
+
+    def predictions_of_batch(self, batch):
+        """Make predictions for a batch of data.
+
+        Note that we use the mask for prediction as part of the input for the
+        transformer, though we don't mask the predictions themselves.
+        """
+        log_neutral_aa_probs, log_selection_factors = self.prediction_pair_of_batch(
+            batch
+        )
+        return self.predictions_of_pair(log_neutral_aa_probs, log_selection_factors)
+
+    def loss_of_batch(self, batch):
+        aa_subs_indicator = batch["subs_indicator"].to(self.device)
+        mask = batch["mask"].to(self.device)
+        aa_parents_idxs = batch["aa_parents_idxs"].to(self.device)
+        aa_subs_indicator = aa_subs_indicator.masked_select(mask)
+        predictions = self.predictions_of_batch(batch)
+        # Add one entry, zero, to the last dimension of the predictions tensor
+        # to handle the ambiguous amino acids. This is the conservative choice.
+        # It might be faster to reassign all the 20s to 0s if we are confident
+        # in our masking. Perhaps we should always output a 21st dimension
+        # for the ambiguous amino acids (see issue #16).
+        # If we change something here we should also change the test code
+        # in test_dasm.py::test_zero_diagonal.
+        predictions = torch.cat(
+            [predictions, torch.zeros_like(predictions[:, :, :1])], dim=-1
+        )
+
+        predictions = zero_predictions_along_diagonal(predictions, aa_parents_idxs)
+
+        # After zeroing out the diagonal, we are effectively summing over the
+        # off-diagonal elements to get the probability of a nonsynonymous
+        # mutation.
+        predictions_of_mut = torch.sum(predictions, dim=-1)
+        predictions_of_mut = predictions_of_mut.masked_select(mask)
+        predictions_of_mut = clamp_probability(predictions_of_mut)
+        return self.bce_loss(predictions_of_mut, aa_subs_indicator)
+
+    def build_selection_matrix_from_parent(self, parent: str):
+        # This is simpler than the equivalent in dnsm.py because we get the selection
+        # matrix directly.
+        parent = translate_sequence(parent)
+        selection_factors = self.model.selection_factors_of_aa_str(parent)
+        parent_idxs = sequences.aa_idx_array_of_str(parent)
+        selection_factors[torch.arange(len(parent_idxs)), parent_idxs] = 1.0
+
+        return selection_factors

netam/dnsm.py

@@ -9,6 +9,7 @@
 
 import copy
 import multiprocessing as mp
+from functools import partial
 
 import torch
 from torch.utils.data import Dataset
@@ -89,7 +90,7 @@ def __init__(
         assert torch.max(self.aa_parents_idxs) <= MAX_AMBIG_AA_IDX
 
         self._branch_lengths = branch_lengths
-        self.update_neutral_aa_mut_probs()
+        self.update_neutral_probs()
 
     @classmethod
     def of_seriess(
@@ -134,9 +135,31 @@ def of_pcp_df(cls, pcp_df, branch_length_multiplier=5.0):
             branch_length_multiplier=branch_length_multiplier,
         )
 
+    @classmethod
+    def train_val_datasets_of_pcp_df(cls, pcp_df, branch_length_multiplier=5.0):
+        """Perform a train-val split based on the 'in_train' column.
+
+        This is a class method so it works for subclasses.
+        """
+        train_df = pcp_df[pcp_df["in_train"]].reset_index(drop=True)
+        val_df = pcp_df[~pcp_df["in_train"]].reset_index(drop=True)
+
+        val_dataset = cls.of_pcp_df(
+            val_df, branch_length_multiplier=branch_length_multiplier
+        )
+
+        if len(train_df) == 0:
+            return None, val_dataset
+        # else:
+        train_dataset = cls.of_pcp_df(
+            train_df, branch_length_multiplier=branch_length_multiplier
+        )
+
+        return train_dataset, val_dataset
+
     def clone(self):
         """Make a deep copy of the dataset."""
-        new_dataset = DNSMDataset(
+        new_dataset = self.__class__(
             self.nt_parents,
             self.nt_children,
             self.all_rates.copy(),
@@ -152,7 +175,7 @@ def subset_via_indices(self, indices):
         depends on `indices`: if `indices` is an iterable of integers, then we
         make a deep copy, otherwise we use slices to make a shallow copy.
         """
-        new_dataset = DNSMDataset(
+        new_dataset = self.__class__(
             self.nt_parents[indices].reset_index(drop=True),
             self.nt_children[indices].reset_index(drop=True),
             self.all_rates[indices],
@@ -181,7 +204,7 @@ def branch_lengths(self, new_branch_lengths):
         )
         assert torch.all(torch.isfinite(new_branch_lengths) & (new_branch_lengths > 0))
         self._branch_lengths = new_branch_lengths
-        self.update_neutral_aa_mut_probs()
+        self.update_neutral_probs()
 
     def export_branch_lengths(self, out_csv_path):
         pd.DataFrame({"branch_length": self.branch_lengths}).to_csv(
@@ -193,7 +216,14 @@ def load_branch_lengths(self, in_csv_path):
             pd.read_csv(in_csv_path)["branch_length"].values
         )
 
-    def update_neutral_aa_mut_probs(self):
+    def update_neutral_probs(self):
+        """Update the neutral mutation probabilities for the dataset.
+
+        This is a somewhat vague name, but that's because it includes both the cases of
+        the DNSM (in which case it's neutral probabilities of any nonsynonymous
+        mutation) and the DASM (in which case it's the neutral probabilities of mutation
+        to the various amino acids).
+        """
         neutral_aa_mut_prob_l = []
 
         for nt_parent, mask, rates, branch_length, subs_probs in zip(
@@ -272,25 +302,6 @@ def to(self, device):
         self.all_subs_probs = self.all_subs_probs.to(device)
 
 
-def train_val_datasets_of_pcp_df(pcp_df, branch_length_multiplier=5.0):
-    """Perform a train-val split based on a "in_train" column.
-
-    Stays here so it can be used in tests.
-    """
-    train_df = pcp_df[pcp_df["in_train"]].reset_index(drop=True)
-    val_df = pcp_df[~pcp_df["in_train"]].reset_index(drop=True)
-    val_dataset = DNSMDataset.of_pcp_df(
-        val_df, branch_length_multiplier=branch_length_multiplier
-    )
-    if len(train_df) == 0:
-        return None, val_dataset
-    # else:
-    train_dataset = DNSMDataset.of_pcp_df(
-        train_df, branch_length_multiplier=branch_length_multiplier
-    )
-    return train_dataset, val_dataset
-
-
 class DNSMBurrito(framework.Burrito):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
@@ -413,10 +424,14 @@ def find_optimal_branch_lengths(self, dataset, **optimization_kwargs):
         # The following can be used when one wants a better traceback.
         # burrito = DNSMBurrito(None, dataset, copy.deepcopy(self.model))
         # return burrito.serial_find_optimal_branch_lengths(dataset, **optimization_kwargs)
+        our_optimize_branch_length = partial(
+            worker_optimize_branch_length,
+            self.__class__,
+        )
         with mp.Pool(worker_count) as pool:
             splits = dataset.split(worker_count)
             results = pool.starmap(
-                worker_optimize_branch_length,
+                our_optimize_branch_length,
                 [(self.model, split, optimization_kwargs) for split in splits],
             )
         return torch.cat(results)
@@ -436,9 +451,9 @@ def to_crepe(self):
         return framework.Crepe(encoder, self.model, training_hyperparameters)
 
 
-def worker_optimize_branch_length(model, dataset, optimization_kwargs):
+def worker_optimize_branch_length(burrito_class, model, dataset, optimization_kwargs):
     """The worker used for parallel branch length optimization."""
-    burrito = DNSMBurrito(None, dataset, copy.deepcopy(model))
+    burrito = burrito_class(None, dataset, copy.deepcopy(model))
     return burrito.serial_find_optimal_branch_lengths(dataset, **optimization_kwargs)
 
 

netam/models.py

@@ -569,6 +569,7 @@ def __init__(
         dim_feedforward: int,
         layer_count: int,
         dropout_prob: float = 0.5,
+        output_dim: int = 1,
     ):
         super().__init__()
         # Note that d_model has to be divisible by nhead, so we make that
@@ -586,7 +587,7 @@ def __init__(
             batch_first=True,
         )
         self.encoder = nn.TransformerEncoder(self.encoder_layer, layer_count)
-        self.linear = nn.Linear(self.d_model, 1)
+        self.linear = nn.Linear(self.d_model, output_dim)
         self.init_weights()
 
     @property
@@ -597,6 +598,7 @@ def hyperparameters(self):
             "dim_feedforward": self.dim_feedforward,
             "layer_count": self.encoder.num_layers,
             "dropout_prob": self.pos_encoder.dropout.p,
+            "output_dim": self.linear.out_features,
         }
 
     def init_weights(self) -> None:

tests/conftest.py

@@ -0,0 +1,17 @@
+import pytest
+from netam.framework import (
+    load_pcp_df,
+    add_shm_model_outputs_to_pcp_df,
+)
+
+
+@pytest.fixture(scope="module")
+def pcp_df():
+    df = load_pcp_df(
+        "data/wyatt-10x-1p5m_pcp_2023-11-30_NI.first100.csv.gz",
+    )
+    df = add_shm_model_outputs_to_pcp_df(
+        df,
+        "data/cnn_joi_sml-shmoof_small",
+    )
+    return df