Merge pull request #13 from badeok0716/main

Correcting Acquisition Function Calculation

lambo/acquisitions/monte_carlo.py

@@ -71,18 +71,19 @@ def forward(self, X: array) -> Tensor:
             baseline_X = self._X_baseline
             baseline_X = baseline_X.expand(*X.shape[:-2], -1, -1)
             X_full = torch.cat([baseline_X, X], dim=-2)
+            q = X.shape[-2]
         else:
             baseline_X = copy(self.X_baseline_string) # ensure contiguity
             baseline_X.resize(
                 baseline_X.shape[:-(X.ndim)] + X.shape[:-1] + baseline_X.shape[-1:]
             )
             X_full = concatenate([baseline_X, X], axis=-1)
+            q = X.shape[-1]
         # Note: it is important to compute the full posterior over `(X_baseline, X)``
         # to ensure that we properly sample `f(X)` from the joint distribution `
         # `f(X_baseline, X) ~ P(f | D)` given that we can already fixed the sampled
         # function values for `f(X_baseline)`
         posterior = self.model.posterior(X_full)
-        q = X.shape[-2]
         self._set_sampler(q=q, posterior=posterior)
         samples = self.sampler(posterior)[..., -q:, :]
         # add previous nehvi from pending points

lambo/candidate.py

@@ -8,13 +8,6 @@
 
 from lambo.utils import StringSubstitution, StringDeletion, StringInsertion, FoldxMutation
 
-
-def apply_mutation(base_seq, mut_pos, mut_res, tokenizer):
-    tokens = tokenizer.decode(tokenizer.encode(base_seq)).split(" ")[1:-1]
-    mut_seq = "".join(tokens[:mut_pos] + [mut_res] + tokens[(mut_pos + 1):])
-    return mut_seq
-
-
 def pdb_to_residues(pdb_path, chain_id='A'):
     """
     :param pdb_path: path to pdb file (str or Path)

lambo/models/base_surrogate.py

@@ -10,7 +10,7 @@
 
 class BaseSurrogate(torch.nn.Module):
     device = torch.device('cuda:0') if torch.cuda.is_available() else torch.device('cpu')
-    dtype = torch.float
+    dtype = torch.double
 
     def _set_transforms(self, tokenizer, max_shift, mask_size, train_prepend=None):
         # convert from string to LongTensor of token indexes

lambo/optimizers/lambo.py

@@ -310,9 +310,7 @@ def optimize(self, candidate_pool, pool_targets, all_seqs, all_targets, log_pref
                     else:
                         raise ValueError
 
-                    # import pdb; pdb.set_trace()
-                    lat_acq_vals = acq_fn(pooled_features.unsqueeze(-2))
-                    # lat_acq_vals = acq_fn(pooled_features.unsqueeze(0))
+                    lat_acq_vals = acq_fn(pooled_features.unsqueeze(0))
                     loss = -lat_acq_vals.mean() + self.entropy_penalty * logit_entropy.mean()
 
                     if self.optimize_latent:
@@ -322,31 +320,20 @@ def optimize(self, candidate_pool, pool_targets, all_seqs, all_targets, log_pref
 
                     tgt_seqs = tokens_to_str(tgt_tok_idxs, self.encoder.tokenizer)
                     with torch.no_grad():
-                        act_acq_vals = acq_fn(tgt_seqs[..., None])
-                    # act_acq_vals = acq_fn(tgt_seqs[None, :]).mean().item()
-
-                    is_improved = (act_acq_vals >= best_scores)
-                    best_scores = torch.where(is_improved, act_acq_vals, best_scores)
-                    best_seqs = np.where(is_improved.cpu().numpy(), tgt_seqs, best_seqs)
-                    # best_scores[is_improved] = act_acq_vals[is_improved]
-                    # best_seqs[is_improved] = tgt_seqs[is_improved]
-
-                    with torch.no_grad():
-                        batch_acq_val = acq_fn(best_seqs[None, :]).mean().item()
-                    curr_score = -1.0 * batch_acq_val
+                        act_acq_vals = acq_fn(tgt_seqs[None, :]).mean().item()
 
                     best_score, best_step, _, stop = check_early_stopping(
                         model=None,
                         best_score=best_score,
                         best_epoch=best_step,
                         best_weights=None,
-                        curr_score=curr_score,
+                        curr_score=-act_acq_vals,
                         curr_epoch=step_idx + 1,
                         patience=self.patience,
                         save_weights=False,
                     )
                     if (step_idx + 1) == best_step:
-                        # best_seqs = tgt_seqs.copy()
+                        best_seqs = tgt_seqs.copy()
                         best_entropy = logit_entropy.mean().item()
                     if stop:
                         print(f"Early stopping at step {step_idx + 1}")

lambo/tasks/surrogate_task.py

@@ -19,7 +19,6 @@ def _evaluate(self, x, out, *args, **kwargs):
             cand_idx, mut_pos, mut_res_idx, op_idx = query_pt
             op_type = self.op_types[op_idx]
             base_seq = self.candidate_pool[cand_idx].mutant_residue_seq
-            mut_pos = mut_pos % len(base_seq)
             mut_res = self.tokenizer.sampling_vocab[mut_res_idx]
             mutant_seq = apply_mutation(base_seq, mut_pos, mut_res, op_type, self.tokenizer)
             candidates.append(mutant_seq)

lambo/utils.py

@@ -432,7 +432,8 @@ def tokens_to_str(tok_idx_array, tokenizer):
 
 
 def apply_mutation(base_seq, mut_pos, mut_res, op_type, tokenizer):
-    tokens = tokenizer.decode(tokenizer.encode(base_seq)).split(" ")[1:-1]
+    tokens = tokenizer.decode(tokenizer.encode(base_seq)).split(" ")
+    mut_pos = mut_pos % len(tokens)
 
     if op_type == 'sub':
         mut_seq = "".join(tokens[:mut_pos] + [mut_res] + tokens[(mut_pos + 1):])