Update app.py

app.py

@@ -1,183 +1,184 @@
-import torch
-import random
-import pandas as pd
-from utils import create_vocab, setup_seed
-from dataset_mlm import  get_paded_token_idx_gen, add_tokens_to_vocab
-import gradio as gr
-from gradio_rangeslider import RangeSlider
-import time
-
-is_stopped = False
-
-seed = random.randint(0,100000)
-setup_seed(seed)
-
-device = torch.device("cpu")
-vocab_mlm = create_vocab()
-vocab_mlm = add_tokens_to_vocab(vocab_mlm)
-save_path = 'mlm-model-27.pt'
-train_seqs = pd.read_csv('C0_seq.csv')
-train_seq = train_seqs['Seq'].tolist()
-model = torch.load(save_path, map_location=torch.device('cpu'))
-model = model.to(device)
-
-def temperature_sampling(logits, temperature):
-    logits = logits / temperature
-    probabilities = torch.softmax(logits, dim=-1)
-    sampled_token = torch.multinomial(probabilities, 1)
-    return sampled_token
-
-def stop_generation():
-    global is_stopped
-    is_stopped = True
-    return "Generation stopped."
-
-def CTXGen(X0, X1, X2, τ, g_num):
-    global is_stopped
-    is_stopped = False
-    X3 = "X" * len(X0)
-    msa_data = pd.read_csv('conoData_C0.csv') 
-    msa = msa_data['Sequences'].tolist()
-    msa = [x for x in msa if x.startswith(f"{X1}|{X2}")]
-    msa = random.choice(msa)
-    X4 = msa.split("|")[3]
-    X5 = msa.split("|")[4]
-    X6 = msa.split("|")[5]
-
-    model.eval()
-    with torch.no_grad():
-        new_seq = None
-        IDs = []
-        generated_seqs = []
-        generated_seqs_FINAL = []
-        cls_probability_all = []
-        act_probability_all = []
-        count = 0
-        gen_num = g_num
-        NON_AA = ["B","O","U","Z","X",'<K16>', '<α1β1γδ>', '<Ca22>', '<AChBP>', '<K13>', '<α1BAR>', '<α1β1ε>', '<α1AAR>', '<GluN3A>', '<α4β2>',
-                        '<GluN2B>', '<α75HT3>', '<Na14>', '<α7>', '<GluN2C>', '<NET>', '<NavBh>', '<α6β3β4>', '<Na11>', '<Ca13>', 
-                        '<Ca12>', '<Na16>', '<α6α3β2>', '<GluN2A>', '<GluN2D>', '<K17>', '<α1β1δε>', '<GABA>', '<α9>', '<K12>', 
-                        '<Kshaker>', '<α3β4>', '<Na18>', '<α3β2>', '<α6α3β2β3>', '<α1β1δ>', '<α6α3β4β3>', '<α2β2>','<α6β4>', '<α2β4>',
-                        '<Na13>', '<Na12>', '<Na15>', '<α4β4>', '<α7α6β2>', '<α1β1γ>', '<NaTTXR>', '<K11>', '<Ca23>', 
-                        '<α9α10>','<α6α3β4>', '<NaTTXS>', '<Na17>','<high>','<low>','[UNK]','[SEP]','[PAD]','[CLS]','[MASK]']
-        
-        seq_parent = [f"{X1}|{X2}|{X0}|{X4}|{X5}|{X6}"]
-        padded_seqseq_parent, _, idx_msaseq_parent, _ = get_paded_token_idx_gen(vocab_mlm, seq_parent, new_seq)
-        idx_msaseq_parent = torch.tensor(idx_msaseq_parent).unsqueeze(0).to(device)
-        seqseq_parent = ["[MASK]" if i=="X" else i for i in padded_seqseq_parent]
-
-        seqseq_parent[1] = "[MASK]"
-        input_ids_parent = vocab_mlm.__getitem__(seqseq_parent)
-        logits_parent = model(torch.tensor([input_ids_parent]).to(device), idx_msaseq_parent)
-
-        cls_mask_logits_parent = logits_parent[0, 1, :]
-        cls_probability_parent, cls_mask_probs_parent = torch.topk((torch.softmax(cls_mask_logits_parent, dim=-1)), k=10)
-
-        seqseq_parent[2] = "[MASK]"
-        input_ids_parent = vocab_mlm.__getitem__(seqseq_parent)
-        logits_parent = model(torch.tensor([input_ids_parent]).to(device), idx_msaseq_parent)
-        act_mask_logits_parent = logits_parent[0, 2, :]
-        act_probability_parent, act_mask_probs_parent = torch.topk((torch.softmax(act_mask_logits_parent, dim=-1)), k=2)
-
-        cls_pos_parent = vocab_mlm.to_tokens(list(cls_mask_probs_parent))
-        act_pos_parent = vocab_mlm.to_tokens(list(act_mask_probs_parent))
-
-        cls_proba_parent = cls_probability_parent[cls_pos_parent.index(X1)].item()
-        act_proba_parent = act_probability_parent[act_pos_parent.index(X2)].item()
-
-        while count < gen_num:
-            gen_len = len(X0)
-            seq = [f"{X1}|{X2}|{X3}|{X4}|{X5}|{X6}"]
-            vocab_mlm.token_to_idx["X"] = 4
-
-            padded_seq, _, _, _ = get_paded_token_idx_gen(vocab_mlm, seq, new_seq)
-            input_text = ["[MASK]" if i=="X" else i for i in padded_seq]
-
-            gen_length = len(input_text)
-            length = gen_length - sum(1 for x in input_text if x != '[MASK]')
-
-            for i in range(length):
-                _, idx_seq, idx_msa, attn_idx = get_paded_token_idx_gen(vocab_mlm, seq, new_seq)
-                idx_seq = torch.tensor(idx_seq).unsqueeze(0).to(device)
-                idx_msa = torch.tensor(idx_msa).unsqueeze(0).to(device)
-                attn_idx = torch.tensor(attn_idx).to(device)
-
-                mask_positions = [j for j in range(gen_length) if input_text[j] == "[MASK]"]
-                mask_position = torch.tensor([mask_positions[torch.randint(len(mask_positions), (1,))]])
-                
-                logits = model(idx_seq,idx_msa, attn_idx) 
-                mask_logits = logits[0, mask_position.item(), :] 
-
-                predicted_token_id = temperature_sampling(mask_logits, τ)
-
-                predicted_token = vocab_mlm.to_tokens(int(predicted_token_id))
-                input_text[mask_position.item()] = predicted_token
-                padded_seq[mask_position.item()] = predicted_token.strip()
-                new_seq = padded_seq
-
-            generated_seq = input_text
-        
-            generated_seq[1] = "[MASK]"
-            input_ids = vocab_mlm.__getitem__(generated_seq)
-            logits = model(torch.tensor([input_ids]).to(device), idx_msa)
-            cls_mask_logits = logits[0, 1, :]
-            cls_probability, cls_mask_probs = torch.topk((torch.softmax(cls_mask_logits, dim=-1)), k=10)
-
-            generated_seq[2] = "[MASK]"
-            input_ids = vocab_mlm.__getitem__(generated_seq)
-            logits = model(torch.tensor([input_ids]).to(device), idx_msa)
-            act_mask_logits = logits[0, 2, :]
-            act_probability, act_mask_probs = torch.topk((torch.softmax(act_mask_logits, dim=-1)), k=2)
-
-            cls_pos = vocab_mlm.to_tokens(list(cls_mask_probs))
-            act_pos = vocab_mlm.to_tokens(list(act_mask_probs))
-            
-            if X1 in cls_pos and X2 in act_pos:
-                cls_proba = cls_probability[cls_pos.index(X1)].item()
-                act_proba = act_probability[act_pos.index(X2)].item()
-                generated_seq = generated_seq[generated_seq.index('[MASK]') + 2:generated_seq.index('[SEP]')]
-                if cls_proba>=cls_proba_parent and act_proba>=act_proba_parent and generated_seq.count('C') % 2 == 0 and len("".join(generated_seq)) == gen_len:
-                    generated_seqs.append("".join(generated_seq))
-                    if "".join(generated_seq) not in train_seq and "".join(generated_seq) not in generated_seqs[0:-1] and all(x not in NON_AA for x in generated_seq):
-                        generated_seqs_FINAL.append("".join(generated_seq))
-                        cls_probability_all.append(cls_proba)
-                        act_probability_all.append(act_proba)
-                        IDs.append(count+1)
-                        out = pd.DataFrame({
-                            'ID':IDs,
-                            'Generated_seq': generated_seqs_FINAL,
-                            'Subtype': X1,
-                            'Subtype_probability': cls_probability_all, 
-                            'Potency': X2, 
-                            'Potency_probability': act_probability_all, 
-                            'Random_seed': seed
-                        })
-                        out.to_csv("output.csv", index=False, encoding='utf-8-sig')
-                        count += 1
-                        yield out, "output.csv"
-    return out, "output.csv"
-
-with gr.Blocks() as demo:
-    gr.Markdown("# Conotoxin Optimization Generation")
-    with gr.Row():
-        X1 = gr.Dropdown(choices=['<α7>','<AChBP>','<α4β2>','<α3β4>','<Ca22>','<α3β2>', '<Na12>','<α9α10>','<K16>', '<α1β1γδ>', 
-                                  '<K13>', '<α1BAR>', '<α1β1ε>', '<α1AAR>', '<GluN3A>', '<GluN2B>', '<α75HT3>', '<Na14>', 
-                                  '<GluN2C>', '<NET>', '<NavBh>', '<α6β3β4>', '<Na11>', '<Ca13>', '<Ca12>', '<Na16>', '<α6α3β2>', 
-                                  '<GluN2A>', '<GluN2D>', '<K17>', '<α1β1δε>', '<GABA>', '<α9>', '<K12>', '<Kshaker>',  '<Na18>', 
-                                  '<α6α3β2β3>', '<α1β1δ>', '<α6α3β4β3>', '<α2β2>','<α6β4>', '<α2β4>','<Na13>', '<Na15>', '<α4β4>', 
-                                  '<α7α6β2>', '<α1β1γ>', '<NaTTXR>', '<K11>', '<Ca23>', '<α6α3β4>', '<NaTTXS>', '<Na17>'], label="Subtype")
-        X2 = gr.Dropdown(choices=['<high>','<low>'], label="Potency")
-        τ = gr.Slider(minimum=1, maximum=2, step=0.1, label="τ")
-        g_num = gr.Dropdown(choices=[1, 10, 20, 30, 40, 50], label="Number of generations")
-    with gr.Row():
-        start_button = gr.Button("Start Generation")
-        stop_button = gr.Button("Stop Generation")
-    with gr.Row():
-        output_df = gr.DataFrame(label="Generated Conotoxins")
-    with gr.Row():
-        output_file = gr.File(label="Download generated conotoxins")
-    
-    start_button.click(CTXGen, inputs=[X1, X2, τ, g_num], outputs=[output_df, output_file])
-    stop_button.click(stop_generation, outputs=None)
-
+import torch
+import random
+import pandas as pd
+from utils import create_vocab, setup_seed
+from dataset_mlm import  get_paded_token_idx_gen, add_tokens_to_vocab
+import gradio as gr
+from gradio_rangeslider import RangeSlider
+import time
+
+is_stopped = False
+
+seed = random.randint(0,100000)
+setup_seed(seed)
+
+device = torch.device("cpu")
+vocab_mlm = create_vocab()
+vocab_mlm = add_tokens_to_vocab(vocab_mlm)
+save_path = 'mlm-model-27.pt'
+train_seqs = pd.read_csv('C0_seq.csv')
+train_seq = train_seqs['Seq'].tolist()
+model = torch.load(save_path, map_location=torch.device('cpu'))
+model = model.to(device)
+
+def temperature_sampling(logits, temperature):
+    logits = logits / temperature
+    probabilities = torch.softmax(logits, dim=-1)
+    sampled_token = torch.multinomial(probabilities, 1)
+    return sampled_token
+
+def stop_generation():
+    global is_stopped
+    is_stopped = True
+    return "Generation stopped."
+
+def CTXGen(X0, X1, X2, τ, g_num):
+    global is_stopped
+    is_stopped = False
+    X3 = "X" * len(X0)
+    msa_data = pd.read_csv('conoData_C0.csv') 
+    msa = msa_data['Sequences'].tolist()
+    msa = [x for x in msa if x.startswith(f"{X1}|{X2}")]
+    msa = random.choice(msa)
+    X4 = msa.split("|")[3]
+    X5 = msa.split("|")[4]
+    X6 = msa.split("|")[5]
+
+    model.eval()
+    with torch.no_grad():
+        new_seq = None
+        IDs = []
+        generated_seqs = []
+        generated_seqs_FINAL = []
+        cls_probability_all = []
+        act_probability_all = []
+        count = 0
+        gen_num = g_num
+        NON_AA = ["B","O","U","Z","X",'<K16>', '<α1β1γδ>', '<Ca22>', '<AChBP>', '<K13>', '<α1BAR>', '<α1β1ε>', '<α1AAR>', '<GluN3A>', '<α4β2>',
+                        '<GluN2B>', '<α75HT3>', '<Na14>', '<α7>', '<GluN2C>', '<NET>', '<NavBh>', '<α6β3β4>', '<Na11>', '<Ca13>', 
+                        '<Ca12>', '<Na16>', '<α6α3β2>', '<GluN2A>', '<GluN2D>', '<K17>', '<α1β1δε>', '<GABA>', '<α9>', '<K12>', 
+                        '<Kshaker>', '<α3β4>', '<Na18>', '<α3β2>', '<α6α3β2β3>', '<α1β1δ>', '<α6α3β4β3>', '<α2β2>','<α6β4>', '<α2β4>',
+                        '<Na13>', '<Na12>', '<Na15>', '<α4β4>', '<α7α6β2>', '<α1β1γ>', '<NaTTXR>', '<K11>', '<Ca23>', 
+                        '<α9α10>','<α6α3β4>', '<NaTTXS>', '<Na17>','<high>','<low>','[UNK]','[SEP]','[PAD]','[CLS]','[MASK]']
+        
+        seq_parent = [f"{X1}|{X2}|{X0}|{X4}|{X5}|{X6}"]
+        padded_seqseq_parent, _, idx_msaseq_parent, _ = get_paded_token_idx_gen(vocab_mlm, seq_parent, new_seq)
+        idx_msaseq_parent = torch.tensor(idx_msaseq_parent).unsqueeze(0).to(device)
+        seqseq_parent = ["[MASK]" if i=="X" else i for i in padded_seqseq_parent]
+
+        seqseq_parent[1] = "[MASK]"
+        input_ids_parent = vocab_mlm.__getitem__(seqseq_parent)
+        logits_parent = model(torch.tensor([input_ids_parent]).to(device), idx_msaseq_parent)
+
+        cls_mask_logits_parent = logits_parent[0, 1, :]
+        cls_probability_parent, cls_mask_probs_parent = torch.topk((torch.softmax(cls_mask_logits_parent, dim=-1)), k=10)
+
+        seqseq_parent[2] = "[MASK]"
+        input_ids_parent = vocab_mlm.__getitem__(seqseq_parent)
+        logits_parent = model(torch.tensor([input_ids_parent]).to(device), idx_msaseq_parent)
+        act_mask_logits_parent = logits_parent[0, 2, :]
+        act_probability_parent, act_mask_probs_parent = torch.topk((torch.softmax(act_mask_logits_parent, dim=-1)), k=2)
+
+        cls_pos_parent = vocab_mlm.to_tokens(list(cls_mask_probs_parent))
+        act_pos_parent = vocab_mlm.to_tokens(list(act_mask_probs_parent))
+
+        cls_proba_parent = cls_probability_parent[cls_pos_parent.index(X1)].item()
+        act_proba_parent = act_probability_parent[act_pos_parent.index(X2)].item()
+
+        while count < gen_num:
+            gen_len = len(X0)
+            seq = [f"{X1}|{X2}|{X3}|{X4}|{X5}|{X6}"]
+            vocab_mlm.token_to_idx["X"] = 4
+
+            padded_seq, _, _, _ = get_paded_token_idx_gen(vocab_mlm, seq, new_seq)
+            input_text = ["[MASK]" if i=="X" else i for i in padded_seq]
+
+            gen_length = len(input_text)
+            length = gen_length - sum(1 for x in input_text if x != '[MASK]')
+
+            for i in range(length):
+                _, idx_seq, idx_msa, attn_idx = get_paded_token_idx_gen(vocab_mlm, seq, new_seq)
+                idx_seq = torch.tensor(idx_seq).unsqueeze(0).to(device)
+                idx_msa = torch.tensor(idx_msa).unsqueeze(0).to(device)
+                attn_idx = torch.tensor(attn_idx).to(device)
+
+                mask_positions = [j for j in range(gen_length) if input_text[j] == "[MASK]"]
+                mask_position = torch.tensor([mask_positions[torch.randint(len(mask_positions), (1,))]])
+                
+                logits = model(idx_seq,idx_msa, attn_idx) 
+                mask_logits = logits[0, mask_position.item(), :] 
+
+                predicted_token_id = temperature_sampling(mask_logits, τ)
+
+                predicted_token = vocab_mlm.to_tokens(int(predicted_token_id))
+                input_text[mask_position.item()] = predicted_token
+                padded_seq[mask_position.item()] = predicted_token.strip()
+                new_seq = padded_seq
+
+            generated_seq = input_text
+        
+            generated_seq[1] = "[MASK]"
+            input_ids = vocab_mlm.__getitem__(generated_seq)
+            logits = model(torch.tensor([input_ids]).to(device), idx_msa)
+            cls_mask_logits = logits[0, 1, :]
+            cls_probability, cls_mask_probs = torch.topk((torch.softmax(cls_mask_logits, dim=-1)), k=10)
+
+            generated_seq[2] = "[MASK]"
+            input_ids = vocab_mlm.__getitem__(generated_seq)
+            logits = model(torch.tensor([input_ids]).to(device), idx_msa)
+            act_mask_logits = logits[0, 2, :]
+            act_probability, act_mask_probs = torch.topk((torch.softmax(act_mask_logits, dim=-1)), k=2)
+
+            cls_pos = vocab_mlm.to_tokens(list(cls_mask_probs))
+            act_pos = vocab_mlm.to_tokens(list(act_mask_probs))
+            
+            if X1 in cls_pos and X2 in act_pos:
+                cls_proba = cls_probability[cls_pos.index(X1)].item()
+                act_proba = act_probability[act_pos.index(X2)].item()
+                generated_seq = generated_seq[generated_seq.index('[MASK]') + 2:generated_seq.index('[SEP]')]
+                if cls_proba>=cls_proba_parent and act_proba>=act_proba_parent and generated_seq.count('C') % 2 == 0 and len("".join(generated_seq)) == gen_len:
+                    generated_seqs.append("".join(generated_seq))
+                    if "".join(generated_seq) not in train_seq and "".join(generated_seq) not in generated_seqs[0:-1] and all(x not in NON_AA for x in generated_seq):
+                        generated_seqs_FINAL.append("".join(generated_seq))
+                        cls_probability_all.append(cls_proba)
+                        act_probability_all.append(act_proba)
+                        IDs.append(count+1)
+                        out = pd.DataFrame({
+                            'ID':IDs,
+                            'Generated_seq': generated_seqs_FINAL,
+                            'Subtype': X1,
+                            'Subtype_probability': cls_probability_all, 
+                            'Potency': X2, 
+                            'Potency_probability': act_probability_all, 
+                            'Random_seed': seed
+                        })
+                        out.to_csv("output.csv", index=False, encoding='utf-8-sig')
+                        count += 1
+                        yield out, "output.csv"
+    return out, "output.csv"
+
+with gr.Blocks() as demo:
+    gr.Markdown("# Conotoxin Optimization Generation")
+    with gr.Row():
+        X0 = gr.Textbox(label="conotoxin")
+        X1 = gr.Dropdown(choices=['<α7>','<AChBP>','<α4β2>','<α3β4>','<Ca22>','<α3β2>', '<Na12>','<α9α10>','<K16>', '<α1β1γδ>', 
+                                  '<K13>', '<α1BAR>', '<α1β1ε>', '<α1AAR>', '<GluN3A>', '<GluN2B>', '<α75HT3>', '<Na14>', 
+                                  '<GluN2C>', '<NET>', '<NavBh>', '<α6β3β4>', '<Na11>', '<Ca13>', '<Ca12>', '<Na16>', '<α6α3β2>', 
+                                  '<GluN2A>', '<GluN2D>', '<K17>', '<α1β1δε>', '<GABA>', '<α9>', '<K12>', '<Kshaker>',  '<Na18>', 
+                                  '<α6α3β2β3>', '<α1β1δ>', '<α6α3β4β3>', '<α2β2>','<α6β4>', '<α2β4>','<Na13>', '<Na15>', '<α4β4>', 
+                                  '<α7α6β2>', '<α1β1γ>', '<NaTTXR>', '<K11>', '<Ca23>', '<α6α3β4>', '<NaTTXS>', '<Na17>'], label="Subtype")
+        X2 = gr.Dropdown(choices=['<high>','<low>'], label="Potency")
+        τ = gr.Slider(minimum=1, maximum=2, step=0.1, label="τ")
+        g_num = gr.Dropdown(choices=[1, 10, 20, 30, 40, 50], label="Number of generations")
+    with gr.Row():
+        start_button = gr.Button("Start Generation")
+        stop_button = gr.Button("Stop Generation")
+    with gr.Row():
+        output_df = gr.DataFrame(label="Generated Conotoxins")
+    with gr.Row():
+        output_file = gr.File(label="Download generated conotoxins")
+    
+    start_button.click(CTXGen, inputs=[X0, X1, X2, τ, g_num], outputs=[output_df, output_file])
+    stop_button.click(stop_generation, outputs=None)
+
 demo.launch()