Update app.py
Browse files
app.py
CHANGED
@@ -114,7 +114,10 @@ def generate_caption(protein, prompt):
|
|
114 |
'''
|
115 |
print("esm embedding generated")
|
116 |
esm_emb = F.pad(esm_emb.t(), (0, 1024 - len(esm_emb))).t().to('cuda')
|
117 |
-
|
|
|
|
|
|
|
118 |
samples = {'name': ['protein_name'],
|
119 |
'image': torch.unsqueeze(esm_emb, dim=0),
|
120 |
'text_input': ['none'],
|
@@ -174,11 +177,11 @@ with gr.Blocks(css=css) as demo:
|
|
174 |
with gr.Column():
|
175 |
input_protein = gr.Textbox(type="text", label="Upload sequence")
|
176 |
# model_selector = gr.Dropdown(choices=list(models.keys()), label="Model", value='microsoft/Florence-2-large')
|
177 |
-
prompt = gr.Textbox(type="text", label="
|
178 |
submit_btn = gr.Button(value="Submit")
|
179 |
with gr.Column():
|
180 |
output_text = gr.Textbox(label="Output Text")
|
181 |
-
|
182 |
gr.Examples(
|
183 |
examples=[
|
184 |
["MKTLLLTLVVVTIVCLDLGNSLKCYVSREGKTQTCPEGEKLCEKYAVSYFHDGRWRYRYECTSACHRGPYNVCCSTDLCNK", 'Micrurus'],
|
@@ -186,7 +189,11 @@ with gr.Blocks(css=css) as demo:
|
|
186 |
["MKTLALFLVLVCVLGLVQSWEWPWNRKPTKFPIPSPNPRDKWCRLNLGPAWGGRC", 'Sophophora'],
|
187 |
["MAARGAMLRYLRVNVNPTIQNPRECVLPFSILLRRFSEEVRGSFLDKSEVTDRVLSVVKNFQKVDPSKVTPKANFQNDLGLDSLDSVEVVMALEEEFGFEIPDNEADKIQSIDLAVDFIASHPQAK", 'Arabidopsis'],
|
188 |
["MAAAGGARLLRAASAVLGGPAGRWLHHAGSRAGSSGLLRNRGPGGSAEASRSLSVSARARSSSEDKITVHFINRDGETLTTKGKVGDSLLDVVVENNLDIDGFGACEGTLACSTCHLIFEDHIYEKLDAITDEENDMLDLAYGLTDRSRLGCQICLTKSMDNMTVRVPETVADARQSIDVGKTS", 'Homo'],
|
189 |
-
['MASAELSREENVYMAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEEGRGNEDRVTLIKDYRGKIETELTKICDGILKLLETHLVPSSTAPESKVFYLKMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACSLAKQAFDEAISELDTLSEESYKDSTLIMQLLRDNLTLWTSDISEDPAEEIREAPKRDSSEGQ', 'Zea']
|
|
|
|
|
|
|
|
|
190 |
],
|
191 |
inputs=[input_protein, prompt],
|
192 |
outputs=[output_text],
|
|
|
114 |
'''
|
115 |
print("esm embedding generated")
|
116 |
esm_emb = F.pad(esm_emb.t(), (0, 1024 - len(esm_emb))).t().to('cuda')
|
117 |
+
if prompt is None:
|
118 |
+
prompt = 'none'
|
119 |
+
else:
|
120 |
+
prompt = prompt.lower()
|
121 |
samples = {'name': ['protein_name'],
|
122 |
'image': torch.unsqueeze(esm_emb, dim=0),
|
123 |
'text_input': ['none'],
|
|
|
177 |
with gr.Column():
|
178 |
input_protein = gr.Textbox(type="text", label="Upload sequence")
|
179 |
# model_selector = gr.Dropdown(choices=list(models.keys()), label="Model", value='microsoft/Florence-2-large')
|
180 |
+
prompt = gr.Textbox(type="text", label="Taxonomy Prompt")
|
181 |
submit_btn = gr.Button(value="Submit")
|
182 |
with gr.Column():
|
183 |
output_text = gr.Textbox(label="Output Text")
|
184 |
+
# train index 99, 127, 266, 738, 1060 test index 4
|
185 |
gr.Examples(
|
186 |
examples=[
|
187 |
["MKTLLLTLVVVTIVCLDLGNSLKCYVSREGKTQTCPEGEKLCEKYAVSYFHDGRWRYRYECTSACHRGPYNVCCSTDLCNK", 'Micrurus'],
|
|
|
189 |
["MKTLALFLVLVCVLGLVQSWEWPWNRKPTKFPIPSPNPRDKWCRLNLGPAWGGRC", 'Sophophora'],
|
190 |
["MAARGAMLRYLRVNVNPTIQNPRECVLPFSILLRRFSEEVRGSFLDKSEVTDRVLSVVKNFQKVDPSKVTPKANFQNDLGLDSLDSVEVVMALEEEFGFEIPDNEADKIQSIDLAVDFIASHPQAK", 'Arabidopsis'],
|
191 |
["MAAAGGARLLRAASAVLGGPAGRWLHHAGSRAGSSGLLRNRGPGGSAEASRSLSVSARARSSSEDKITVHFINRDGETLTTKGKVGDSLLDVVVENNLDIDGFGACEGTLACSTCHLIFEDHIYEKLDAITDEENDMLDLAYGLTDRSRLGCQICLTKSMDNMTVRVPETVADARQSIDVGKTS", 'Homo'],
|
192 |
+
['MASAELSREENVYMAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEEGRGNEDRVTLIKDYRGKIETELTKICDGILKLLETHLVPSSTAPESKVFYLKMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACSLAKQAFDEAISELDTLSEESYKDSTLIMQLLRDNLTLWTSDISEDPAEEIREAPKRDSSEGQ', 'Zea'],
|
193 |
+
['MIKAAVTKESLYRMNTLMEAFQGFLGLDLGEFTFKVKPGVFLLTDVKSYLIGDKYDDAFNALIDFVLRNDRDAVEGTETDVSIRLGLSPSDMVVKRQDKTFTFTHGDLEFEVHWINL', 'Bacteriophage'],
|
194 |
+
['MQMYKLTAGTTGYHTLLTRTQAEHMLSLWGDKYSIDDCTPSNPIYSPSRYTKLELVYMAANATA', 'Bacteriophage'],
|
195 |
+
['MSITAMDAKLQRILEESTCFGIGHDPNVKECKMCDVREQCKAKTQGMNVPTPTRKKPEDVAPAKEKPTTKKTTAKKSTAKEEKKETAPKAKETKAKPKSKPKKAKAPENPNLPNFKEMSFEELVELAKERNVEWKDYNSPNITRMRLIMALKASY', 'Bacteriophage'],
|
196 |
+
['MNDLMIQLLDQFEMGLRERAIKVMATINDEKHRFPMELNKKQCSLMLLGTTDTTTFDMRFNSKKDFPRIKGAREKYPRDAVIEWYHQNWMRTEVKQ', 'Bacteriophage'],
|
197 |
],
|
198 |
inputs=[input_protein, prompt],
|
199 |
outputs=[output_text],
|