Update README.md

README.md

@@ -49,8 +49,73 @@ This model does not rank over the full vocabulary. It first masks non-gene token
 ```python
 with torch.no_grad():
     messages = [
-    {"role": "user", "content": "[PUT THE PROMPT GENERATED FROM https://phenogemini.org]"}
-]
+        {
+          "role": "user",
+          "content": (
+              "For a patient who presents with Intellectual disability, movement disorder, "
+              "memory impairment, abnormal posture, falls, dysarthria, leukodystrophy, "
+              "developmental regression, muscle weakness, elevated liver transaminases, "
+              "atopic dermatitis, rash, pruritus.\n"
+              "We can find some patients with similar phenotypes, such as:\n"
+              "A patient presents with Seizure, Global developmental delay, Intellectual "
+              "disability, Gait disturbance, Hyperornithinemia, Childlike behavior, "
+              "Clumsiness, Spasticity, Myoclonus, Ataxic gait, Falls, Drop attacks, "
+              "Spastic gait, Ataxic gait, Depressive episode, Suicidal behavior, "
+              "Asthenia, Fatigue, Dysarthria, Urinary incontinence, Fecal incontinence, "
+              "Intervertebral disc degeneration, Syringomyelia, Cerebral atrophy, "
+              "Leukoencephalopathy, Pons hyperdensity, Myelopathy, Peripheral neuropathy, "
+              "Wheelchair bound, Proximal muscle weakness, Hypotonia, Hyperreflexia, "
+              "Babinski sign, Memory impairment, Cognitive decline, Dysphagia, "
+              "Impaired self-care. This patient has a mutation in "
+              "<|PhenoGemini-Special-Token-Entrez-ID-10166|>.\n"
+              "A patient presents with Irritability, Seizure, Developmental regression, "
+              "Failure to thrive, Food aversion, Tremor, Head nodding, Global developmental "
+              "delay, Hepatomegaly, Aggressive behavior, Attention deficit hyperactivity "
+              "disorder, Intellectual disability, Spastic paraplegia, Hyperreflexia, "
+              "Clonus, Babinski sign, Impaired verbal comprehension, Short-term memory "
+              "impairment, Gait disturbance, Frequent falls, Inability to walk, Dystonia, "
+              "Impaired arithmetic ability, Impaired performance on psychometric tests, "
+              "Postural instability, Muscle weakness, Gait ataxia, Circumduction gait, "
+              "Shuffling gait, Muscle wasting, Spasticity, Proximal muscle weakness. "
+              "This patient has a mutation in "
+              "<|PhenoGemini-Special-Token-Entrez-ID-10166|>.\n"
+              "A patient presents with Cognitive impairment, Absent speech, Gait "
+              "disturbance, Hypotonia, Alacrima, Constipation, Tremor, Hyperkinesia, "
+              "Abnormality of the electroencephalogram, Seizure, Elevated hepatic "
+              "transaminase, Failure to thrive, Sleep disturbance, Dysphagia, Scoliosis, "
+              "Small hands, Small feet, Abnormality of the skin, Corneal opacity, "
+              "Peripheral neuropathy, Hearing impairment, Recurrent infections, "
+              "Strabismus, Abnormality of metabolism/homeostasis, Neurodevelopmental "
+              "regression, Hypospadias, Recurrent pneumonia, Airway obstruction, "
+              "Recurrent fractures, Osteopenia, Laryngomalacia, Hirschsprung disease, "
+              "Anxiety, Eosinophilic esophagitis, Microcephaly, Skin hypopigmentation, "
+              "Skin hyperpigmentation, Exocrine pancreatic insufficiency, "
+              "Abnormality of vision. This patient has a mutation in "
+              "<|PhenoGemini-Special-Token-Entrez-ID-55768|>.\n"
+              "A patient presents with Chronic kidney disease, Gout, Action tremor, "
+              "Myoclonus, Gait disturbance, Falls, Dysarthria, Distal sensory loss, "
+              "Sensorineural hearing impairment, Stuttering, Motor delay, Axial ataxia, "
+              "Dysmetria, Slow saccadic eye movements, Ptosis, Abnormality of the Romberg "
+              "sign, Dystonia, Muscle weakness, Axonal neuropathy, Impaired temperature "
+              "sensation, Cerebellar atrophy, Cortical atrophy, Impaired working memory, "
+              "Perseveration, Impaired concentration, Bradyphrenia, Glomerulonephritis, "
+              "Nephronophthisis, Cytochrome c oxidase deficiency, Ragged red muscle "
+              "fibers, Abnormality of mitochondrial morphology. This patient has a "
+              "mutation in <|PhenoGemini-Special-Token-Entrez-ID-63929|>.\n"
+              "A patient presents with Developmental delay, Hypotonia, Microcephaly, "
+              "Failure to thrive, Gastroesophageal reflux, Absence of speech, Drooling, "
+              "Abnormal ocular pursuit, Ataxia, Dysmetria, Areflexia, Limb weakness, "
+              "Abnormal involuntary movements, Axonal neuropathy, Sensorimotor "
+              "neuropathy, Unilateral hearing impairment, Abnormal visual evoked "
+              "potentials, Skeletal deformities, Muscle wasting, Gait disturbance, "
+              "Chorea, Orofacial dyskinesia, Chewing difficulty, Optic atrophy, "
+              "Increased CSF lactate, Dysarthria. This patient has a mutation in "
+              "<|PhenoGemini-Special-Token-Entrez-ID-9927|>.\n"
+              "Based on all the information above, and my own general knowledge, "
+              "this patient is likely to have a mutation in"
+            ),
+        }
+    ]
     text = tokenizer.apply_chat_template(
     messages,
     tokenize=False,