Update README.md

README.md

@@ -109,6 +109,29 @@ with torch.no_grad():
 > **Special Gene Token Example**  
 > In `<|PhenoGemini-Special-Token-Entrez-ID-64087|>`, the numeric value after the final hyphen represents the Entrez Gene ID.  
 
+# Usage Example
+### Patient Phenotypes:
+Gait disturbance, Scoliosis, Tall stature, Musculoskeletal abnormality, Positive wrist sign, Positive thumb sign, Pectus carinatum, Redundant skin, Scapular winging, Prominent vertebral column, Increased intervertebral disc space, Congenital hip dislocation
+### Prompt Generated From https://phenogemini.org:
+```text
+For a patient who presents with Gait disturbance, Scoliosis, Tall stature, Musculoskeletal abnormality, Positive wrist sign, Positive thumb sign, Pectus carinatum, Redundant skin, Scapular winging, Prominent vertebral column, Increased intervertebral disc space, Congenital hip dislocation.
+We can find some patients with similar phenotypes, such as: 
+A patient presents with skeletal dysplasia, abnormal skeletal development starting with a ‘hump’ in the back that later evolved into scoliosis, short stature, abnormal chest appearance, deformed wrists and elbows, progressive difficulty in walking and holding objects with her hands, myopia, malar hypoplasia, hazy cornea with a hyper-pigmented spot in the sclera, short neck, pectus carinatum, flaring lower ribs, kyphoscoliosis with gibbus, markedly redundant umbilical skin, thickened wrists and elbows, fixed flexion deformity of knees, heel prominence, flat feet, overriding of lateral toes, joint hypermobility. This patient has a mutation in <|PhenoGemini-Special-Token-Entrez-ID-2588|>.
+A patient presents with weak lower extremities, trigger fingers, tight hamstrings, proximal muscle weakness in his lower extremities that caused him difficulties with squatting, balancing, and walking with a stable gait, short stature, barrel-shaped chest, pectus carinatum, short neck and trunk, longer limbs, hyperextensible joints, thoracic kyphosis, mildly coarse facial features along with a flat midface, flat vertebrae, hypoplastic odontoid with a stable relationship to C1/C2, lumbar hyperlordosis, proximal tapering and shortened metacarpal bones, small and irregular carpal and tarsal bones, platyspondyly, hip dysplasia, flared lower coastal margin, elevated mucopolysaccharide levels in his urine, abnormal band pattern of urine oligosaccharides on electrophoresis, reduced β-galactosidase activity in white blood cells (12.3 nmol/h/mg protein), thoracic kyphosis measuring 4° and narrowing of the spinal canal diameter, diffuse lumbar spinal stenosis, narrow lumbar nerve root exit foramina, anterior beaking of the C3–T2 vertebral bodies, low bone mass for his age, ankle valgus (32° bilaterally at age 10), able to walk >1 km slowly with custom bilateral UCBL in-shoe orthotics, but preferred wheelchair, bilateral triggering fingers (right thumb, right index finger, right long digits, left ring digit), relative ulnar shortening compared to the radius, good wrist strength with normal pronation and supination, genu valgum, right-sided inguinal hernia (surgically repaired at age 7), soft systolic ejection murmur at the mid-left sternal border, redundant cords to the anterior mitral leaflet with leaflet thickening (age 6), mitral regurgitation (grade 2/6 pansystolic murmur at age 8), mild corneal clouding, normal polysomnogram, audiology, cognition assessment, nerve conduction study (age 5–7), stable kyphosis at the thoracolumbar junction, broad-based kyphosis centered on the thoracolumbar junction, anterior subluxation of T12 with respect to L1, full range of motion in the neck, no significant cervical instability clinically or radiographically, elevated ferritin levels, chronic pain in hips and legs with gait deterioration requiring wheelchair use for longer distances in adolescence, sleeping problems related to stiffness, pain, and anxiety, slightly elevated intraocular pressure on the right, collapsed left foot arch compared to the right, weak hands and intrinsics, finger escape during sustained finger adduction, Trendelenburg gait. This patient has a mutation in <|PhenoGemini-Special-Token-Entrez-ID-2720|>.
+...
+Based on all the information above, and my own general knowledge, this patient is likely to have a mutation in
+```
+### Output:
+| Token | Gene Symbol | Probability |
+|-------|-------------|-------|
+| `<\|PhenoGemini-Special-Token-Entrez-ID-2200\|>` | FBN1   | 0.560 |
+| `<\|PhenoGemini-Special-Token-Entrez-ID-7043\|>` | TGFB3  | 0.120 |
+| `<\|PhenoGemini-Special-Token-Entrez-ID-2588\|>` | GALNS  | 0.040 |
+| `<\|PhenoGemini-Special-Token-Entrez-ID-4087\|>` | SMAD2  | 0.020 |
+| `<\|PhenoGemini-Special-Token-Entrez-ID-7048\|>` | TGFBR2 | 0.020 |
+| `<\|PhenoGemini-Special-Token-Entrez-ID-1280\|>` | COL2A1 | 0.017 |
+| `<\|PhenoGemini-Special-Token-Entrez-ID-2317\|>` | FLNB   | 0.016 |
+
 # Contact
 For questions about individual modules or accessing additional data, please email `dr.wunan@pumch.cn`, `jeffchenmed@gmail.com`, or `caijh09@gmail.com`.