sentence-transformers How to use ksg-dfci/TrialSpace-1225 with sentence-transformers:
from sentence_transformers import SentenceTransformer
model = SentenceTransformer("ksg-dfci/TrialSpace-1225")
sentences = [
"Instruct: Given a cancer patient summary, retrieve clinical trial options that are reasonable for that patient; or, given a clinical trial option, retrieve cancer patients who are reasonable candidates for that trial. Age: 5 \nSex: Male \nCancer type: Medulloblastoma \nPrimary site: Cerebellum (posterior fossa) \nHistology: WHO Grade IV, Group 4 embryonal tumor (small round blue cell) \n\nCurrent extent: Localized persistent residual disease confined to the posterior fossa (vermian nodule ~1.5 cm plus several <3 mm cerebellar cortical foci); no leptomeningeal, spinal, or distant metastases on latest MRI (11/2024); disease considered stable. \n\nBiomarkers: \n• YAP1 positive, β‑catenin negative (consistent with Group 4) \n• Ki‑67 proliferation index ≈60 % on repeat biopsy (↑ from 40 % at diagnosis) \n• Chromosome 17q gain (+3 copies) – present at diagnosis and retained \n• CDK6 amplification, OTX2 amplification, TERT promoter −124 C>T mutation – present at diagnosis and retained \n• KMT2C frameshift, low‑level MYCN gain – present at diagnosis \n• Acquired homozygous CDKN2A deletion (loss of CDK inhibitor) – identified on recurrence NGS (8/2022) \n• SMARCA4 p.Glu1579Lys missense mutation – acquired on recurrence NGS (8/2022) \n• No MYC, TP53, CTNNB1 mutations; no actionable target per current FDA‑approved pediatric drugs. \n\nTreatment history: \n# 12/2020 – 12/2020: Gross‑total resection of right cerebellar/brainstem medulloblastoma via right suboccipital/craniotomy; margins negative. \n# 8/2022 (≈age 3.1 yr): Oral prednisone 1 mg/kg twice daily × 14 days for peritumoral edema associated with recurrence. \n# 8/2022 – present: Low‑dose dexamethasone (range 0.05–0.15 mg/kg daily) continuously for symptom control (edema, nausea, ataxia). No systemic chemotherapy, no craniospinal irradiation, and no enrolment in a clinical trial yet (investigation pending).",
"Instruct: Given a cancer patient summary, retrieve clinical trial options that are reasonable for that patient; or, given a clinical trial option, retrieve cancer patients who are reasonable candidates for that trial. Age range allowed: 1 Year to 39 Years. Sex allowed: Male and Female. Cancer type allowed: Myeloid sarcoma. Histology allowed: Extramedullary presentation of myeloid malignancy. Cancer burden allowed: Relapsed or refractory disease. Prior treatment required: Full recovery from prior hematopoietic stem cell transplantation or anthracycline exposure. Prior treatment excluded: Current administration of anticancer agents (except intrathecal agents or hydroxyurea). Biomarkers required: NA. Biomarkers excluded: Philadelphia chromosome/BCR‑ABL1 fusion, KMT2A rearrangement, acute promyelocytic leukemia characteristics, Down‑syndrome‑associated leukemia.",
"Instruct: Given a cancer patient summary, retrieve clinical trial options that are reasonable for that patient; or, given a clinical trial option, retrieve cancer patients who are reasonable candidates for that trial. Age range allowed: ≥ 36 months and < 22 years. Sex allowed: Both. Cancer type allowed: Primary malignant cerebellar brain tumor – Giant cell glioblastoma. Histology allowed: Giant cell glioblastoma. Cancer burden allowed: Single cerebellar lesion measurable 1.0–3.0 cm, surgially accessible, recurrent or progressive after standard therapy, not diffuse across ≥3 brain lobes, not involving ventricles or brainstem. Prior treatment required: Surgical resection and/or radiotherapy and/or systemic chemotherapy. Prior treatment excluded: NA. Biomarkers required: NA. Biomarkers excluded: NA.",
"Instruct: Given a cancer patient summary, retrieve clinical trial options that are reasonable for that patient; or, given a clinical trial option, retrieve cancer patients who are reasonable candidates for that trial. Age range allowed: ≥ 36 months and < 22 years. Sex allowed: Both. Cancer type allowed: Primary malignant cerebellar brain tumor – Giant cell glioblastoma. Histology allowed: Giant cell glioblastoma. Cancer burden allowed: Single cerebellar lesion measurable 1.0–3.0 cm, surgially accessible, recurrent or progressive after standard therapy, not diffuse across ≥3 brain lobes, not involving ventricles or brainstem. Prior treatment required: Surgical resection and/or radiotherapy and/or systemic chemotherapy. Prior treatment excluded: NA. Biomarkers required: NA. Biomarkers excluded: NA."
]
embeddings = model.encode(sentences)
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [4, 4] 
