Patients must have histologically or cytologically confirmed alveolar soft part sarcoma that is not curable by surgery; diagnosis of malignancy must be confirmed by the department of pathology at the institution where the patient is enrolled prior to patient enrollment Histologically confirmed diagnosis of adenocarcinoma of the rectum Patients must have a biopsy with histologically confirmed diagnosis of recurrent endometrial cancer confined to the pelvis and/or vagina and no evidence of extrapelvic disease Histologically confirmed diagnosis of WHO grade II meningioma confirmed by central pathology review prior to step registration Histologically confirmed, new diagnosis of PTCL Histologically or cytologically confirmed diagnosis of limited or extensive stage SCLC which failed one prior platinum-containing regimen and with a chemotherapy-free interval (CTFI, time from the last dose of first-line chemotherapy to the occurrence of progressive disease) ? days. Small-cell carcinoma of unknown primary site with or without neuroendocrine features confirmed in histology test(s) performed on metastatic lesion(s) are eligible, if Ki-/MIB- is expressed in >% of tumor cells. Histologically confirmed advanced malignant melanoma, regardless of subtype (for screening and treatment phases) Patients must have histologically or cytologically confirmed invasive breast cancer, with stage IV disease; patients without pathologic or cytologic confirmation of metastatic disease should have unequivocal evidence of metastasis from physical examination or radiologic evaluation Histologically confirmed presence of BCG-unresponsive CIS (with or without Ta or T disease) or histologically confirmed presence of BCG-unresponsive high-grade Ta or T disease. COHORT D: Histologically confirmed diagnosis of melanoma Have a histologically-confirmed diagnosis of MB, NB, ES, or ARMS Patients must have persistent or recurrent histologically confirmed USC The diagnosis must be histologically confirmed by a gynecologic pathologist as containing >= % uterine papillary serous (UPSC) adenocarcinoma in the specimen Participants must have histologically or cytologically confirmed stage IV invasive breast cancer. Participants without pathologic or cytologic confirmation of metastatic disease should have unequivocal evidence of metastasis from physical examination or radiologic evaluation Epithelial Endometrial Cancer: histologically confirmed diagnosis (by either primary surgical specimen or biopsy for recurrence) of recurrent previously treated EEC. Histologically confirmed diagnosis of GIST histologically confirmed diagnosis of metastatic CRPC Participants must have histologically or cytologically confirmed invasive breast cancer, with metastatic disease; participants without pathologic or cytologic confirmation of metastatic disease should have unequivocal evidence of metastasis from physical examination or radiologic evaluation New diagnosis of brain metastases from a histologically or cytologically confirmed primary or metastatic NSCLC tumor within years of registration on the study. If the original histological proof of malignancy is greater than years, then pathological confirmation is required (i.e.: from extra-cranial or intracranial disease). Histologically confirmed lymphoma (WHO classification), or confirmed MM (IMWG), that is relapsed and/or refractory. Patient must have biopsy-confirmed diagnosis of Langerhans cell histiocytosis Part : HNSCC, with confirmed p mutations Histologically confirmed diagnosis of one of the following: Stratum D: Patients must have a histologically confirmed diagnosis of ependymoma that is recurrent, progressive or refractory following therapy which included radiotherapy Stratum E: Patients must have a histologically confirmed diagnosis of medulloblastoma that is recurrent, progressive or refractory following therapy which included radiotherapy Histologically confirmed CAH or grade EC Histologically confirmed neurotropic primary melanoma Histologically confirmed diagnosis of cHL. Prior diagnosis of Langerhans cell histiocytosis (strata A and B) or LCH-related disorder (stratum C) established by standard diagnostic criteria and confirmed histologically Participants must have histologically or cytologically confirmed invasive breast cancer, with metastatic disease; participants without pathologic or cytologic confirmation of metastatic disease should have unequivocal evidence of metastasis from physical examination or radiologic evaluation Have histologically or cytologically confirmed diagnosis of SCCHN irrespective of PD-L status, which is either inoperable and recurrent, or metastatic Histologically confirmed advanced TET (thymoma or thymic carcinoma) Patients with chemo-sensitive histologically confirmed NHL will be eligible for this treatment protocol contingent on histologic sub-classification Histologically confirmed malignancy of the bladder Patients must have histologically or cytologically confirmed epithelial endometrial carcinoma; all histologies are accepted; patients with diagnosis of endometrial carcinosarcoma will be enrolled in the exploratory cohort (arm C) and will receive combination of cabozantinib and nivolumab Histologically confirmed prostate cancer of any stage undergoing RP Patients must have histologically confirmed diagnosis of chordoma; the pathologic confirmation may be from another metastatic site Patients must be diagnosed with relapse of previously histologically confirmed PFEPN Subjects with histologically confirmed metastatic breast cancer that is either TNBC or HR-positive Patients must have histologically confirmed diagnosis of melanoma; the pathologic confirmation may be from another metastatic site or from metastatic brain or spine lesions Histologically confirmed DLBCL (WHO classification). Patients must have a histologically confirmed diagnosis of endometrial cancer and no clinical evidence of extra-uterine disease on preoperative evaluation Histologically confirmed diagnosis of melanoma Patients must have histologically confirmed diagnosis of osteosarcoma or Ewing sarcoma by central review, except if the diagnosis was already confirmed by the RRePS (Rseau de Rfrence en Pathologie des Sarcomes et des Tissus Mous et des Viscres) network Advanced malignancies (except leukemias), histologically proven at diagnosis; Histologically confirmed advanced malignancies that are known to be sensitive to PF- inhibition, e.g. ALK, c-MET and ROS New diagnosis of histologically confirmed adenocarcinoma of the rectum Histologically confirmed metastatic or recurrent HER-negative (via IHC or FISH per ASCO/CAP guidelines ) breast cancer or histologically confirmed metastatic solid tumor Histologically confirmed cancer by a Mount Sinai pathologist Histologically confirmed diagnosis of cancer as per the cohort specifications Histologically confirmed diagnosis of epithelial cancer; subject must have a measurable disease for enrollment consideration Patients with histologically or cytologically confirmed metastatic clear cell RCC who are eligible for cytoreductive nephrectomy, metastasectomy or post-treatment biopsy; diagnosis must be confirmed by pathologist review of screening biopsy; the determination of resectability will ultimately lie in the clinical judgment of the urologist and medical oncologist involved in the care of the patient Participants must have histologically confirmed primary cancer of the uterus or cervix with histologically confirmed metastasis to one or more parametrial, pelvic, or para-aortic nodes prior to enrollment; participants diagnosed at other institutions must have pathology reviewed and confirmed at Massachusetts General Hospital (MGH) or another Dana-Farber (DF)/Harvard Cancer Center (HCC) institution Patient must have suspected intrahepatic or hilar cholangiocarcinoma with minimal extrahepatic disease; diagnosis must be histologically or cytologically confirmed for continued treatment on study after pump placement Histologically confirmed diagnosis of chordoma or chondrosarcoma Patients must have histologically confirmed malignancy with brain metastases and are being recommended palliative WBRT Histologically positive margins Histologically confirmed invasive well-moderately differentiated rectal adenocarcinoma diagnosed within days prior to enrollment. Histologically confirmed diagnosis of ACC according to Weiss system by a national reference pathologist who has to be nominated before study initiation. Histologically-confirmed Tb, T or T gallbladder cancer discovered incidentally at the time of or following routine cholecystectomy for presumed benign disease Patients with histologically-confirmed Tis, Ta, or T tumors Women with biopsy confirmed high grade cervical intraepithelial lesions (diagnosis confirmed by\r\npositive p immunohistochemistry staining) within weeks of baseline visit Histologically confirmed diagnosis of a CD+ B-cell malignancy; Patients with histologically confirmed carcinoma of the female breast with any or unknown hormone receptors (HRs)/HER status Histologically confirmed plasmacytoma amenable for biopsy Subjects with histologically confirmed diagnosis of recurrent germ cell tumor Patients must have histologically confirmed localized or locally advanced breast cancer for which the treatment plan includes chemotherapy with cycles of standard TC (docetaxel mg/m^ and cyclophosphamide mg/m^) Histologically or cytologically confirmed diagnosis of biliary tract adenocarcinoma/ cholangiocarcinoma (including primary intra- and extrahepatic diseases); pathologic confirmation may be made from the primary or a metastatic site Must have histologically confirmed diagnosis of MPNST Patients with a histologically-confirmed diagnosis of melanoma who have imaging findings suggestive of to brain metastases Patients with chemotherapy (chemo)-sensitive histologically confirmed NHL will be eligible for this treatment protocol contingent on histologic subclassification The diagnosis must be histologically confirmed by a gynecologic pathologist as containing >= % UPSC adenocarcinoma in the specimen Has one of the following histologically confirmed tumors: (NOTE: Evidence of diagnostic pathology of original biopsy confirmed by a CLIA/CAP certified laboratory must be available) Has one of the following histologically confirmed tumors: Part : histologically confirmed disease in specific tumor types Patients with histologically confirmed intrahepatic, perihilar or extra-hepatic CCA. Based on RECIST v. criteria on current nivolumab treatment (prior to initiation of this study), has a best response of confirmed stable disease (SD) or confirmed progressive disease (PD). Confirmed SD or confirmed PD refers to a response that is confirmed by a nd scan which is at least weeks apart from the previous scan. Histologically-confirmed disease Histologically confirmed non-keratinizing differentiated NPC or undifferentiated NPC Specific eligibility criteria for Part CRPC expansion cohort: Histologically or cytologically confirmed diagnosis of prostate adenocarcinoma, surgically castrated or continuously medically castrated (for >= weeks prior to pre-screening). Histologically confirmed diagnosis of DLBCL Histologically-confirmed epithelial or biphasic MPM; biphasic tumors must have a predominantly (?%) epithelial component Histologically confirmed diagnosis of R/R AITL (eligibility needs to be confirmed by central pathological review). Have a histologically or cytologically confirmed diagnosis of non-resectable, recurrent, or metastatic biliary tract adenocarcinoma (intrahepatic or extrahepatic cholangiocarcinoma, gallbladder cancer, or Ampulla of Vater) . Participants must have histologically confirmed B-cell NHL Histologically confirmed diagnosis of melanoma Histologically confirmed diagnosis of malignant melanoma. Histologically confirmed melanoma of cutaneous origin Confirmed or suspected endocarditis Confirmed HER positive status Participant has histologically or cytologically confirmed adenocarcinoma of the breast that is now metastatic or locally-recurrent and inoperable with curative intent. Every effort should be made to make paraffin-embedded tissue or slides from the diagnostic biopsy or surgical specimen available for confirmation of diagnosis Histologically documented diagnosis of DLBCL. Patients must have histologically-confirmed endometrial carcinoma (endometrioid and mixed endometrioid tumors, any grade). Patients must have a histologically confirmed diagnosis of Ph+ ALL Histologically confirmed diagnosis of advanced (metastatic, recurrent, or unresectable) cancer with mutations in any of the following genes: TSC, TSC, NF, NF, or STK Histologically confirmed recurrent or metastatic SCCHN Histologically confirmed papillary serous adenocarcinoma or endometrioid type of endometrial carcinoma (histological documentation of recurrence is not required); Patients with unresectable or metastatic histologically confirmed sporadic or NF associated high grade MPNST Histologically confirmed squamous cell carcinoma of the cervix (any grade) or histologically confirmed grade or adenocarcinoma of cervix Histologically confirmed AML with >% blasts Histologically confirmed intrahepatic cholangiocarcinoma (also variously reported as peripheral cholangiocarcinoma, cholangiolar carcinoma or cholangiocellular carcinoma) (ICC); confirmation of the diagnosis must be made at MSKCC or at the participating institution prior to initiating protocol therapy Histologically-confirmed non-germinal center B-cell subtype DLBCL Patients must have histologically-confirmed advanced or recurrent endometrial carcinoma (endometrioid and mixed tumors, any grade) that is refractory to curative therapy or established treatments A histologically confirmed rectal cancer with measurable or evaluable disease on imaging or endoscopy Histologically confirmed diagnosis of mycosis fungoides (MF) or Sezary Syndrome (SS) Histologically confirmed AL or LCDD (from any time prior to screening) Have a confirmed diagnosis of endometrial hyperplasia without atypia based upon endometrial biopsy histologically-confirmed diagnosis according to REAL/WHO classification, of the following B-cell lymphomas : Patients must have a histologically confirmed diagnosis of endometrial cancer and no clinical evidence of extra-uterine disease on preoperative evaluation Histologically confirmed diagnosis of melanoma Patients must have histologically or cytologically confirmed invasive breast cancer, with metastatic disease; patients without pathologic or cytologic confirmation of metastatic disease should have unequivocal evidence of metastasis by physical exam or radiologic study Subjects must have histologically-confirmed chordoma Patients biopsies must be histologically confirmed CD positive within months of enrollment Patients must have histologically confirmed adenocarcinoma of the small bowel or ampulla of Vater that is either unresectable or metastatic Histologically-confirmed HL Confirmed pathologic diagnosis of a solid tumor that is not curable with available therapies for which HKI- plus vinorelbine is a reasonable treatment option (part only) or Confirmed pathologic diagnosis of ErbB--positive breast cancer (current stage IV) in female subjects for which vinorelbine plus HKI- is a reasonable treatment option (part only). Histologically confirmed MCL Histologically confirmed diagnosis of B-lineage ALL. Verification of CD expression is not required Histologically confirmed DLBCL(Cohort C) Histologically confirmed CD positive primary B-cell CNS lymphoma (PCNSL) confirmed by one of the following: Patients must be males with histologically confirmed and clinically localized low-grade and low-volume prostate cancer demonstrated at the time of initial diagnosis Patients in Parts and must have histologically confirmed diagnosis of CD-positive DLBCL Histologically confirmed biliary tract or gallbladder cancer that have relapsed or are refractory after one prior gemcitabine-based chemotherapy regimen for advanced biliary cancer Histologically confirmed diagnosis of osteosarcoma with lung metastasis, who have progressed on the prior line of therapy, or relapsed LUNG ADENOCARCINOMA COHORT (COHORT ONLY): Subjects must have histologically confirmed advanced (stage IIIB/IV) lung adenocarcinoma; the diagnosis will be confirmed by the Laboratory of Pathology/CCR/NCI Histologically confirmed non-squamous histologies are not allowed; an exception is made for WHO type I-III nasopharynx histologies Patients in the phase I portion must have:\r\n* Histologically confirmed diagnosis of metastatic, genitourinary solid tumor\r\n* Metastatic disease defined as new or progressive lesions on cross-sectional imaging; patients must have at least:\r\n** One evaluable site of disease \r\n** Or, appearance of one new bone lesion Histologically confirmed: Histologically confirmed uterine leiomyosarcoma with disease limited to the uterus (determined by surgical staging or radiologic imaging). Histologically documented leiomyosarcoma Participants must have histologically confirmed intrahepatic cholangiocarcinoma (IHC) without evidence of extrahepatic metastasis within months prior to study registration Subjects with histologically or cytologically confirmed mCRC, Kirsten rat sarcoma wild-type (KRAS WT) at initial diagnosis Histologically confirmed diagnosis of PTCL Histologically confirmed endometrial cancer Histologically confirmed angiosarcoma Patients must have histologically confirmed metastatic alveolar soft part sarcoma that is not curable by surgery; diagnosis of malignancy must be confirmed by the department of pathology at the institution where the patient is enrolled prior to patient enrollment Histologically- or cytologically-confirmed MPeM; epithelial, sarcomatoid, biphasic, multi-cystic, or well-differentiated papillary subtypes are allowed Histologically confirmed diagnosis of conventional chondrosarcoma of any grade. Histologically confirmed medulloblastoma located in the posterior fossa \r\n* Standard-risk disease Histologically confirmed diagnosis, measurable disease and evidence of disease progression of MM. Patients must have histologically confirmed diagnosis of recurrent, persistent or advanced (stage IVB) squamous, adenocarcinoma or adenosquamous cervical cancer Histologically confirmed diagnosis of metastatic melanoma with the presence of the B-Raf proto-oncogene, serine/threonine kinase (BRAFV) mutation Histologically confirmed cancer diagnosis Histologically confirmed diagnosis for which an allogeneic transplant is utilized Patients must have histologically or cytologically confirmed stage IV invasive breast cancer; patients without pathologic or cytologic confirmation of metastatic disease should have unequivocal evidence of metastasis from physical examination or radiologic evaluation Subject has a diagnosis of high grade myxoid liposarcoma / myxoid round cell liposarcoma confirmed histologically and by the presence of the reciprocal chromosomal translocation t(;)(q;p) or t(; ) (q;q) Must have a histologically confirmed cancer diagnosis Adolescents and young adults (AYA) with histologically confirmed cancer who have completed primary treatment Patients must have histologically confirmed T-T and N-N, M adenocarcinoma of the rectum with the inferior margin within cm from the anal verge Histologically confirmed breast cancer and no evidence of metastatic disease with a recommendation to begin chemotherapy within weeks Adult men of all races and body size with histologically confirmed localized PCa on AS Have histologically confirmed cancer CANCER PATIENT GROUP: Histologically confirmed non-metastatic PCa Patients with histologically confirmed diagnosis of cancer; NOTE: patients with active cancer or post treatment are allowed on the study Nave or non-nave patient with histologically, and/or cytologically (or imaging in the case of brain tumors) confirmed malignant disease. Subject must have histologically confirmed at last relapse aggressive B-cell NHL according to \The revision of the WHO classification of lymphoid neoplasms\ defined as: If, based on surgeons assessment, the patient is recommended to undergo surgical staging for histologically confirmed endometrial cancer or if IB cervical cancer is deemed eligible for surgical treatment of disease History of histologically confirmed melanoma as assessed per medical record review Patients must have histologically confirmed primary or metastatic cancer; if biopsies were performed at an outside facility, the histology must be reviewed and confirmed by the Department of Pathology at the City of Hope Subjects must have:\r\n* Diagnosis of NF with a lesion concerning for MPNST\r\n** Criteria include pain, growth of a known plexiform neurofibroma, abnormality on functional imaging study (FDG-PET) or change in clinical exam OR\r\n* Diagnosis of NF with a histologically confirmed MPNST Participants must have histologically confirmed intracranial meningioma, grade II-III, that has recurred or progressed after previous treatment Mediastinal nodal metastases (N) disease must be confirmed histologically Patients must have histologically-confirmed HNSCC with surgically resectable disease Histologically confirmed: Histologically confirmed recurrent or metastatic carcinoma of the nasopharynx is allowed, but these participants will not be included as response-evaluable participants for efficacy analysis of HNSCC. Participants must have histologically or cytologically confirmed diagnosis of one of the following differentiated thyroid cancer (DTC) subtypes: