Functions — github.com/bunnelab/mtbbench

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Functions164 in github.com/bunnelab/mtbbench

⨍ Functions 164◇ Types & classes 22

Method__init__

(self)

neurips25/tools/pubmed.py:24

Method__init__

(self, local: bool = True, out_path: str = "data/drugbank")

neurips25/tools/drugbank.py:16

Method__init__

(self, device: str, post_process_size=1024)

neurips25/tools/conch.py:8

Method__init__

(self, patient_id: str)

neurips25/utils/hancock_patient.py:26

Method__init__

(self, input_feature_dim=1536, n_heads=1, head_dim=512, dropout=0.2, gated=True, hidden_dim=512)

neurips25/utils/train_abmil.py:16

Method__init__

(self, sample_id: str)

neurips25/utils/patient.py:27

Method__init__

(self, patient_id: str)

neurips25/utils/patient.py:80

Method__init__

(self, model_name, hf_token=None)

neurips25/eval/gemma_3.py:11

Method__init__

(self, model_name, hf_token=None)

neurips25/eval/base_hf_eval.py:9

Method__init__

(self, tools=False, use_all_but_last_device=False, *args, **kwargs)

neurips25/eval/hf_eval_text2text.py:97

Method__init__

(self, model_name, hf_token=None)

neurips25/eval/internvl.py:12

Method__init__

(self, model_name, hf_token=None, openai_token=None)

neurips25/eval/gpt_4o.py:8

Method__init__

(self, tools=False, *args, **kwargs)

neurips25/eval/vllm_eval_multimodal.py:56

Method__init__

(self, model_name, hf_token=None, use_last_device_for_eval=False)

neurips25/eval/qwen_25_vl.py:10

Method__init__

Initialize the PatientAgent with the main LLM and oracle LLM for answers.

neurips25/models/agent_with_tools_msk.py:16

Method__init__

Initialize the PatientAgent with the main LLM and oracle LLM for answers.

neurips25/models/agent_with_tools.py:14

Method__init__

Initialize the PatientAgent with the main LLM and oracle LLM for answers.

neurips25/models/agent.py:12

Method__len__

(self)

neurips25/utils/train_abmil.py:117

Method__missing__

(key)

neurips25/utils/patient.py:201

Methodcollapse_list_values

(row)

neurips25/tools/drugbank.py:112

Methodconvert_to_chat_format

Convert the input messages to the chat format required by the model.

neurips25/eval/base_hf_eval.py:30

Methoddecode_response

Decode the generated response into human-readable text.

neurips25/eval/gemma_3.py:83

Methoddecode_response

Decode the generated response to a human-readable format.

neurips25/eval/hf_eval_text2text.py:86

Methoddecode_response

Decode the generated response to a human-readable format.

neurips25/eval/hf_eval_text2text.py:163

Methoddecode_response

Decode the generated response into human-readable text.

neurips25/eval/internvl.py:81

Methoddecode_response

Decode the response from the model into a human-readable text.

neurips25/eval/gpt_4o.py:77

Methoddecode_response

Decode the generated response to a human-readable format.

neurips25/eval/vllm_eval_multimodal.py:115

Methoddecode_response

(self, response)

neurips25/eval/vllm_eval_multimodal.py:179

Methoddecode_response

Decode the generated response into human-readable text.

neurips25/eval/qwen_25_vl.py:78

Methoddefault_format

(event)

neurips25/utils/patient.py:203

Functionextract_prompt

(text, word)

neurips25/tools/pubmed.py:17

Methodforward

(self, x)

neurips25/utils/train_abmil.py:40

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/gemma_3.py:73

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/hf_eval_text2text.py:70

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/hf_eval_text2text.py:157

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/internvl.py:73

Methodgenerate_response

Generate a response using the chat client based on the processed inputs.

neurips25/eval/gpt_4o.py:65

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/vllm_eval_multimodal.py:98

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/vllm_eval_multimodal.py:162

Methodgenerate_response

Generate a response from the model based on the inputs.

neurips25/eval/qwen_25_vl.py:66

Methodimage_to_image_retrieval

Finds the most similar image from a list of images given a reference image. Args: image_path (str): The path to a histop

neurips25/tools/conch.py:46

Methodload_model

Load the model from the specified model name.

neurips25/eval/base_hf_eval.py:15

Methodload_model

(self)

neurips25/eval/gpt_4o.py:13

Methodload_processor

Load the processor from the specified model name.

neurips25/eval/base_hf_eval.py:22

Methodload_processor

(self)

neurips25/eval/hf_eval_text2text.py:19

Methodload_processor

(self)

neurips25/eval/hf_eval_text2text.py:105

Methodload_processor

(self)

neurips25/eval/gpt_4o.py:16

Methodparse_ICD_OPS_codes

(icd_codes_text: str)

neurips25/utils/hancock_patient.py:130

Functionplot_wsi

Plot the WSI with the annotations overlayed.

neurips25/utils/create_patient_cases.py:13

Methodprocess_text

(self, messages)

neurips25/eval/gemma_3.py:64

Methodprocess_text

Process the input text and prepare it for the model.

neurips25/eval/hf_eval_text2text.py:54

Methodprocess_text

Process the input text and prepare it for the model.

neurips25/eval/hf_eval_text2text.py:150

Methodprocess_text

(self, messages)

neurips25/eval/internvl.py:65

Methodprocess_text

Process the text and vision inputs.

neurips25/eval/gpt_4o.py:58

Methodprocess_text

Process the input text and prepare it for the model.

neurips25/eval/vllm_eval_multimodal.py:86

Methodprocess_text

Process the input text and prepare it for the model.

neurips25/eval/vllm_eval_multimodal.py:150

Methodprocess_text

(self, messages)

neurips25/eval/qwen_25_vl.py:50

Methodrun_case

Run the agent on a single patient case.

neurips25/models/agent_with_tools_msk.py:137

Methodrun_case

Run the agent on a single patient case.

neurips25/models/agent_with_tools.py:182

Functionsearch_pubmed

Search PubMed for articles related to a given search term or fetch a specific article by its PubMed ID. Args: search_text: (str) The

neurips25/tools/pubmed.py:106

Methodtest

Test printing the timelines of 10 random patients

neurips25/utils/patient.py:254

Methodtext_to_image_retrieval

Finds the most relevant image based on a given text prompt from a list of images. Args: prompt (str): The text prompt us

neurips25/tools/conch.py:77

Methodto_markdown

(self)

neurips25/utils/patient.py:68

Methodvalue_status

(row)

neurips25/utils/hancock_patient.py:67

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