Initial config export (README, examples)

README.md

@@ -1,3 +1,46 @@
----
-license: mit
----
+---
+license: mit
+language: en
+tags:
+  - medical
+  - config
+  - med-vllm
+library_name: medvllm
+pipeline_tag: token-classification
+---
+
+# Med vLLM (Config-first Repository)
+
+This repository serves as a config-first landing for the Med vLLM stack.
+
+It contains example configuration files and is intended to help users discover
+and consume the `MedicalModelConfig` from the Hub via `from_pretrained`, and to
+use these as starting points for training or inference in medical NLP tasks.
+
+## Contents
+
+- NER config example (`examples/ner/`)
+- Classification config example (`examples/classification/`)
+- Generation config example (`examples/generation/`)
+
+## Usage (Python)
+
+```python
+from medvllm.medical.config.models.medical_config import MedicalModelConfig
+cfg = MedicalModelConfig.from_pretrained("Junaidi-AI/med-vllm")
+print(cfg.task_type)
+```
+
+Or directly load a specific example folder if exported as a subfolder with
+its own config files.
+
+## Medical Disclaimer
+
+This repository and associated configurations are provided for research and
+engineering purposes only. They are not intended for clinical decision-making.
+Always involve qualified healthcare professionals and ensure compliance with
+applicable regulations (e.g., HIPAA, GDPR). Avoid using PHI/PII.
+
+## License
+
+MIT

examples/classification/config.json

@@ -0,0 +1,103 @@
+{
+  "_serializing": true,
+  "activation_recompute": false,
+  "adapter_config": null,
+  "adapter_type": null,
+  "allow_tf32": false,
+  "anatomical_regions": [
+    "head"
+  ],
+  "attention_impl": null,
+  "batch_size": 16,
+  "cache_ttl": 3600,
+  "classification_labels": [
+    "diagnosis",
+    "treatment",
+    "follow-up"
+  ],
+  "config_version": "1.0.0",
+  "cudnn_benchmark": null,
+  "document_types": [
+    "clinical_note",
+    "discharge_summary",
+    "radiology_report"
+  ],
+  "domain_adaptation": false,
+  "domain_adaptation_lambda": 0.1,
+  "domain_specific_vocab": null,
+  "emit_trace": false,
+  "enable_flash_attention": null,
+  "enable_memory_pooling": false,
+  "enable_mixed_precision": false,
+  "enable_profiling": false,
+  "enable_uncertainty_estimation": false,
+  "enforce_eager": false,
+  "entity_linking": {
+    "confidence_threshold": 0.8,
+    "enabled": false,
+    "knowledge_bases": [
+      "umls",
+      "snomed_ct",
+      "loinc"
+    ]
+  },
+  "eos": -1,
+  "file_path": null,
+  "flash_attention_config": null,
+  "gpu_memory_utilization": 0.9,
+  "grad_checkpointing": false,
+  "hf_config": "namespace(model_type='unknown', max_position_embeddings=4096)",
+  "imaging_modalities": [
+    "xray"
+  ],
+  "kvcache_block_size": 256,
+  "max_entity_span_length": 10,
+  "max_medical_seq_length": 4096,
+  "max_model_len": 4096,
+  "max_num_batched_tokens": 32768,
+  "max_num_seqs": 512,
+  "max_retries": 3,
+  "medical_entity_types": [
+    "disease"
+  ],
+  "medical_specialties": [
+    "cardiology"
+  ],
+  "memory_efficient": true,
+  "mixed_precision_dtype": "fp16",
+  "model": "emilyalsentzer/Bio_ClinicalBERT",
+  "model_type": "medical_llm",
+  "ner_confidence_threshold": 0.5,
+  "num_kvcache_blocks": -1,
+  "pool_device": "auto",
+  "pool_max_bytes": null,
+  "pretrained_model_name_or_path": "emilyalsentzer/Bio_ClinicalBERT",
+  "profiler_device": "auto",
+  "quantization_bits": null,
+  "quantization_method": null,
+  "recompute_granularity": null,
+  "regulatory_compliance": [
+    "hipaa",
+    "gdpr"
+  ],
+  "request_timeout": 30,
+  "section_headers": [
+    "history_of_present_illness",
+    "past_medical_history",
+    "medications",
+    "allergies",
+    "family_history",
+    "social_history",
+    "review_of_systems",
+    "physical_exam",
+    "assessment_and_plan"
+  ],
+  "task_type": "classification",
+  "tensor_parallel_size": 1,
+  "torch_matmul_precision": null,
+  "trace_dir": "profiles",
+  "uncertainty_threshold": 0.7,
+  "use_cuda_graphs": false,
+  "use_medical_adapter": true,
+  "version": "0.1.0"
+}

examples/classification/config.yaml

@@ -0,0 +1,91 @@
+_serializing: true
+activation_recompute: false
+adapter_config: null
+adapter_type: null
+allow_tf32: false
+anatomical_regions:
+- head
+attention_impl: null
+batch_size: 16
+cache_ttl: 3600
+classification_labels:
+- diagnosis
+- treatment
+- follow-up
+config_version: 1.0.0
+cudnn_benchmark: null
+document_types:
+- clinical_note
+- discharge_summary
+- radiology_report
+domain_adaptation: false
+domain_adaptation_lambda: 0.1
+domain_specific_vocab: null
+emit_trace: false
+enable_flash_attention: null
+enable_memory_pooling: false
+enable_mixed_precision: false
+enable_profiling: false
+enable_uncertainty_estimation: false
+enforce_eager: false
+entity_linking:
+  confidence_threshold: 0.8
+  enabled: false
+  knowledge_bases:
+  - umls
+  - snomed_ct
+  - loinc
+eos: -1
+file_path: null
+flash_attention_config: null
+gpu_memory_utilization: 0.9
+grad_checkpointing: false
+hf_config: namespace(model_type='unknown', max_position_embeddings=4096)
+imaging_modalities:
+- xray
+kvcache_block_size: 256
+max_entity_span_length: 10
+max_medical_seq_length: 4096
+max_model_len: 4096
+max_num_batched_tokens: 32768
+max_num_seqs: 512
+max_retries: 3
+medical_entity_types:
+- disease
+medical_specialties:
+- cardiology
+memory_efficient: true
+mixed_precision_dtype: fp16
+model: emilyalsentzer/Bio_ClinicalBERT
+model_type: medical_llm
+ner_confidence_threshold: 0.5
+num_kvcache_blocks: -1
+pool_device: auto
+pool_max_bytes: null
+pretrained_model_name_or_path: emilyalsentzer/Bio_ClinicalBERT
+profiler_device: auto
+quantization_bits: null
+quantization_method: null
+recompute_granularity: null
+regulatory_compliance:
+- hipaa
+- gdpr
+request_timeout: 30
+section_headers:
+- history_of_present_illness
+- past_medical_history
+- medications
+- allergies
+- family_history
+- social_history
+- review_of_systems
+- physical_exam
+- assessment_and_plan
+task_type: classification
+tensor_parallel_size: 1
+torch_matmul_precision: null
+trace_dir: profiles
+uncertainty_threshold: 0.7
+use_cuda_graphs: false
+use_medical_adapter: true
+version: 0.1.0

examples/generation/config.json

@@ -0,0 +1,99 @@
+{
+  "_serializing": true,
+  "activation_recompute": false,
+  "adapter_config": null,
+  "adapter_type": null,
+  "allow_tf32": false,
+  "anatomical_regions": [
+    "head"
+  ],
+  "attention_impl": null,
+  "batch_size": 1,
+  "cache_ttl": 3600,
+  "classification_labels": [],
+  "config_version": "1.0.0",
+  "cudnn_benchmark": null,
+  "document_types": [
+    "clinical_note",
+    "discharge_summary",
+    "radiology_report"
+  ],
+  "domain_adaptation": false,
+  "domain_adaptation_lambda": 0.1,
+  "domain_specific_vocab": null,
+  "emit_trace": false,
+  "enable_flash_attention": null,
+  "enable_memory_pooling": false,
+  "enable_mixed_precision": false,
+  "enable_profiling": false,
+  "enable_uncertainty_estimation": false,
+  "enforce_eager": false,
+  "entity_linking": {
+    "confidence_threshold": 0.8,
+    "enabled": false,
+    "knowledge_bases": [
+      "umls",
+      "snomed_ct",
+      "loinc"
+    ]
+  },
+  "eos": -1,
+  "file_path": null,
+  "flash_attention_config": null,
+  "gpu_memory_utilization": 0.9,
+  "grad_checkpointing": false,
+  "hf_config": "namespace(model_type='unknown', max_position_embeddings=4096)",
+  "imaging_modalities": [
+    "xray"
+  ],
+  "kvcache_block_size": 256,
+  "max_entity_span_length": 10,
+  "max_medical_seq_length": 1024,
+  "max_model_len": 1024,
+  "max_num_batched_tokens": 32768,
+  "max_num_seqs": 512,
+  "max_retries": 3,
+  "medical_entity_types": [
+    "disease"
+  ],
+  "medical_specialties": [
+    "cardiology"
+  ],
+  "memory_efficient": true,
+  "mixed_precision_dtype": "fp16",
+  "model": "gpt2",
+  "model_type": "medical_llm",
+  "ner_confidence_threshold": 0.5,
+  "num_kvcache_blocks": -1,
+  "pool_device": "auto",
+  "pool_max_bytes": null,
+  "pretrained_model_name_or_path": "gpt2",
+  "profiler_device": "auto",
+  "quantization_bits": null,
+  "quantization_method": null,
+  "recompute_granularity": null,
+  "regulatory_compliance": [
+    "hipaa",
+    "gdpr"
+  ],
+  "request_timeout": 30,
+  "section_headers": [
+    "history_of_present_illness",
+    "past_medical_history",
+    "medications",
+    "allergies",
+    "family_history",
+    "social_history",
+    "review_of_systems",
+    "physical_exam",
+    "assessment_and_plan"
+  ],
+  "task_type": "generation",
+  "tensor_parallel_size": 1,
+  "torch_matmul_precision": null,
+  "trace_dir": "profiles",
+  "uncertainty_threshold": 0.7,
+  "use_cuda_graphs": false,
+  "use_medical_adapter": true,
+  "version": "0.1.0"
+}

examples/generation/config.yaml

@@ -0,0 +1,88 @@
+_serializing: true
+activation_recompute: false
+adapter_config: null
+adapter_type: null
+allow_tf32: false
+anatomical_regions:
+- head
+attention_impl: null
+batch_size: 1
+cache_ttl: 3600
+classification_labels: []
+config_version: 1.0.0
+cudnn_benchmark: null
+document_types:
+- clinical_note
+- discharge_summary
+- radiology_report
+domain_adaptation: false
+domain_adaptation_lambda: 0.1
+domain_specific_vocab: null
+emit_trace: false
+enable_flash_attention: null
+enable_memory_pooling: false
+enable_mixed_precision: false
+enable_profiling: false
+enable_uncertainty_estimation: false
+enforce_eager: false
+entity_linking:
+  confidence_threshold: 0.8
+  enabled: false
+  knowledge_bases:
+  - umls
+  - snomed_ct
+  - loinc
+eos: -1
+file_path: null
+flash_attention_config: null
+gpu_memory_utilization: 0.9
+grad_checkpointing: false
+hf_config: namespace(model_type='unknown', max_position_embeddings=4096)
+imaging_modalities:
+- xray
+kvcache_block_size: 256
+max_entity_span_length: 10
+max_medical_seq_length: 1024
+max_model_len: 1024
+max_num_batched_tokens: 32768
+max_num_seqs: 512
+max_retries: 3
+medical_entity_types:
+- disease
+medical_specialties:
+- cardiology
+memory_efficient: true
+mixed_precision_dtype: fp16
+model: gpt2
+model_type: medical_llm
+ner_confidence_threshold: 0.5
+num_kvcache_blocks: -1
+pool_device: auto
+pool_max_bytes: null
+pretrained_model_name_or_path: gpt2
+profiler_device: auto
+quantization_bits: null
+quantization_method: null
+recompute_granularity: null
+regulatory_compliance:
+- hipaa
+- gdpr
+request_timeout: 30
+section_headers:
+- history_of_present_illness
+- past_medical_history
+- medications
+- allergies
+- family_history
+- social_history
+- review_of_systems
+- physical_exam
+- assessment_and_plan
+task_type: generation
+tensor_parallel_size: 1
+torch_matmul_precision: null
+trace_dir: profiles
+uncertainty_threshold: 0.7
+use_cuda_graphs: false
+use_medical_adapter: true
+version: 0.1.0

examples/ner/config.json

@@ -0,0 +1,101 @@
+{
+  "_serializing": true,
+  "activation_recompute": false,
+  "adapter_config": null,
+  "adapter_type": null,
+  "allow_tf32": false,
+  "anatomical_regions": [
+    "head"
+  ],
+  "attention_impl": null,
+  "batch_size": 1,
+  "cache_ttl": 3600,
+  "classification_labels": [],
+  "config_version": "1.0.0",
+  "cudnn_benchmark": null,
+  "document_types": [
+    "clinical_note",
+    "discharge_summary",
+    "radiology_report"
+  ],
+  "domain_adaptation": false,
+  "domain_adaptation_lambda": 0.1,
+  "domain_specific_vocab": null,
+  "emit_trace": false,
+  "enable_flash_attention": null,
+  "enable_memory_pooling": false,
+  "enable_mixed_precision": false,
+  "enable_profiling": false,
+  "enable_uncertainty_estimation": false,
+  "enforce_eager": false,
+  "entity_linking": {
+    "confidence_threshold": 0.8,
+    "enabled": false,
+    "knowledge_bases": [
+      "umls",
+      "snomed_ct",
+      "loinc"
+    ]
+  },
+  "eos": -1,
+  "file_path": null,
+  "flash_attention_config": null,
+  "gpu_memory_utilization": 0.9,
+  "grad_checkpointing": false,
+  "hf_config": "namespace(model_type='unknown', max_position_embeddings=4096)",
+  "imaging_modalities": [
+    "xray"
+  ],
+  "kvcache_block_size": 256,
+  "max_entity_span_length": 10,
+  "max_medical_seq_length": 4096,
+  "max_model_len": 4096,
+  "max_num_batched_tokens": 32768,
+  "max_num_seqs": 512,
+  "max_retries": 3,
+  "medical_entity_types": [
+    "disease",
+    "drug",
+    "procedure"
+  ],
+  "medical_specialties": [
+    "cardiology"
+  ],
+  "memory_efficient": true,
+  "mixed_precision_dtype": "fp16",
+  "model": "dmis-lab/biobert-base-cased-v1.2",
+  "model_type": "medical_llm",
+  "ner_confidence_threshold": 0.85,
+  "num_kvcache_blocks": -1,
+  "pool_device": "auto",
+  "pool_max_bytes": null,
+  "pretrained_model_name_or_path": "dmis-lab/biobert-base-cased-v1.2",
+  "profiler_device": "auto",
+  "quantization_bits": null,
+  "quantization_method": null,
+  "recompute_granularity": null,
+  "regulatory_compliance": [
+    "hipaa",
+    "gdpr"
+  ],
+  "request_timeout": 30,
+  "section_headers": [
+    "history_of_present_illness",
+    "past_medical_history",
+    "medications",
+    "allergies",
+    "family_history",
+    "social_history",
+    "review_of_systems",
+    "physical_exam",
+    "assessment_and_plan"
+  ],
+  "task_type": "ner",
+  "tensor_parallel_size": 1,
+  "torch_matmul_precision": null,
+  "trace_dir": "profiles",
+  "uncertainty_threshold": 0.7,
+  "use_cuda_graphs": false,
+  "use_medical_adapter": true,
+  "version": "0.1.0"
+}

examples/ner/config.yaml

@@ -0,0 +1,90 @@
+_serializing: true
+activation_recompute: false
+adapter_config: null
+adapter_type: null
+allow_tf32: false
+anatomical_regions:
+- head
+attention_impl: null
+batch_size: 1
+cache_ttl: 3600
+classification_labels: []
+config_version: 1.0.0
+cudnn_benchmark: null
+document_types:
+- clinical_note
+- discharge_summary
+- radiology_report
+domain_adaptation: false
+domain_adaptation_lambda: 0.1
+domain_specific_vocab: null
+emit_trace: false
+enable_flash_attention: null
+enable_memory_pooling: false
+enable_mixed_precision: false
+enable_profiling: false
+enable_uncertainty_estimation: false
+enforce_eager: false
+entity_linking:
+  confidence_threshold: 0.8
+  enabled: false
+  knowledge_bases:
+  - umls
+  - snomed_ct
+  - loinc
+eos: -1
+file_path: null
+flash_attention_config: null
+gpu_memory_utilization: 0.9
+grad_checkpointing: false
+hf_config: namespace(model_type='unknown', max_position_embeddings=4096)
+imaging_modalities:
+- xray
+kvcache_block_size: 256
+max_entity_span_length: 10
+max_medical_seq_length: 4096
+max_model_len: 4096
+max_num_batched_tokens: 32768
+max_num_seqs: 512
+max_retries: 3
+medical_entity_types:
+- disease
+- drug
+- procedure
+medical_specialties:
+- cardiology
+memory_efficient: true
+mixed_precision_dtype: fp16
+model: dmis-lab/biobert-base-cased-v1.2
+model_type: medical_llm
+ner_confidence_threshold: 0.85
+num_kvcache_blocks: -1
+pool_device: auto
+pool_max_bytes: null
+pretrained_model_name_or_path: dmis-lab/biobert-base-cased-v1.2
+profiler_device: auto
+quantization_bits: null
+quantization_method: null
+recompute_granularity: null
+regulatory_compliance:
+- hipaa
+- gdpr
+request_timeout: 30
+section_headers:
+- history_of_present_illness
+- past_medical_history
+- medications
+- allergies
+- family_history
+- social_history
+- review_of_systems
+- physical_exam
+- assessment_and_plan
+task_type: ner
+tensor_parallel_size: 1
+torch_matmul_precision: null
+trace_dir: profiles
+uncertainty_threshold: 0.7
+use_cuda_graphs: false
+use_medical_adapter: true
+version: 0.1.0