Training in progress, step 10

adapter_config.json

@@ -0,0 +1,34 @@
+{
+  "alpha_pattern": {},
+  "auto_mapping": null,
+  "base_model_name_or_path": "meta-llama/Llama-3.2-11B-Vision-Instruct",
+  "bias": "none",
+  "fan_in_fan_out": false,
+  "inference_mode": true,
+  "init_lora_weights": "gaussian",
+  "layer_replication": null,
+  "layers_pattern": null,
+  "layers_to_transform": null,
+  "loftq_config": {},
+  "lora_alpha": 8,
+  "lora_dropout": 0.1,
+  "megatron_config": null,
+  "megatron_core": "megatron.core",
+  "modules_to_save": null,
+  "peft_type": "LORA",
+  "r": 8,
+  "rank_pattern": {},
+  "revision": null,
+  "target_modules": [
+    "k_proj",
+    "o_proj",
+    "down_proj",
+    "q_proj",
+    "gate_proj",
+    "up_proj",
+    "v_proj"
+  ],
+  "task_type": "CAUSAL_LM",
+  "use_dora": false,
+  "use_rslora": false
+}

adapter_model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7b9b9f4c1084cf509324c602c4ad2237d5fd736d3b15695b1c9ba2296ff5d3d6
+size 118097288

instruct.ipynb

@@ -173,18 +173,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "#source_model_id = \"HuggingFaceM4/Idefics3-8B-Llama3\"\n",
     "source_model_id = \"meta-llama/Llama-3.2-11B-Vision-Instruct\"\n",
-    "destination_model_id = \"eltorio/IDEFICS3_medical_instruct\"\n",
+    "detination_model_id = \"eltorio/IDEFICS3_medical_instruct\"\n",
     "dataset_id = \"ruslanmv/ai-medical-dataset\"\n",
     "prompt= \"You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor\"\n",
-    "output_dir = \"IDEFICS3_medical_instruct\"\n",
-    "os.environ[\"output_dir\"] = output_dir\n",
-    "os.environ[\"source_model_id\"] = source_model_id\n",
-    "os.environ[\"destination_model_id\"] = destination_model_id\n",
-    "os.environ[\"dataset_id\"] = dataset_id\n",
-    "os.environ[\"prompt\"] = prompt"
+    "output_dir = \"IDEFICS3_medical_instruct\""
    ]
   },
   {
@@ -200,20 +194,10 @@
    "execution_count": 4,
    "id": "f6510468-c903-4bd2-80fd-2511b7fb2f72",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "eltorio/IDEFICS3_medical_instruct\n",
-      "fatal: destination path 'IDEFICS3_medical_instruct' already exists and is not an empty directory.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# clone Hugging Face model repository\n",
-    "!echo $destination_model_id\n",
-    "!git clone https://huggingface.co/$destination_model_id $output_dir"
+    "# !git clone https://huggingface.co/$destination_model_id $output_dir"
    ]
   },
   {
@@ -226,7 +210,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 15,
    "id": "1efffd3f-aece-4858-b615-8fb1f2997068",
    "metadata": {
     "scrolled": true
@@ -235,7 +219,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f24e4d53f709483b95188d8de72e8d54",
+       "model_id": "b39d97f2fb434903b0521f5dea2fd37c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -249,7 +233,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7200c855b9ce46b3bf2e73177255a366",
+       "model_id": "da3388e8f61e4aee98971ce520785c0c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -263,7 +247,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "695a9eda242f4bae9b6bff10902e996b",
+       "model_id": "db11101162ff455baed085d8c25a2c77",
        "version_major": 2,
        "version_minor": 0
       },
@@ -297,7 +281,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 16,
    "id": "86163110-f084-429e-bc70-5b281a679d1c",
    "metadata": {
     "colab": {
@@ -341,7 +325,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a02e8ed0f3b1470ab2f9341b5e5f4aeb",
+       "model_id": "591a95a8c90143a39a5616131c605ed3",
        "version_major": 2,
        "version_minor": 0
       },
@@ -403,18 +387,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 17,
    "id": "f2c2fd34-e1e4-427d-86d0-73bf74ff0005",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{'question': 'What is the percentage of adult malignancies?',\n",
-       " 'context': 'Renal cell carcinoma accounts for about 3% of adult malignancies and 85% of neoplasms arising from the kidney. To identify potential progression markers for kidney cancer we examined non-neoplastic and neoplastic kidney tissue from three groups of patients, which represent different tumor stages (pT1, pT2, pT3) by a fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) approach combined with MALDI-ToF-MS/MS. Delta2D software package was used for gel image based quantification and statistical analysis. Thereby, a comprehensive Principal Component Analysis (PCA) could be performed and allowed a robust quality control of the experiment as well as a classification of the analyzed samples, which correlated with the predicted stages from the pathological examination. Additionally for selected candidate proteins we detected a correlation to the tumor grading as revealed by immunohistochemistry. On the 2D protein map 176 spots out of 989 were detected as at least 2-fold differentially expressed. These spots were analyzed by MALDI-ToF-MS/MS and 187 different proteins were identified. The functional clustering of the identified proteins revealed ten groups. Within these groups we found 86 enzymes, 63 proteins of unknown function, 14 transporter, 8 peptidases and 7 kinases. From the systems biology approach we could map many of these proteins in major pathways involved in remodelling of cytoskeleton, mitochondrial dysfunctions and changes in lipid metabolism. Due to complexity of the highly interconnected pathway network, further expression and functional validation of these proteins might provide new insights in kidney cancer progression to design novel diagnostic and therapeutic strategies.'}"
+       "{'question': 'What was the goal of the study?',\n",
+       " 'context': 'The aim of this study was to evaluate the success of steroid (PRED) withdrawal due to replacement by mycophenolate mofetil (MMF) in orthotopic liver transplant (OLT) recipients with autoimmune hepatitis (AIH). Thirty patients with AIH > 12 months after OLT randomized to receive either PRED and tacrolimus (TAC) or MMF and TAC were followed for 24 months. Withdrawal of steroids showed no difference regarding graft and patient survival. Also we demonstrated significantly lower glucose levels with lower HbA1c and a reduced need for insulin as well as a significantly lower serum cholesterol in the MMF group. Patients without steroids showed a lower incidence of osteopenia. Maintenance therapy in OLT patients with AIH may be performed safely using MMF instead of prednisone.'}"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -436,7 +420,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 57,
    "id": "29d96aea-445d-482d-b7dc-861635a5389c",
    "metadata": {
     "executionInfo": {
@@ -486,6 +470,7 @@
     "                }\n",
     "            ]\n",
     "            text = processor.apply_chat_template(messages, add_generation_prompt=False)\n",
+    "            print(text)\n",
     "            texts.append(text.strip())\n",
     "\n",
     "        batch = processor(text=texts, return_tensors=\"pt\", padding=True)\n",
@@ -511,7 +496,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 58,
    "id": "f3cda658-05f6-4078-8d71-2d1c0352ecfa",
    "metadata": {
     "executionInfo": {
@@ -559,7 +544,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 59,
    "id": "e6569265-5941-4482-84e2-faf1b61b685c",
    "metadata": {
     "colab": {
@@ -619,7 +604,194 @@
     "id": "WQA84KnTAMtI",
     "outputId": "ebb15160-f56e-4899-e608-b0d5fd0ba117"
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the cross sensitivity with acetaminophen in aspirin-<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "Cross sensitivity with acetaminophen in aspirin-sensitive subjects with asthma.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the study of blood pressure control rate in Chinese hypertensive outpatients?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "[National survey of blood pressure control rate in Chinese hypertensive outpatients-China STATUS].<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the pH of the late secretory pathway?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "An autocatalytic cleavage in the C terminus of the human MUC2 mucin occurs at the low pH of the late secretory pathway.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the name of the uncontrolled diabetes mellitus mellitus mell<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "- Uncontrolled diabetes mellitus mellitus (as indicated by metabolic derangements and/or severe diabetes mellitus related uncontrolled organ complications)<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the name of the two unrelated yeast strains?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "The genome variability and meiotic gene expression patterns in two unrelated laboratory yeast strains, SK1 and W303, have been characterized using high-density oligonucleotide arrays. The statistical analysis and comparison of the data has allowed identification of: (1) genes with functional importance to meiosis and sporulation in yeast and (2) genes expressed in a strain-specific manner. The genome-wide data also reveal potential reasons why these strains display significant differences in the ability to make fertile spores. Molecularly tagged yeast deletion strains have been used to determine the contribution of each gene to the execution of the sporulation/germination pathway. The application of genetics and the new genomic technologies have allowed a quantum jump in our understanding of yeast molecular biology.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the name of the endproducts that are used in patients with systemic l<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "Accumulation of advanced glycation endproducts in patients with systemic lupus erythematosus.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the potential for developing small molecules antagonists?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "The development of specific targeted therapies, such as anti-TNF-alpha treatment, for chronic inflammatory disorders such as rheumatoid arthritis, has significantly improved treatment, although not all patients respond. Targeting cellular adhesion molecules and chemokines/chemokine receptors as regulators of the extravasation and migration of leukocytes may provide a novel approach for the treatment of these diseases. Moreover, the possibility of developing small-molecule antagonists offers an excellent method for the oral delivery of compounds with a short half-life.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the name of the type of cancer that is undergoing upper endoscopy?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "- People who are undergoing upper endoscopy as part of their medical care with a history of esophageal cancer, Barrett's esophagus, or upper gastrointestinal symptoms.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the purpose of the investigators' research?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "The investigators propose to find out how much Latino men know about the benefits and risks of prostate cancer screening and what factors influence how they decide whether or not to have screening. The investigators are also interested in learning how providing education information, both verbally and in print, about the risks and benefits of prostate cancer screening affects men's interest and knowledge.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the effectiveness of scalp cooling in preventing alopecia?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "The effectiveness of scalp cooling in preventing alopecia for patients receiving epirubicin and docetaxel.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "What is the PET/CT PET/CT PET/CT PET/CT PET/CT PET<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "68GA-BMV101 PET/CT IN PATIENTS WITH IDIOPATHIC PULMONARY FIBROSIS:<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "How many patients were enrolled in the MXF group?<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "OBJECTIVE: To investigate whether adding moxifloxacin (MXF) to the standard anti-tuberculosis regimen can shorten the time to sputum culture conversion in pulmonary tuberculosis (PTB). METHODS: Adults with culture-positive PTB were divided into two treatment groups by their choice: standard regimen alone (HERZ group) and standard regimen plus daily 400 mg MXF in the first 2 months (MXF group). Sputum samples were collected thrice weekly in the first 8 weeks. The propensity score was calculated to estimate the conditional probability of entering the MXF group. Factors influencing time to culture conversion were investigated using Cox proportional hazards regression analysis stratified by propensity score. RESULTS: Sixty-two patients were enrolled in the MXF group and 88 in the HERZ group; respectively 51 and 72 completed the study. The regimen was modified before culture conversion in respectively 6 (12%) and 12 (16%; P = 0.47) patients, due to adverse effects. The time to culture conversion was shorter in the MXF group (HR 2.1, 95%CI 1.4-3.2). The culture conversion rate after 6 weeks of treatment was respectively 82% and 61% (P = 0.011, <0.05/4, calculated using the modified Bonferroni method). CONCLUSIONS: Adding MXF to the standard anti-tuberculosis regimen in the first 2 months was associated with a shorter time to culture conversion, a higher 6-week culture conversion rate and reduced transmission of tuberculosis.<|eot_id|>\n",
+      "<|begin_of_text|><|start_header_id|>system<|end_header_id|>\n",
+      "\n",
+      "Cutting Knowledge Date: December 2023\n",
+      "Today Date: 16 Nov 2024\n",
+      "\n",
+      "[{'type': 'text', 'text': 'You are a medical doctor with 15 year of experience verifying the knowledge of a new diploma medical doctor'}]<|eot_id|><|start_header_id|>user<|end_header_id|>\n",
+      "\n",
+      "Pyrimethamine.<|eot_id|><|start_header_id|>assistant<|end_header_id|>\n",
+      "\n",
+      "- Pyrimethamine.<|eot_id|>\n"
+     ]
+    }
+   ],
    "source": [
     "trainer.train()"
    ]

training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9165ed00e86ed104c65895923502c69ad704adc6569417f95dcd29493970793f
+size 5304