From a119304a152300089b466d4be3067a3dc6bafe91 Mon Sep 17 00:00:00 2001
From: Ivan Pavlovich <ivan.pavlovic@hes-so.ch>
Date: Thu, 20 Mar 2025 12:46:32 +0100
Subject: [PATCH] =?UTF-8?q?Ajout=20de=20gemini=20host=C3=A9=20dans=20mon?=
=?UTF-8?q?=20systeme=20de=20teste?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
models/LLM/Cohere/cohereCommand.py | 7 +-
models/LLM/Gemini/gemini.py | 18 +-
testModel/launch_tests.py | 2 +-
...aurer-DeBERTa_v3_base_mnli_fever_anli.json | 40236 ---------------
.../MoritzLaurer-bge_m3_zeroshot_v2_0.json | 87 -
...-deberta_v3_base_zeroshot_v1_1_all_33.json | 40107 ---------------
...er-multilingual_MiniLMv2_L6_mnli_xnli.json | 39751 ---------------
testModel/results/deepseek_v2.json | 40716 ----------------
.../results/facebook-bart_large_mnli.json | 39939 ---------------
testModel/results/llama3_2.json | 40275 ---------------
testModel/results/mistral_small.json | 40442 ---------------
testModel/test.py | 15 +-
variables/models.py | 21 +-
13 files changed, 40 insertions(+), 281576 deletions(-)
delete mode 100644 testModel/results/MoritzLaurer-DeBERTa_v3_base_mnli_fever_anli.json
delete mode 100644 testModel/results/MoritzLaurer-bge_m3_zeroshot_v2_0.json
delete mode 100644 testModel/results/MoritzLaurer-deberta_v3_base_zeroshot_v1_1_all_33.json
delete mode 100644 testModel/results/MoritzLaurer-multilingual_MiniLMv2_L6_mnli_xnli.json
delete mode 100644 testModel/results/deepseek_v2.json
delete mode 100644 testModel/results/facebook-bart_large_mnli.json
delete mode 100644 testModel/results/llama3_2.json
delete mode 100644 testModel/results/mistral_small.json
diff --git a/models/LLM/Cohere/cohereCommand.py b/models/LLM/Cohere/cohereCommand.py
index 443d7ea9e..86e4fe160 100644
--- a/models/LLM/Cohere/cohereCommand.py
+++ b/models/LLM/Cohere/cohereCommand.py
@@ -1,15 +1,16 @@
import cohere
import json
-co = cohere.ClientV2("hNdIrXFRGTzxSK4bnEXONMMIYukcMuPqOLHV6P28")
+def cohere_create_client():
+ return cohere.ClientV2("hNdIrXFRGTzxSK4bnEXONMMIYukcMuPqOLHV6P28")
-def cohere_classify(sequence, labels):
+def cohere_classify(client, sequence, labels):
prompt = f'I need you to give me the labels that could be given to the text (keep in mind that u can put multiple labels and select only the labels that i give you):\
text: {sequence}\
labels: {labels}\
Give the response in json format {{ "labels": [] }}'
- response = co.chat(
+ response = client.chat(
model="command-r-plus",
messages=[{"role": "user", "content": prompt}]
)
diff --git a/models/LLM/Gemini/gemini.py b/models/LLM/Gemini/gemini.py
index 5c988e612..3d62929c2 100644
--- a/models/LLM/Gemini/gemini.py
+++ b/models/LLM/Gemini/gemini.py
@@ -13,10 +13,11 @@ def gemini_start_chat():
def gemini_classify(chat, sequence, labels):
- prompt = f'I need you to give me the labels that could be given to the text (keep in mind that u can put multiple labels and select only the labels that i give you):\
- text: {sequence}\
- labels: {labels}\
- Give the response in json format "labels": []'
+ prompt = 'I need you to give me the labels that could be given to the text (keep in mind that u can put multiple labels and select only the labels that i give you):\n'
+ prompt += 'text: ' + sequence + '\n'
+ prompt += 'labels: ' + "[" + ", ".join(labels) + ']\n'
+ prompt += 'Give the response in json format: { "labels": [] }. Follow this writing to the letter and don t add text around it. Only put the labels that you select between [].'
+ prompt += 'Even if you have no labels give me a response like: { "labels": [] }. And also put labels between "".'
waitingTime = 1
while(waitingTime <= 500):
@@ -38,4 +39,11 @@ def gemini_classify(chat, sequence, labels):
responce_json = json.loads(json_str)
- return responce_json
\ No newline at end of file
+ print(responce_json)
+
+ res = {}
+
+ for label in labels:
+ res[label] = label in responce_json["labels"]
+
+ return res
\ No newline at end of file
diff --git a/testModel/launch_tests.py b/testModel/launch_tests.py
index 690789d15..6d992b45b 100644
--- a/testModel/launch_tests.py
+++ b/testModel/launch_tests.py
@@ -14,7 +14,7 @@ file_path = os.path.abspath(os.path.join(os.path.dirname(__file__), TEST_SCRIPT_
parser = argparse.ArgumentParser(description="Launch your_script.py with optional arguments.")
parser.add_argument(
- "--mode", choices=["ollama", "huggingface"], help="Choose mode: ollama or huggingface", default=None
+ "--mode", choices=["ollama", "huggingface", "hosted"], help="Choose mode: ollama or huggingface", default=None
)
parser.add_argument("-r", "--remake", action="store_true", help="Run the test scripts with remake flag")
diff --git a/testModel/results/MoritzLaurer-DeBERTa_v3_base_mnli_fever_anli.json b/testModel/results/MoritzLaurer-DeBERTa_v3_base_mnli_fever_anli.json
deleted file mode 100644
index 1ae9c046b..000000000
--- a/testModel/results/MoritzLaurer-DeBERTa_v3_base_mnli_fever_anli.json
+++ /dev/null
@@ -1,40236 +0,0 @@
-{
- "treshold": 0.7,
- "articles": [
- {
- "PMID": "39737510",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Adult",
- "Middle Aged",
- "India",
- "Male",
- "Female",
- "Noncommunicable Diseases",
- "Risk Factors",
- "Aged",
- "Poverty Areas",
- "Adolescent",
- "Prevalence",
- "Smoking",
- "Alcohol Drinking",
- "Obesity",
- "Cross-Sectional Studies",
- "Young Adult",
- "Urban Population"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Cardiovascular diseases"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "39737504",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "India",
- "Stem Cell Transplantation",
- "Cell- and Tissue-Based Therapy",
- "Noncommunicable Diseases"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Selected Labels": [
- "Non-Communicable Diseases"
- ],
- "confusion matrix": [
- [
- 1,
- 0
- ],
- [
- 0,
- 7
- ]
- ]
- },
- {
- "PMID": "39736607",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Noncommunicable Diseases",
- "Female",
- "Male",
- "Sex Factors",
- "Employment",
- "Socioeconomic Factors",
- "Poverty",
- "Universal Health Insurance",
- "Cost of Illness"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": true,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": true,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Chronic respiratory disease",
- "Cardiovascular diseases",
- "Diabetes type 1",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 4
- ],
- [
- 0,
- 3
- ]
- ]
- },
- {
- "PMID": "39732655",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Noncommunicable Diseases",
- "Machine Learning",
- "Bias",
- "Population Health",
- "Algorithms"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 2
- ],
- [
- 0,
- 5
- ]
- ]
- },
- {
- "PMID": "39732436",
- "Labels": [
- "Non-Communicable Diseases",
- "Cardiovascular diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Male",
- "Female",
- "Middle Aged",
- "Prospective Studies",
- "Japan",
- "Aged",
- "Sodium, Dietary",
- "Noncommunicable Diseases",
- "Cohort Studies",
- "Potassium, Dietary",
- "Mortality, Premature",
- "Cause of Death",
- "Risk Factors",
- "Cardiovascular Diseases",
- "Diet",
- "Potassium",
- "East Asian People"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": true,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Cancer",
- "Cardiovascular diseases"
- ],
- "confusion matrix": [
- [
- 2,
- 1
- ],
- [
- 0,
- 5
- ]
- ]
- },
- {
- "PMID": "39731009",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Republic of Korea",
- "Male",
- "Female",
- "Middle Aged",
- "Longitudinal Studies",
- "Noncommunicable Diseases",
- "Exercise",
- "Employment",
- "Aged",
- "Risk Factors"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": true,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Selected Labels": [
- "Diabetes",
- "Chronic respiratory disease"
- ],
- "confusion matrix": [
- [
- 0,
- 2
- ],
- [
- 1,
- 5
- ]
- ]
- },
- {
- "PMID": "39725416",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "New Zealand",
- "Cross-Sectional Studies",
- "Male",
- "Female",
- "Middle Aged",
- "Aged",
- "Noncommunicable Diseases",
- "Adult",
- "Comorbidity",
- "Censuses",
- "Adolescent",
- "Young Adult",
- "Aged, 80 and over",
- "Prevalence",
- "Child",
- "Child, Preschool"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": true,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Cardiovascular diseases",
- "Mental Health"
- ],
- "confusion matrix": [
- [
- 1,
- 2
- ],
- [
- 0,
- 5
- ]
- ]
- },
- {
- "PMID": "39722627",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Sugar-Sweetened Beverages",
- "Taxes",
- "Tobacco Products",
- "Mediterranean Region",
- "Noncommunicable Diseases"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes",
- "Cardiovascular diseases",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 3
- ],
- [
- 0,
- 4
- ]
- ]
- },
- {
- "PMID": "39709790",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "NF-E2-Related Factor 2",
- "Humans",
- "Animals",
- "Noncommunicable Diseases",
- "Oxidative Stress",
- "Reactive Oxygen Species",
- "Oxidation-Reduction",
- "Disease Models, Animal",
- "Inflammation",
- "Gene Expression Regulation"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": true,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes type 1",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 2
- ],
- [
- 0,
- 5
- ]
- ]
- },
- {
- "PMID": "39702198",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Aged",
- "Female",
- "Male",
- "India",
- "Middle Aged",
- "Aged, 80 and over",
- "Noncommunicable Diseases",
- "Cost of Illness",
- "Disability-Adjusted Life Years",
- "Sex Factors",
- "Age Factors",
- "Global Burden of Disease",
- "Wounds and Injuries"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": true,
- "Chronic respiratory disease": true,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": true,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes",
- "Cancer",
- "Chronic respiratory disease",
- "Cardiovascular diseases",
- "Diabetes type 1",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 6
- ],
- [
- 0,
- 1
- ]
- ]
- },
- {
- "PMID": "39699459",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Absenteeism",
- "Male",
- "Female",
- "Brazil",
- "Cross-Sectional Studies",
- "Adult",
- "Middle Aged",
- "Chronic Disease",
- "Noncommunicable Diseases",
- "Prevalence",
- "Health Surveys",
- "Young Adult",
- "Adolescent",
- "Sex Distribution",
- "Socioeconomic Factors",
- "Cost of Illness",
- "Multimorbidity",
- "Sociodemographic Factors"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": true,
- "Diabetes type 1": true,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes",
- "Cardiovascular diseases",
- "Mental Health",
- "Diabetes type 1",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 5
- ],
- [
- 0,
- 2
- ]
- ]
- },
- {
- "PMID": "39697299",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Humans",
- "Middle Aged",
- "Male",
- "Female",
- "Cross-Sectional Studies",
- "Multimorbidity",
- "Noncommunicable Diseases",
- "Health Expenditures",
- "Prevalence",
- "Aged",
- "Adult",
- "Surveys and Questionnaires"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes",
- "Cardiovascular diseases",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 3
- ],
- [
- 0,
- 4
- ]
- ]
- },
- {
- "PMID": "39696316",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
- "Thailand",
- "Humans",
- "Noncommunicable Diseases",
- "Stakeholder Participation",
- "Health Policy",
- "Sustainable Development",
- "Intersectoral Collaboration",
- "Cooperative Behavior"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": true,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": true,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Chronic respiratory disease",
- "Cardiovascular diseases",
- "Diabetes type 1",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 4
- ],
- [
- 0,
- 3
- ]
- ]
- },
- {
- "PMID": "39696309",
- "Labels": [
- "Non-Communicable Diseases",
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Middle Aged",
- "Adult",
- "Male",
- "Female",
- "Diabetes Mellitus, Type 2",
- "Prevalence",
- "Aged",
- "Risk Factors",
- "Adolescent",
- "Young Adult",
- "Cabo Verde",
- "Prediabetic State",
- "Noncommunicable Diseases",
- "World Health Organization",
- "Cross-Sectional Studies",
- "Surveys and Questionnaires"
- ],
- "Wanted": {
- "Non-Communicable Diseases": true,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 2,
- 1
- ],
- [
- 0,
- 5
- ]
- ]
- },
- {
- "PMID": "39695503",
- "Labels": [
- "Non-Communicable Diseases",
- "Mental Health"
- ],
- "MeshTerms": [
- "Humans",
- "Indonesia",
- "Adolescent",
- "Male",
- "Female",
- "Noncommunicable Diseases",
- "Cross-Sectional Studies",
- "Risk Factors",
- "Mental Health",
- "Quality of Life",
- "Prevalence"
- ],
- "Wanted": {
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\ No newline at end of file
diff --git a/testModel/results/MoritzLaurer-bge_m3_zeroshot_v2_0.json b/testModel/results/MoritzLaurer-bge_m3_zeroshot_v2_0.json
deleted file mode 100644
index ff8920bfc..000000000
--- a/testModel/results/MoritzLaurer-bge_m3_zeroshot_v2_0.json
+++ /dev/null
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-{
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\ No newline at end of file
diff --git a/testModel/results/MoritzLaurer-deberta_v3_base_zeroshot_v1_1_all_33.json b/testModel/results/MoritzLaurer-deberta_v3_base_zeroshot_v1_1_all_33.json
deleted file mode 100644
index 01a3b5df3..000000000
--- a/testModel/results/MoritzLaurer-deberta_v3_base_zeroshot_v1_1_all_33.json
+++ /dev/null
@@ -1,40107 +0,0 @@
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- "Diabetes type 2": true
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- "Selected Labels": [
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- {
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- "Wanted": {
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- "Diabetes": false,
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- "Cardiovascular diseases": false,
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- "Diabetes type 1": false,
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- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
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- },
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- "confusion matrix": [
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- "Bile Acids and Salts",
- "Animals",
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- "Diabetes type 2": true
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- "Selected Labels": [
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- {
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- "Middle Aged",
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- "Glycated Hemoglobin",
- "Aged",
- "Remission Induction",
- "Blood Glucose",
- "Treatment Outcome",
- "Glycemic Control",
- "Glucagon-Like Peptide-2 Receptor",
- "Gastric Inhibitory Polypeptide",
- "Tirzepatide"
- ],
- "Wanted": {
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- "Diabetes": false,
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- "Diabetes type 2": true
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- "results": {
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- "ALL": {
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- 690,
- 379
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- 209,
- 5122
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- 93
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- 76,
- 1286
- ]
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- "TPR": 0.6561085972850679,
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- },
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- 165,
- 84
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- 76
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- "VERY LONG": {
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- 126
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- "TPR": 0.8464912280701754,
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- "F1": 0.7056672760511884
- }
- }
-}
\ No newline at end of file
diff --git a/testModel/results/MoritzLaurer-multilingual_MiniLMv2_L6_mnli_xnli.json b/testModel/results/MoritzLaurer-multilingual_MiniLMv2_L6_mnli_xnli.json
deleted file mode 100644
index b2f163d9e..000000000
--- a/testModel/results/MoritzLaurer-multilingual_MiniLMv2_L6_mnli_xnli.json
+++ /dev/null
@@ -1,39751 +0,0 @@
-{
- "treshold": 0.7,
- "articles": [
- {
- "PMID": "39737510",
- "Labels": [
- "Non-Communicable Diseases"
- ],
- "MeshTerms": [
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- "Middle Aged",
- "India",
- "Male",
- "Female",
- "Noncommunicable Diseases",
- "Risk Factors",
- "Aged",
- "Poverty Areas",
- "Adolescent",
- "Prevalence",
- "Smoking",
- "Alcohol Drinking",
- "Obesity",
- "Cross-Sectional Studies",
- "Young Adult",
- "Urban Population"
- ],
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- "Mental Health": false,
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- },
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- "Stem Cell Transplantation",
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- "Noncommunicable Diseases"
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- ],
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- },
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\ No newline at end of file
diff --git a/testModel/results/deepseek_v2.json b/testModel/results/deepseek_v2.json
deleted file mode 100644
index 0e0717dae..000000000
--- a/testModel/results/deepseek_v2.json
+++ /dev/null
@@ -1,40716 +0,0 @@
-{
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\ No newline at end of file
diff --git a/testModel/results/facebook-bart_large_mnli.json b/testModel/results/facebook-bart_large_mnli.json
deleted file mode 100644
index 79fe9ca8f..000000000
--- a/testModel/results/facebook-bart_large_mnli.json
+++ /dev/null
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\ No newline at end of file
diff --git a/testModel/results/llama3_2.json b/testModel/results/llama3_2.json
deleted file mode 100644
index 707cfe530..000000000
--- a/testModel/results/llama3_2.json
+++ /dev/null
@@ -1,40275 +0,0 @@
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- }
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-}
\ No newline at end of file
diff --git a/testModel/results/mistral_small.json b/testModel/results/mistral_small.json
deleted file mode 100644
index ee6d0f60d..000000000
--- a/testModel/results/mistral_small.json
+++ /dev/null
@@ -1,40442 +0,0 @@
-{
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- "Acute Disease",
- "Adult",
- "Glucagon-Like Peptide-1 Receptor Agonists"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "39084811",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Pregnancy",
- "Diabetes, Gestational",
- "Diabetes Mellitus, Type 2",
- "Female",
- "Hyperglycemia",
- "Hypoglycemic Agents",
- "Pregnancy in Diabetics"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "39069090",
- "Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Blood Glucose",
- "Glucose Tolerance Test",
- "Female",
- "Male",
- "Black People",
- "Middle Aged",
- "Diabetes Mellitus",
- "Adult",
- "Diabetes Mellitus, Type 2",
- "United States",
- "African People"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": true,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": false
- },
- "Selected Labels": [
- "Non-Communicable Diseases",
- "Diabetes"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 1,
- 5
- ]
- ]
- },
- {
- "PMID": "39028078",
- "Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Glycated Hemoglobin",
- "Hypoglycemic Agents",
- "Body Mass Index",
- "Diabetes Mellitus, Type 2",
- "Weight Gain",
- "Diabetes Mellitus"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 2,
- 0
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "38988282",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Diabetes Mellitus, Type 2",
- "Algorithms",
- "Japan",
- "Hypoglycemic Agents",
- "Consensus",
- "Societies, Medical"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "38971377",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Diabetes Mellitus, Type 2",
- "Glucagon",
- "Female",
- "Male",
- "Middle Aged",
- "Glucose",
- "Dietary Carbohydrates",
- "Postprandial Period",
- "Blood Glucose",
- "Sex Characteristics",
- "Aged",
- "Sex Factors"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "38950981",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Sodium-Glucose Transporter 2 Inhibitors",
- "Heart Failure",
- "Renal Insufficiency, Chronic",
- "Diabetes Mellitus, Type 2",
- "Randomized Controlled Trials as Topic"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": true,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Cardiovascular diseases",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "38926031",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Bile Acids and Salts",
- "Animals",
- "Gastrointestinal Microbiome",
- "Acylation",
- "Diabetes Mellitus, Type 2",
- "Bacteroides"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 0
- ],
- [
- 0,
- 7
- ]
- ]
- },
- {
- "PMID": "38922299",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Humans",
- "Neurosyphilis",
- "Male",
- "Treponema pallidum",
- "Diabetes Mellitus, Type 2",
- "Anti-Bacterial Agents",
- "Middle Aged",
- "Antibodies, Bacterial"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "38897878",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Animals",
- "Humans",
- "Mitochondrial Dynamics",
- "Mice",
- "Mitochondria, Liver",
- "Diabetes Mellitus, Type 2",
- "Food",
- "Liver"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- },
- {
- "PMID": "38889536",
- "Labels": [
- "Diabetes type 2"
- ],
- "MeshTerms": [
- "Diabetes Mellitus, Type 2",
- "Humans",
- "Middle Aged",
- "Male",
- "Female",
- "Hypoglycemic Agents",
- "Glycated Hemoglobin",
- "Aged",
- "Remission Induction",
- "Blood Glucose",
- "Treatment Outcome",
- "Glycemic Control",
- "Glucagon-Like Peptide-2 Receptor",
- "Gastric Inhibitory Polypeptide",
- "Tirzepatide"
- ],
- "Wanted": {
- "Non-Communicable Diseases": false,
- "Diabetes": false,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Predictions": {
- "Non-Communicable Diseases": false,
- "Diabetes": true,
- "Cancer": false,
- "Chronic respiratory disease": false,
- "Cardiovascular diseases": false,
- "Mental Health": false,
- "Diabetes type 1": false,
- "Diabetes type 2": true
- },
- "Selected Labels": [
- "Diabetes",
- "Diabetes type 2"
- ],
- "confusion matrix": [
- [
- 1,
- 1
- ],
- [
- 0,
- 6
- ]
- ]
- }
- ],
- "results": {
- "prediction time": 457.2930645942688,
- "ALL": {
- "confusion matrix": [
- [
- 819,
- 468
- ],
- [
- 80,
- 5033
- ]
- ],
- "TPR": 0.9110122358175751,
- "TNR": 0.9149245591710599,
- "Precision": 0.6363636363636364,
- "F1": 0.7493138151875572
- },
- "SHORT": {
- "confusion matrix": [
- [
- 181,
- 106
- ],
- [
- 40,
- 1273
- ]
- ],
- "TPR": 0.8190045248868778,
- "TNR": 0.9231327048585932,
- "Precision": 0.6306620209059234,
- "F1": 0.7125984251968503
- },
- "MEDIUM": {
- "confusion matrix": [
- [
- 200,
- 106
- ],
- [
- 18,
- 1276
- ]
- ],
- "TPR": 0.9174311926605505,
- "TNR": 0.9232995658465991,
- "Precision": 0.6535947712418301,
- "F1": 0.7633587786259541
- },
- "LONG": {
- "confusion matrix": [
- [
- 221,
- 113
- ],
- [
- 11,
- 1255
- ]
- ],
- "TPR": 0.9525862068965517,
- "TNR": 0.9173976608187134,
- "Precision": 0.6616766467065869,
- "F1": 0.7809187279151943
- },
- "VERY LONG": {
- "confusion matrix": [
- [
- 217,
- 143
- ],
- [
- 11,
- 1229
- ]
- ],
- "TPR": 0.9517543859649122,
- "TNR": 0.8957725947521866,
- "Precision": 0.6027777777777777,
- "F1": 0.738095238095238
- }
- }
-}
\ No newline at end of file
diff --git a/testModel/test.py b/testModel/test.py
index 346dad6f8..4e4626890 100644
--- a/testModel/test.py
+++ b/testModel/test.py
@@ -66,8 +66,11 @@ if data["treshold"] is None:
pmids = [article["PMID"] for article in data["articles"]]
-if MODELS[model]["isHuggingFace"]:
- pipline = MODELS[model]["pipline"](model)
+if MODELS[model]["requiresDependency"]:
+ if MODELS[model]["category"] == "huggingface":
+ dependency = MODELS[model]["dependency"](model)
+ elif MODELS[model]["category"] == "hosted":
+ dependency = MODELS[model]["dependency"]()
print("---------------------------------")
print(f"MODEL: {model}")
@@ -105,10 +108,12 @@ for ncd in NCDS:
start = time.time()
- if MODELS[model]["isHuggingFace"]:
- predictions = MODELS[model]["predict"](pipline, title+abstract, NCDS, data["treshold"])
- else:
+ if MODELS[model]["category"] == "huggingface":
+ predictions = MODELS[model]["predict"](dependency, title+abstract, NCDS, data["treshold"])
+ elif MODELS[model]["category"] == "ollama":
predictions = MODELS[model]["predict"](model, title+abstract, NCDS)
+ elif MODELS[model]["category"] == "hosted":
+ predictions = MODELS[model]["predict"](dependency, title+abstract, NCDS)
end = time.time()
diff --git a/variables/models.py b/variables/models.py
index 3acfc32c7..ec03a0300 100644
--- a/variables/models.py
+++ b/variables/models.py
@@ -6,19 +6,22 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '../')))
from models.ZeroShotClassifier.HuggingFace.zero_shot_classification import create_classifier, classify
import models.LLM.Ollama.ollama_wrapper as ollama
+from models.LLM.Gemini.gemini import gemini_start_chat, gemini_classify
MODELS_CATEGORIES = [
"huggingface",
- "ollama"
+ "ollama",
+ "hosted"
]
MODELS = {
- 'facebook/bart-large-mnli': {'category': "huggingface", 'predict': classify, 'isHuggingFace': True, 'pipline': create_classifier},
- # 'MoritzLaurer/bge-m3-zeroshot-v2.0': {'category': "huggingface", 'predict': classify, 'isHuggingFace': True, 'pipline': create_classifier},
- 'MoritzLaurer/DeBERTa-v3-base-mnli-fever-anli': {'category': "huggingface", 'predict': classify, 'isHuggingFace': True, 'pipline': create_classifier},
- 'MoritzLaurer/deberta-v3-base-zeroshot-v1.1-all-33': {'category': "huggingface", 'predict': classify, 'isHuggingFace': True, 'pipline': create_classifier},
- 'MoritzLaurer/multilingual-MiniLMv2-L6-mnli-xnli': {'category': "huggingface", 'predict': classify, 'isHuggingFace': True, 'pipline': create_classifier},
- 'llama3.2': {'category': "ollama", 'predict': ollama.classify, 'isHuggingFace': False, 'pipline': None},
- 'mistral-small': {'category': "ollama", 'predict': ollama.classify, 'isHuggingFace': False, 'pipline': None},
- 'deepseek-v2': {'category': "ollama", 'predict': ollama.classify, 'isHuggingFace': False, 'pipline': None}
+ 'facebook/bart-large-mnli': {'category': "huggingface", 'predict': classify, 'requiresDependency': True, 'dependency': create_classifier},
+ # 'MoritzLaurer/bge-m3-zeroshot-v2.0': {'category': "huggingface", 'predict': classify, 'requiresDependency': True, 'dependency': create_classifier},
+ 'MoritzLaurer/DeBERTa-v3-base-mnli-fever-anli': {'category': "huggingface", 'predict': classify, 'requiresDependency': True, 'dependency': create_classifier},
+ 'MoritzLaurer/deberta-v3-base-zeroshot-v1.1-all-33': {'category': "huggingface", 'predict': classify, 'requiresDependency': True, 'dependency': create_classifier},
+ 'MoritzLaurer/multilingual-MiniLMv2-L6-mnli-xnli': {'category': "huggingface", 'predict': classify, 'requiresDependency': True, 'dependency': create_classifier},
+ 'llama3.2': {'category': "ollama", 'predict': ollama.classify, 'requiresDependency': False, 'dependency': None},
+ 'mistral-small': {'category': "ollama", 'predict': ollama.classify, 'requiresDependency': False, 'dependency': None},
+ 'deepseek-v2': {'category': "ollama", 'predict': ollama.classify, 'requiresDependency': False, 'dependency': None},
+ 'gemini-hosted': {'category': "hosted", 'predict': gemini_classify, 'requiresDependency': True, 'dependency': gemini_start_chat}
}
\ No newline at end of file
--
GitLab