agent-smith-ai
Project description
Agent Smith (AI)
Agent smith makes it easy to instantiate AI agents that can safely and easily call APIs and locally defined functions to interact with the world.
Be aware of the following:
- It is designed to use OpenAI's function-calling models and thus requires an OpenAI API key.
Examples
The examples directory provides some examples, including:
monarch_basic.py: Illustrates how to extend the basic UtilityAgent to register APIs and define callable local methods, and how to interact with the agent by processing produced Message objects.monarch_cli.py: Illustrates extending the CLIAgent, which itself extends the UtilityAgent to provide a command-line chat interface.
Here's an example conversation from monarch_cli.py (sadly, markdown-defined colors and links are not shown here):
╭──────────────────────────────────────────── Welcome ─────────────────────────────────────────────╮
│ Hello! I'm the Monarch Assistant, an AI-powered chatbot that can answer questions about genes, │
│ diseases, and phenotypes, based on information hosted at https://monarchinitiative.org. │
│ │
│ • You can exit by saying 'exit', and you can request that I turn on or off function call │
│ responses by saying 'show function calls' or 'hide function calls' at any time. They are │
│ shown by default. │
│ • I do not currently implement context-window management, so after a while your conversation │
│ will produce an error. │
│ • For a bit of fun, try asking me to describe my plan. For example, "What are the symptoms of │
│ Cystic Fibrosis? Describe your plan before you execute it." │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
User: What are the symptoms of Cystic Fibrosis? Describe your plan before you execute it.
╭─ Monarch Assistant -> Monarch Assistant (monarch-search_entity function) ────────────────────────╮
│ To find the symptoms of Cystic Fibrosis, I will first search for the disease using the term │
│ "Cystic Fibrosis" in the Monarch Initiative knowledge graph. Once I have the ontology identifier │
│ for Cystic Fibrosis, I will use it to retrieve the associated phenotypes. These phenotypes │
│ represent the symptoms of the disease. I will then provide a description of the symptoms of │
│ Cystic Fibrosis based on the retrieved information. │
│ │
│ Here is my plan: │
│ │
│ 1 Search for the disease "Cystic Fibrosis" in the Monarch Initiative knowledge graph. │
│ 2 Retrieve the ontology identifier for Cystic Fibrosis. │
│ 3 Use the ontology identifier to retrieve the associated phenotypes. │
│ 4 Provide a description of the symptoms of Cystic Fibrosis based on the retrieved information. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> Monarch Assistant (monarch-search_entity function) ────────────────────────╮
│ │
│ monarch-search_entity(params = {'term': 'Cystic Fibrosis', 'category': 'biolink:Disease', │
│ 'limit': 1}) │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant (monarch-search_entity function) -> Monarch Assistant ────────────────────────╮
│ │
│ { │
│ "results": [ │
│ { │
│ "id": "MONDO:0009061", │
│ "name": "cystic fibrosis", │
│ "categories": [ │
│ "biolink:Disease" │
│ ], │
│ "description": "Cystic fibrosis (CF) is a genetic disorder characterized by the │
│ production of sweat with a high salt content and mucus secretions with an abnormal viscosity." │
│ } │
│ ], │
│ "total": 3 │
│ } │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> Monarch Assistant (monarch-get_disease_phenotype_associations function) ───╮
│ │
│ monarch-get_disease_phenotype_associations(params = {'disease_id': 'MONDO:0009061', 'limit': │
│ 10}) │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant (monarch-get_disease_phenotype_associations function) -> Monarch Assistant ───╮
│ │
│ { │
│ "associations": [ │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0004401", │
│ "label": "Meconium ileus (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0006528", │
│ "label": "Chronic lung disease (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0006538", │
│ "label": "Recurrent bronchopulmonary infections (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0100582", │
│ "label": "Nasal polyposis (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0002035", │
│ "label": "Rectal prolapse (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0002099", │
│ "label": "Asthma (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0002150", │
│ "label": "Hypercalciuria (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0002595", │
│ "label": "Ileus (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0002613", │
│ "label": "Biliary cirrhosis (HPO)" │
│ } │
│ }, │
│ { │
│ "metadata": { │
│ "frequency_qualifier": null, │
│ "onset_qualifier": null │
│ }, │
│ "publications": [], │
│ "phenotype": { │
│ "metadata": {}, │
│ "publications": [], │
│ "phenotype_id": "HP:0003251", │
│ "label": "Male infertility (HPO)" │
│ } │
│ } │
│ ], │
│ "total": 62, │
│ "phenotype_url_template": "https://monarchinitiative.org/phenotype/{phenotype_id}" │
│ } │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> User ──────────────────────────────────────────────────────────────────────╮
│ The symptoms of Cystic Fibrosis include: │
│ │
│ 1 Meconium ileus: This is a condition where the meconium, the first stool of a newborn, is │
│ thick and sticky, causing a blockage in the intestines. More information │
│ 2 Chronic lung disease: Cystic Fibrosis can lead to the development of chronic lung disease, │
│ characterized by persistent respiratory symptoms such as coughing, wheezing, and shortness │
│ of breath. More information │
│ 3 Recurrent bronchopulmonary infections: Individuals with Cystic Fibrosis are prone to │
│ frequent and recurrent infections in the bronchial tubes and lungs. More information │
│ 4 Nasal polyposis: Cystic Fibrosis can cause the development of polyps in the nasal passages, │
│ leading to nasal congestion and difficulty breathing through the nose. More information │
│ 5 Rectal prolapse: In some cases, Cystic Fibrosis can result in the protrusion of the rectum │
│ through the anus. More information │
│ 6 Asthma: Individuals with Cystic Fibrosis may also experience symptoms of asthma, such as │
│ wheezing and difficulty breathing. More information │
│ 7 Hypercalciuria: Cystic Fibrosis can lead to increased levels of calcium in the urine, which │
│ may result in the formation of kidney stones. More information │
│ 8 Ileus: This refers to a blockage or obstruction in the intestines, which can occur in │
│ individuals with Cystic Fibrosis. More information │
│ 9 Biliary cirrhosis: In rare cases, Cystic Fibrosis can lead to the development of liver │
│ disease, specifically biliary cirrhosis. More information │
│ 10 Male infertility: Men with Cystic Fibrosis may experience infertility due to the absence or │
│ blockage of the vas deferens, the tube that carries sperm from the testes. More information │
│ │
│ Please note that this is not an exhaustive list of symptoms, and the severity and presentation │
│ of symptoms can vary among individuals with Cystic Fibrosis. It is important to consult with a │
│ healthcare professional for a comprehensive evaluation and diagnosis. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
User: That's nice. I know you can call local functions too - can you do that and tell me what time it is?
╭─ Monarch Assistant -> Monarch Assistant (time function) ─────────────────────────────────────────╮
│ │
│ time(params = {}) │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant (time function) -> Monarch Assistant ─────────────────────────────────────────╮
│ │
│ "08/02/23 10:28" │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> User ──────────────────────────────────────────────────────────────────────╮
│ The current time is 10:28 AM on August 2, 2023. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
User: Fun! Can you hide the function calls, and then tell me the entropy of a standard scrabble set?
╭─ Monarch Assistant -> Monarch Assistant (hide_function_calls function) ──────────────────────────╮
│ │
│ hide_function_calls(params = {}) │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> User ──────────────────────────────────────────────────────────────────────╮
│ The entropy of a standard Scrabble set is approximately 4.37. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
User: Nice :) What time is it now?
╭─ Monarch Assistant -> User ──────────────────────────────────────────────────────────────────────╮
│ The current time is 10:29 AM on August 2, 2023. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
User: Ok, show the function calls again, and tell me more about the CFTR gene.
╭─ Monarch Assistant (show_function_calls function) -> Monarch Assistant ──────────────────────────╮
│ │
│ null │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> Monarch Assistant (monarch-search_entity function) ────────────────────────╮
│ │
│ monarch-search_entity(params = {'term': 'CFTR', 'category': 'biolink:Gene', 'limit': 1}) │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant (monarch-search_entity function) -> Monarch Assistant ────────────────────────╮
│ │
│ { │
│ "results": [ │
│ { │
│ "id": "HGNC:1884", │
│ "name": "CFTR", │
│ "categories": [ │
│ "biolink:Gene" │
│ ], │
│ "description": null │
│ } │
│ ], │
│ "total": 41 │
│ } │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> Monarch Assistant (monarch-get_gene_disease_associations function) ────────╮
│ │
│ monarch-get_gene_disease_associations(params = {'gene_id': 'HGNC:1884', 'limit': 10}) │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant (monarch-get_gene_disease_associations function) -> Monarch Assistant ────────╮
│ │
│ { │
│ "associations": [ │
│ { │
│ "metadata": { │
│ "relationship": "causal" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0009061", │
│ "label": "cystic fibrosis" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "causal" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0010178", │
│ "label": "congenital bilateral aplasia of vas deferens from CFTR mutation" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0008185", │
│ "label": "hereditary chronic pancreatitis" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0008185", │
│ "label": "hereditary chronic pancreatitis" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0008887", │
│ "label": "bronchiectasis with or without elevated sweat chloride 1" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0009061", │
│ "label": "cystic fibrosis" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0018393", │
│ "label": "male infertility with azoospermia or oligozoospermia due to single │
│ gene mutation" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0018801", │
│ "label": "congenital bilateral absence of vas deferens" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0018956", │
│ "label": "idiopathic bronchiectasis" │
│ }, │
│ "type": null │
│ }, │
│ { │
│ "metadata": { │
│ "relationship": "correlated" │
│ }, │
│ "publications": [], │
│ "disease": { │
│ "metadata": {}, │
│ "publications": [], │
│ "disease_id": "MONDO:0044663", │
│ "label": "aquagenic palmoplantar keratoderma" │
│ }, │
│ "type": null │
│ } │
│ ], │
│ "total": 10, │
│ "disease_url_template": "https://monarchinitiative.org/disease/{disease_id}" │
│ } │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Monarch Assistant -> User ──────────────────────────────────────────────────────────────────────╮
│ The CFTR gene, also known as the Cystic Fibrosis Transmembrane Conductance Regulator gene, is │
│ associated with several diseases. Here are some of the diseases associated with the CFTR gene: │
│ │
│ 1 Cystic Fibrosis: The CFTR gene is causally associated with Cystic Fibrosis, a genetic │
│ disorder characterized by the production of sweat with a high salt content and mucus │
│ secretions with an abnormal viscosity. More information │
│ 2 Congenital Bilateral Aplasia of Vas Deferens from CFTR Mutation: Mutations in the CFTR gene │
│ can lead to the congenital absence of the vas deferens, which can cause infertility in males. │
│ More information │
│ 3 Hereditary Chronic Pancreatitis: The CFTR gene is correlated with hereditary chronic │
│ pancreatitis, a condition characterized by inflammation of the pancreas that persists over │
│ time. More information │
│ 4 Bronchiectasis with or without Elevated Sweat Chloride 1: Mutations in the CFTR gene can also │
│ be correlated with bronchiectasis, a condition characterized by the abnormal widening of the │
│ bronchial tubes. More information │
│ │
│ Please note that this is not an exhaustive list of diseases associated with the CFTR gene. The │
│ CFTR gene plays a crucial role in various physiological processes, and mutations in this gene │
│ can have diverse effects on different organ systems. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
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