diff --git a/biochatter/api_agent/__init__.py b/biochatter/api_agent/__init__.py index e69de29b..6897e400 100644 --- a/biochatter/api_agent/__init__.py +++ b/biochatter/api_agent/__init__.py @@ -0,0 +1,9 @@ +from .abc import BaseQueryBuilder, BaseFetcher, BaseInterpreter +from .api_agent import APIAgent +from .blast import ( + BlastQueryParameters, + BlastQueryBuilder, + BlastFetcher, + BlastInterpreter, +) +from .oncokb import OncoKBQueryBuilder, OncoKBFetcher, OncoKBInterpreter diff --git a/docs/api-reference.md b/docs/api-reference.md new file mode 100644 index 00000000..745d0118 --- /dev/null +++ b/docs/api-reference.md @@ -0,0 +1,20 @@ +# API Agent Reference + +Here we handle the connection to external software tools via the +parameterisation of API calls by the LLM. + +## The abstract base classes + +::: biochatter.api_agent.abc + +## The API Agent + +::: biochatter.api_agent.api_agent + +## The API Agent for the BLAST tool + +::: biochatter.api_agent.blast + +## The API Agent for the OncoKB tool + +::: biochatter.api_agent.oncokb \ No newline at end of file diff --git a/docs/images/boxplot-naive-vs-biochatter.pdf b/docs/images/boxplot-naive-vs-biochatter.pdf index 217ed722..d07cf1ea 100644 Binary files a/docs/images/boxplot-naive-vs-biochatter.pdf and b/docs/images/boxplot-naive-vs-biochatter.pdf differ diff --git a/docs/images/dotplot-per-task.pdf b/docs/images/dotplot-per-task.pdf index b751391d..2224d505 100644 Binary files a/docs/images/dotplot-per-task.pdf and b/docs/images/dotplot-per-task.pdf differ diff --git a/docs/images/dotplot-per-task.png b/docs/images/dotplot-per-task.png index 0e627893..15fd59c4 100644 Binary files a/docs/images/dotplot-per-task.png and b/docs/images/dotplot-per-task.png differ diff --git a/docs/images/scatter-per-quantisation-name.pdf b/docs/images/scatter-per-quantisation-name.pdf index a8b5897f..85c11271 100644 Binary files a/docs/images/scatter-per-quantisation-name.pdf and b/docs/images/scatter-per-quantisation-name.pdf differ diff --git a/docs/images/scatter-per-quantisation-name.png b/docs/images/scatter-per-quantisation-name.png index 753a6272..1c56a4ed 100644 Binary files a/docs/images/scatter-per-quantisation-name.png and b/docs/images/scatter-per-quantisation-name.png differ diff --git a/docs/images/scatter-quantisation-accuracy.pdf b/docs/images/scatter-quantisation-accuracy.pdf index 50d28716..4c66f2c9 100644 Binary files a/docs/images/scatter-quantisation-accuracy.pdf and b/docs/images/scatter-quantisation-accuracy.pdf differ diff --git a/docs/images/scatter-size-accuracy.pdf b/docs/images/scatter-size-accuracy.pdf index f5a735c8..7fe91ad7 100644 Binary files a/docs/images/scatter-size-accuracy.pdf and b/docs/images/scatter-size-accuracy.pdf differ diff --git a/docs/images/stripplot-extraction-tasks.png b/docs/images/stripplot-extraction-tasks.png index bac81e3b..b3e40491 100644 Binary files a/docs/images/stripplot-extraction-tasks.png and b/docs/images/stripplot-extraction-tasks.png differ diff --git a/docs/images/stripplot-per-model.png b/docs/images/stripplot-per-model.png index 7438f983..53db934c 100644 Binary files a/docs/images/stripplot-per-model.png and b/docs/images/stripplot-per-model.png differ diff --git a/docs/images/stripplot-rag-tasks.pdf b/docs/images/stripplot-rag-tasks.pdf index 2330c64a..b1850bea 100644 Binary files a/docs/images/stripplot-rag-tasks.pdf and b/docs/images/stripplot-rag-tasks.pdf differ diff --git a/docs/images/stripplot-rag-tasks.png b/docs/images/stripplot-rag-tasks.png index 8473d422..84f5db1f 100644 Binary files a/docs/images/stripplot-rag-tasks.png and b/docs/images/stripplot-rag-tasks.png differ diff --git a/docs/kg-reference.md b/docs/kg-reference.md new file mode 100644 index 00000000..9e44a936 --- /dev/null +++ b/docs/kg-reference.md @@ -0,0 +1,12 @@ +# Knowledge Graph Agent Reference + +Here we handle generation of use case-specific database prompts and their +execution against a database using the database agent. + +## Dynamic prompt generation for BioCypher knowledge graphs + +::: biochatter.prompts + +## Execution of prompts against the database + +::: biochatter.database_agent \ No newline at end of file diff --git a/docs/llm_connect-reference.md b/docs/llm_connect-reference.md index a5ac81f7..a4ff9f80 100644 --- a/docs/llm_connect-reference.md +++ b/docs/llm_connect-reference.md @@ -1,4 +1,4 @@ -# LLM connectivity module +# LLM Connectivity Reference Here we handle connections to various LLM services, proprietary and open source. diff --git a/docs/podcast-reference.md b/docs/podcast-reference.md index 0f724ae7..c56ce7cd 100644 --- a/docs/podcast-reference.md +++ b/docs/podcast-reference.md @@ -1,4 +1,4 @@ -# Podcast module +# Podcast Reference Here we handle generation of podcasts from texts. diff --git a/docs/prompts-reference.md b/docs/prompts-reference.md deleted file mode 100644 index 21dc065a..00000000 --- a/docs/prompts-reference.md +++ /dev/null @@ -1,5 +0,0 @@ -# Prompts module - -Here we handle generation of use case-specific prompts. - -::: biochatter.prompts diff --git a/docs/reflexion-reference.md b/docs/reflexion-reference.md new file mode 100644 index 00000000..e3f8f049 --- /dev/null +++ b/docs/reflexion-reference.md @@ -0,0 +1,12 @@ +# Reflexion Agent Reference + +Here we handle the implementation of a LangGraph-based multi-agent system for +reflexion on a user-defined task. + +## The base module + +::: biochatter.langgraph_agent_base + +## The KG-based reflexion agent + +::: biochatter.kg_langgraph_agent \ No newline at end of file diff --git a/docs/vectorstore-reference.md b/docs/vectorstore-reference.md index 7205f3af..dfb345e5 100644 --- a/docs/vectorstore-reference.md +++ b/docs/vectorstore-reference.md @@ -1,6 +1,13 @@ -# Vectorstore module +# Vectorstore Agent Reference Here we handle the application of vectorstore services to retrieval-augmented -generation tasks by embedding documents. +generation tasks by embedding documents and connections/management of +vectorstore services and semantic search. + +## Vectorstore Implementation ::: biochatter.vectorstore + +## Vectorstore Agent + +::: biochatter.vectorstore_agent \ No newline at end of file diff --git a/docs/vectorstore_agent-reference.md b/docs/vectorstore_agent-reference.md deleted file mode 100644 index 1353323c..00000000 --- a/docs/vectorstore_agent-reference.md +++ /dev/null @@ -1,6 +0,0 @@ -# Vectorstore agent module - -Here we handle connections and management of various vectorstore services and -semantic seach. - -::: biochatter.vectorstore_agent diff --git a/mkdocs.yml b/mkdocs.yml index 1650e4d5..cfa21419 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -69,9 +69,10 @@ nav: - Customising BioChatter Light - Advanced: vignette-custom-bclight-advanced.md - API Reference: - LLM Connectivity: llm_connect-reference.md - - Vectorstore: vectorstore-reference.md - - Vectorstore Agent: vectorstore_agent-reference.md - - Prompt Engine: prompts-reference.md + - Vectorstore Agent: vectorstore-reference.md + - Knowledge Graph Agent: kg-reference.md + - API Agent: api-reference.md + - Reflexion Agent: reflexion-reference.md - Podcast: podcast-reference.md repo_url: https://github.com/biocypher/biochatter