bioservices

Kosmos is an open-source implementation of an autonomous AI scientist that can:

• Generate hypotheses from literature and data analysis
• Design experiments to test those hypotheses
• Execute code in sandboxed Docker containers
• Validate discoveries using an 8-dimension quality framework
• Build knowledge graphs to track relationships between concepts

The system runs autonomous research cycles, generating tasks, executing analyses, and synthesizing findings into validated discoveries.

Requirements

• Python 3.11+
• Anthropic API key or OpenAI API key
• Docker (recommended for code execution)

Without Docker, code runs via exec() with static validation. See "Code Execution Security" below.

Installation

```bash

git clone https://github.com/jimmc414/Kosmos.git

cd Kosmos

pip install -e .

cp .env.example .env

# Edit .env and set ANTHROPIC_API_KEY or OPENAI_API_KEY

```

Verify Installation

```bash

# Run smoke tests

python scripts/smoke_test.py

# Run unit tests

pytest tests/unit/ -v --tb=short

```

Run Research Workflow

```python

import asyncio

from kosmos.workflow.research_loop import ResearchWorkflow

async def run():

workflow = ResearchWorkflow(

research_objective="Your research question here",

artifacts_dir="./artifacts"

)

result = await workflow.run(num_cycles=5, tasks_per_cycle=10)

report = await workflow.generate_report()

print(report)

asyncio.run(run())

```

CLI Usage

```bash

# Run research with default settings

kosmos run "What metabolic pathways differ between cancer and normal cells?" --domain biology

# With budget limit

kosmos run "How do perovskites optimize efficiency?" --domain materials --budget 50

# Interactive mode (recommended for first time)

kosmos run --interactive

# Maximum verbosity

kosmos run "Your question" --domain biology --trace

# Real-time streaming display

kosmos run "Your question" --stream

# Streaming with token display disabled

kosmos run "Your question" --stream --no-stream-tokens

# Show system information

kosmos info

# Run diagnostics

kosmos doctor

```

Core Capabilities

| Feature | Description | Status |

|---------|-------------|--------|

| Research Loop | Multi-cycle autonomous research with hypothesis generation | Complete |

| Literature Search | ArXiv, PubMed, Semantic Scholar integration | Complete |

| Code Execution | Docker-sandboxed Jupyter notebooks | Complete |

| Knowledge Graph | Neo4j-based relationship storage (optional) | Complete |

| Context Compression | Query-based hierarchical compression (20:1 ratio) | Complete |

| Discovery Validation | 8-dimension ScholarEval quality framework | Complete |

| Multi-Provider LLM | Anthropic, OpenAI, LiteLLM (100+ providers) | Complete |

| Budget Enforcement | Cost tracking with configurable limits and enforcement | Complete |

| Error Recovery | Exponential backoff with circuit breaker | Complete |

| Debug Mode | 4-level verbosity with stage tracking | Complete |

| Real-time Streaming | SSE/WebSocket events, CLI --stream flag | Complete |

Code Execution Security

AI-generated code runs in isolated Docker containers:

| Layer | Implementation |

|-------|---------------|

| Container Isolation | --cap-drop=ALL, no privileged access |

| Network | Disabled (--network=none) |

| Filesystem | Read-only root, tmpfs for scratch |

| Resources | CPU: 2 cores, Memory: 2GB, Timeout: 300s |

| Pooling | Pre-warmed containers reduce cold start |

See: kosmos/execution/sandbox.py, docker_manager.py

Without Docker, falls back to CodeValidator static analysis + exec(). Not recommended for untrusted inputs.

Agent Architecture

| Agent | Role |

|-------|------|

| Research Director | Master orchestrator coordinating all agents |

| Hypothesis Generator | Generates testable hypotheses from literature |

| Experiment Designer | Creates experimental protocols |

| Data Analyst | Analyzes results and interprets findings |

| Literature Analyzer | Searches and synthesizes papers |

| Plan Creator/Reviewer | Strategic task generation with 70/30 exploration/exploitation |

How Context Compression Works

The system processes literature in batches, not bulk:

1. Relevance Sorting: Papers ranked by query relevance before processing
2. Batch Size: Top 10 papers per batch
3. Statistics Extraction: Regex-based extraction of p-values, sample sizes, effect sizes
4. Tiered Summarization:

- Task: 42K lines code to 2-line summary + extracted stats

- Cycle: 10 task summaries to cycle overview

- Synthesis: 20 cycles to final narrative

- Detail: Full content lazy-loaded when needed

Effective ratio: ~20:1. See kosmos/compression/compressor.py.

All configuration via environment variables. See .env.example for the full list.

LLM Provider

```bash

# Anthropic (default)

LLM_PROVIDER=anthropic

ANTHROPIC_API_KEY=sk-ant-...

# OpenAI

LLM_PROVIDER=openai

OPENAI_API_KEY=sk-...

# LiteLLM (supports 100+ providers including local models)

LLM_PROVIDER=litellm

LITELLM_MODEL=ollama/llama3.1:8b

LITELLM_API_BASE=http://localhost:11434

```

Budget Control

```bash

BUDGET_ENABLED=true

BUDGET_LIMIT_USD=10.00

```

Budget enforcement raises BudgetExceededError when the limit is reached, gracefully transitioning the research to completion.

Concurrency

Three independent limits in kosmos/config.py:

| Setting | Default | Range |

|---------|---------|-------|

| max_parallel_hypotheses | 3 | 1-10 |

| max_concurrent_experiments | 10 | 1-16 |

| max_concurrent_llm_calls | 5 | 1-20 |

The paper describes 10 parallel tasks. Default now matches paper specification.

Optional Services

```bash

# Neo4j (optional, for knowledge graph features)

NEO4J_URI=bolt://localhost:7687

NEO4J_PASSWORD=your-password

# Redis (optional, for distributed caching)

REDIS_URL=redis://localhost:6379

```

#### Docker Setup for Optional Services

Start Neo4j, Redis, and PostgreSQL with Docker Compose:

```bash

# Start all optional services (Neo4j, Redis, PostgreSQL)

docker compose --profile dev up -d

# Or start individual services

docker compose up -d neo4j

docker compose up -d redis

docker compose up -d postgres

# Stop services

docker compose --profile dev down

```

Service URLs when running via Docker:

• Neo4j Browser: http://localhost:7474 (user: neo4j, password: kosmos-password)
• PostgreSQL: localhost:5432 (user: kosmos, password: kosmos-dev-password)
• Redis: localhost:6379

#### Semantic Scholar API

Literature search via Semantic Scholar works without authentication. An API key is optional but increases rate limits:

```bash

# Optional: Get API key from https://www.semanticscholar.org/product/api

SEMANTIC_SCHOLAR_API_KEY=your-key-here

```

Debug Mode

```bash

# Enable debug mode with level 1-3

DEBUG_MODE=true

DEBUG_LEVEL=2

# Or use CLI flag for maximum verbosity

kosmos run "Your research question" --trace

```

See [docs/DEBUG_MODE.md](docs/DEBUG_MODE.md) for comprehensive debug documentation.

```

kosmos/

├── agents/ # Research agents (director, hypothesis, experiment, etc.)

├── compression/ # Context compression (20:1 ratio)

├── core/ # LLM providers, metrics, configuration

│ └── providers/ # Anthropic, OpenAI, LiteLLM with async support

├── execution/ # Dock