POPPER
Automated Hypothesis Testing with Agentic Sequential Falsifications
Stars: 123
Popper is an agentic framework for automated validation of free-form hypotheses using Large Language Models (LLMs). It follows Karl Popper's principle of falsification and designs falsification experiments to validate hypotheses. Popper ensures strict Type-I error control and actively gathers evidence from diverse observations. It delivers robust error control, high power, and scalability across various domains like biology, economics, and sociology. Compared to human scientists, Popper achieves comparable performance in validating complex biological hypotheses while reducing time by 10 folds, providing a scalable, rigorous solution for hypothesis validation.
README:
This repository hosts the code base for the paper
Automated Agentic Hypothesis Validation with Sequential Falsifications
Kexin Huang*, Ying Jin*, Ryan Li*, Michael Y. Li, Emmanuel Candès, Jure Leskovec
Link to Paper
If you find this work useful, please consider cite:
@misc{popper,
title={Automated Hypothesis Validation with Agentic Sequential Falsifications},
author={Kexin Huang and Ying Jin and Ryan Li and Michael Y. Li and Emmanuel Candès and Jure Leskovec},
year={2025},
eprint={2502.09858},
archivePrefix={arXiv}
}
Hypotheses are central to information acquisition, decision-making, and discovery. However, many real-world hypotheses are abstract, high-level statements that are difficult to validate directly. This challenge is further intensified by the rise of hypothesis generation from Large Language Models (LLMs), which are prone to hallucination and produce hypotheses in volumes that make manual validation impractical. Here we propose Popper, an agentic framework for rigorous automated validation of free-form hypotheses. Guided by Karl Popper's principle of falsification, Popper validates a hypothesis using LLM agents that design and execute falsification experiments targeting its measurable implications. A novel sequential testing framework ensures strict Type-I error control while actively gathering evidence from diverse observations, whether drawn from existing data or newly conducted procedures. We demonstrate Popper on six domains including biology, economics, and sociology. Popper delivers robust error control, high power, and scalability. Furthermore, compared to human scientists, Popper achieved comparable performance in validating complex biological hypotheses while reducing time by 10 folds, providing a scalable, rigorous solution for hypothesis validation.
We highly recommend using a virtual environment to manage the dependencies.
conda create -n popper_env python=3.10
conda activate popper_envFor direct usage of Popper, you can install the package via pip:
pip install popper_agentFor source code development, you can clone the repository and install the package:
git clone https://github.com/snap-stanford/POPPER.git
cd POPPER
pip install -r requirements.txtAdd the OpenAI/Anthropic API key to the environment variables:
export OPENAI_API_KEY="YOUR_API_KEY"
export ANTHROPIC_API_KEY="YOUR_API_KEY"Datasets will be automatically downloaded to specified data folder when you run the code.
A demo is provided in here to show how to use the Popper agent to validate a hypothesis and basic functionalities of the Popper agent.
from popper import Popper
# Initialize the Popper agent
agent = Popper(llm="claude-3-5-sonnet-20240620")
# Register data for hypothesis testing;
# for bio/discoverybench data in the paper,
# it will be automatically downloaded to your specified data_path
agent.register_data(data_path='path/to/data', loader_type='bio')
# Configure the agent with custom parameters
agent.configure(
alpha=0.1,
max_num_of_tests=5,
max_retry=3,
time_limit=2,
aggregate_test='E-value',
relevance_checker=True,
use_react_agent=True
)
# Validate a hypothesis
results = agent.validate(hypothesis="Your hypothesis here")
# Print the results
print(results)Popper supports inferencing with local LLM servers such as vLLM, SGLang, and llama.cpp, as long as they support OpenAI-compatible API. Here are some example usage with locally hosted LLMs:
Using SGLang:
# mistral large 2 with SGLang, using 4 GPUs with 8-bit quantization
python -m sglang.launch_server --model-path mistralai/Mistral-Large-Instruct-2411 --port 40000 --host 0.0.0.0 --tp 4 --quantization fp8 --mem-fraction-static 0.8 --trust-remote-codefrom popper import Popper
agent = Popper(llm="mistralai/Mistral-Large-Instruct-2411", is_locally_served=True, server_port=40000)
agent.configure(alpha=0.1)
agent.register_data(data_path='path/to/data', loader_type='bio')
agent.validate(hypothesis = 'YOUR HYPOTHESIS')Using vLLM:
vllm serve NousResearch/Meta-Llama-3-8B-Instruct --dtype auto --api-key token-abc123from popper import Popper
agent = Popper(llm="NousResearch/Meta-Llama-3-8B-Instruct", is_locally_served=True, server_port=8000, api_key="token-abc123")Using llama.cpp:
llama-server -m model.gguf --port 8080from popper import Popper
agent = Popper(llm="qwen2 1.5B", is_locally_served=True, server_port=8080)You can simply dump in a set of datasets in your domain (e.g. business, economics, political science, etc.) and run Popper on your own hypothesis. We only expect every file is in a csv or pkl format.
from popper import Popper
agent = Popper(llm="claude-3-5-sonnet-20240620")
agent.configure(alpha = 0.1)
agent.register_data(data_path='path/to/data', loader_type='custom')
agent.validate(hypothesis = 'YOUR HYPOTHESIS')You can arbitrarily define any free-form hypothesis. In the paper, we provide two types of hypothesis: biological hypothesis and discovery-bench hypothesis.
You can load the biological hypothesis with:
from popper.benchmark import gene_perturb_hypothesis
bm = gene_perturb_hypothesis(num_of_samples = samples, permuted=False, dataset = 'IL2', path = path)
example = bm.get_example(0)It will return something like:
{'prompt': 'Gene VAV1 regulates the production of Interleukin-2 (IL-2).',
'gene': 'VAV1',
'answer': 2.916,
'binary_answer': True}
num_of_samples is the number of samples you want to generate, permuted is whether you want to permute the dataset for type I error estimation, and dataset is the dataset you want to use and you can choose from IL2 and IFNG.
For discovery-bench, you can load the hypothesis with:
from popper.benchmark import discovery_bench_hypothesis
bm = discovery_bench_hypothesis(num_samples = samples, path = path)
example = bm.get_example(0)It will return something like:
{'task': 'archaeology',
'domain': 'humanities',
'metadataid': 5,
'query_id': 0,
'prompt': 'From 1700 BCE onwards, the use of hatchets and swords increased while the use of daggers decreased.',
'data_loader': <popper.utils.DiscoveryBenchDataLoader at 0x7c20793e9f70>,
'answer': True}
As each hypothesis in discoverybench has its own associated dataset, the example will return data_loader its own dataset.
Bash scripts for reproducing the paper is provided in the benchmark_scripts/run_targetval.sh for TargetVal benchmark and benchmark_scripts/run_discoverybench.sh for DiscoveryBench benchmark.
Note: the Popper agent can read or write files to your filesystem. We recommend running the benchmark scripts inside a containerized environments. We have provided a working Dockerfile and an example script to launch a Docker container and execute the scripts in benchmark_scripts/run_discoverybench_docker.sh.
To run paper benchmarks with locally-served models, you can simply passed in the extra parameters to the benchmark script, e.g.,
python benchmark_scripts/run_discovery_bench.py --exp_name discovery_bench --model llama-3.3-70b --num_tests 5 --samples 100 --permute --e_value --react --relevance_checker --is_locally_served --server_port 30000 --path PATH_TO_YOUR_DATASETYou can deploy a simple UI interface with one line of code using your datasets or our bio dataset - a gradio UI will be generated and you can interact with it to validate your hypothesis.
agent.launch_UI()An interface like this will be popped up:
The DiscoveryBench benchmark and some of the baseline agents are built on top of allenai/discoverybench. Thanks for their awsome work!
For any questions, please raise an issue in the GitHub or contact Kexin Huang ([email protected]).
For Tasks:
Click tags to check more tools for each tasksFor Jobs:
Alternative AI tools for POPPER
Similar Open Source Tools
POPPER
Popper is an agentic framework for automated validation of free-form hypotheses using Large Language Models (LLMs). It follows Karl Popper's principle of falsification and designs falsification experiments to validate hypotheses. Popper ensures strict Type-I error control and actively gathers evidence from diverse observations. It delivers robust error control, high power, and scalability across various domains like biology, economics, and sociology. Compared to human scientists, Popper achieves comparable performance in validating complex biological hypotheses while reducing time by 10 folds, providing a scalable, rigorous solution for hypothesis validation.
minions
Minions is a communication protocol that enables small on-device models to collaborate with frontier models in the cloud. By only reading long contexts locally, it reduces cloud costs with minimal or no quality degradation. The repository provides a demonstration of the protocol.
web-llm
WebLLM is a modular and customizable javascript package that directly brings language model chats directly onto web browsers with hardware acceleration. Everything runs inside the browser with no server support and is accelerated with WebGPU. WebLLM is fully compatible with OpenAI API. That is, you can use the same OpenAI API on any open source models locally, with functionalities including json-mode, function-calling, streaming, etc. We can bring a lot of fun opportunities to build AI assistants for everyone and enable privacy while enjoying GPU acceleration.
dbt-airflow
A Python package that helps Data and Analytics engineers render dbt projects in Apache Airflow DAGs. It enables teams to automatically render their dbt projects in a granular level, creating individual Airflow tasks for every model, seed, snapshot, and test within the dbt project. This allows for full control at the task-level, improving visibility and management of data models within the team.
paper-qa
PaperQA is a minimal package for question and answering from PDFs or text files, providing very good answers with in-text citations. It uses OpenAI Embeddings to embed and search documents, and includes a process of embedding docs, queries, searching for top passages, creating summaries, using an LLM to re-score and select relevant summaries, putting summaries into prompt, and generating answers. The tool can be used to answer specific questions related to scientific research by leveraging citations and relevant passages from documents.
VMind
VMind is an open-source solution for intelligent visualization, providing an intelligent chart component based on LLM by VisActor. It allows users to create chart narrative works with natural language interaction, edit charts through dialogue, and export narratives as videos or GIFs. The tool is easy to use, scalable, supports various chart types, and offers one-click export functionality. Users can customize chart styles, specify themes, and aggregate data using LLM models. VMind aims to enhance efficiency in creating data visualization works through dialogue-based editing and natural language interaction.
ontogpt
OntoGPT is a Python package for extracting structured information from text using large language models, instruction prompts, and ontology-based grounding. It provides a command line interface and a minimal web app for easy usage. The tool has been evaluated on test data and is used in related projects like TALISMAN for gene set analysis. OntoGPT enables users to extract information from text by specifying relevant terms and provides the extracted objects as output.
kvpress
This repository implements multiple key-value cache pruning methods and benchmarks using transformers, aiming to simplify the development of new methods for researchers and developers in the field of long-context language models. It provides a set of 'presses' that compress the cache during the pre-filling phase, with each press having a compression ratio attribute. The repository includes various training-free presses, special presses, and supports KV cache quantization. Users can contribute new presses and evaluate the performance of different presses on long-context datasets.
storm
STORM is a LLM system that writes Wikipedia-like articles from scratch based on Internet search. While the system cannot produce publication-ready articles that often require a significant number of edits, experienced Wikipedia editors have found it helpful in their pre-writing stage. **Try out our [live research preview](https://storm.genie.stanford.edu/) to see how STORM can help your knowledge exploration journey and please provide feedback to help us improve the system 🙏!**
monitors4codegen
This repository hosts the official code and data artifact for the paper 'Monitor-Guided Decoding of Code LMs with Static Analysis of Repository Context'. It introduces Monitor-Guided Decoding (MGD) for code generation using Language Models, where a monitor uses static analysis to guide the decoding. The repository contains datasets, evaluation scripts, inference results, a language server client 'multilspy' for static analyses, and implementation of various monitors monitoring for different properties in 3 programming languages. The monitors guide Language Models to adhere to properties like valid identifier dereferences, correct number of arguments to method calls, typestate validity of method call sequences, and more.
LeanCopilot
Lean Copilot is a tool that enables the use of large language models (LLMs) in Lean for proof automation. It provides features such as suggesting tactics/premises, searching for proofs, and running inference of LLMs. Users can utilize built-in models from LeanDojo or bring their own models to run locally or on the cloud. The tool supports platforms like Linux, macOS, and Windows WSL, with optional CUDA and cuDNN for GPU acceleration. Advanced users can customize behavior using Tactic APIs and Model APIs. Lean Copilot also allows users to bring their own models through ExternalGenerator or ExternalEncoder. The tool comes with caveats such as occasional crashes and issues with premise selection and proof search. Users can get in touch through GitHub Discussions for questions, bug reports, feature requests, and suggestions. The tool is designed to enhance theorem proving in Lean using LLMs.
LazyLLM
LazyLLM is a low-code development tool for building complex AI applications with multiple agents. It assists developers in building AI applications at a low cost and continuously optimizing their performance. The tool provides a convenient workflow for application development and offers standard processes and tools for various stages of application development. Users can quickly prototype applications with LazyLLM, analyze bad cases with scenario task data, and iteratively optimize key components to enhance the overall application performance. LazyLLM aims to simplify the AI application development process and provide flexibility for both beginners and experts to create high-quality applications.
raft
RAFT (Reusable Accelerated Functions and Tools) is a C++ header-only template library with an optional shared library that contains fundamental widely-used algorithms and primitives for machine learning and information retrieval. The algorithms are CUDA-accelerated and form building blocks for more easily writing high performance applications.
lotus
LOTUS (LLMs Over Tables of Unstructured and Structured Data) is a query engine that provides a declarative programming model and an optimized query engine for reasoning-based query pipelines over structured and unstructured data. It offers a simple and intuitive Pandas-like API with semantic operators for fast and easy LLM-powered data processing. The tool implements a semantic operator programming model, allowing users to write AI-based pipelines with high-level logic and leaving the rest of the work to the query engine. LOTUS supports various semantic operators like sem_map, sem_filter, sem_extract, sem_agg, sem_topk, sem_join, sem_sim_join, and sem_search, enabling users to perform tasks like mapping records, filtering data, aggregating records, and more. The tool also supports different model classes such as LM, RM, and Reranker for language modeling, retrieval, and reranking tasks respectively.
py-vectara-agentic
The `vectara-agentic` Python library is designed for developing powerful AI assistants using Vectara and Agentic-RAG. It supports various agent types, includes pre-built tools for domains like finance and legal, and enables easy creation of custom AI assistants and agents. The library provides tools for summarizing text, rephrasing text, legal tasks like summarizing legal text and critiquing as a judge, financial tasks like analyzing balance sheets and income statements, and database tools for inspecting and querying databases. It also supports observability via LlamaIndex and Arize Phoenix integration.
pg_vectorize
pg_vectorize is a Postgres extension that automates text to embeddings transformation, enabling vector search and LLM applications with minimal function calls. It integrates with popular LLMs, provides workflows for vector search and RAG, and automates Postgres triggers for updating embeddings. The tool is part of the VectorDB Stack on Tembo Cloud, offering high-level APIs for easy initialization and search.
For similar tasks
POPPER
Popper is an agentic framework for automated validation of free-form hypotheses using Large Language Models (LLMs). It follows Karl Popper's principle of falsification and designs falsification experiments to validate hypotheses. Popper ensures strict Type-I error control and actively gathers evidence from diverse observations. It delivers robust error control, high power, and scalability across various domains like biology, economics, and sociology. Compared to human scientists, Popper achieves comparable performance in validating complex biological hypotheses while reducing time by 10 folds, providing a scalable, rigorous solution for hypothesis validation.
For similar jobs
weave
Weave is a toolkit for developing Generative AI applications, built by Weights & Biases. With Weave, you can log and debug language model inputs, outputs, and traces; build rigorous, apples-to-apples evaluations for language model use cases; and organize all the information generated across the LLM workflow, from experimentation to evaluations to production. Weave aims to bring rigor, best-practices, and composability to the inherently experimental process of developing Generative AI software, without introducing cognitive overhead.
LLMStack
LLMStack is a no-code platform for building generative AI agents, workflows, and chatbots. It allows users to connect their own data, internal tools, and GPT-powered models without any coding experience. LLMStack can be deployed to the cloud or on-premise and can be accessed via HTTP API or triggered from Slack or Discord.
VisionCraft
The VisionCraft API is a free API for using over 100 different AI models. From images to sound.
kaito
Kaito is an operator that automates the AI/ML inference model deployment in a Kubernetes cluster. It manages large model files using container images, avoids tuning deployment parameters to fit GPU hardware by providing preset configurations, auto-provisions GPU nodes based on model requirements, and hosts large model images in the public Microsoft Container Registry (MCR) if the license allows. Using Kaito, the workflow of onboarding large AI inference models in Kubernetes is largely simplified.
PyRIT
PyRIT is an open access automation framework designed to empower security professionals and ML engineers to red team foundation models and their applications. It automates AI Red Teaming tasks to allow operators to focus on more complicated and time-consuming tasks and can also identify security harms such as misuse (e.g., malware generation, jailbreaking), and privacy harms (e.g., identity theft). The goal is to allow researchers to have a baseline of how well their model and entire inference pipeline is doing against different harm categories and to be able to compare that baseline to future iterations of their model. This allows them to have empirical data on how well their model is doing today, and detect any degradation of performance based on future improvements.
tabby
Tabby is a self-hosted AI coding assistant, offering an open-source and on-premises alternative to GitHub Copilot. It boasts several key features: * Self-contained, with no need for a DBMS or cloud service. * OpenAPI interface, easy to integrate with existing infrastructure (e.g Cloud IDE). * Supports consumer-grade GPUs.
spear
SPEAR (Simulator for Photorealistic Embodied AI Research) is a powerful tool for training embodied agents. It features 300 unique virtual indoor environments with 2,566 unique rooms and 17,234 unique objects that can be manipulated individually. Each environment is designed by a professional artist and features detailed geometry, photorealistic materials, and a unique floor plan and object layout. SPEAR is implemented as Unreal Engine assets and provides an OpenAI Gym interface for interacting with the environments via Python.
Magick
Magick is a groundbreaking visual AIDE (Artificial Intelligence Development Environment) for no-code data pipelines and multimodal agents. Magick can connect to other services and comes with nodes and templates well-suited for intelligent agents, chatbots, complex reasoning systems and realistic characters.