TIERIA

TIERIA is a prototype quantum framework for closest-pair search over biological sequences using k-mer distributions, Bhattacharyya overlap, QAE-based similarity estimation, and Grover/Dürr--Høyer-style search.

Repository layout

virtue/
  virtue.py              # Core Python implementation and Q# simulation helpers
  qsharp/                # Q# project for correctness/search simulation
  qsharp_resource/       # Q# project for logical resource counting and resource estimation
  experiments/           # Experiment scripts, parameters, README, and generated outputs

Environment setup

A Python virtual environment is recommended.

python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip

The core Python code mainly uses the Python standard library. To run the Q# simulation and resource-estimation parts, install the Q# Python package:

python -m pip install qsharp==1.26.0

If you only want to inspect the classical preprocessing and run the small demo entry point, start with the basic Python environment above. If you want to reproduce the Q# experiments, make sure the qsharp package is installed and available in the same virtual environment.

Quick demo

From the repository root, run:

cd virtue
python virtue.py

This runs a small built-in demonstration of the closest-pair search workflow on a toy sequence set and prints the observed k-mer basis, exact pair overlaps, and the search trace.

Experiments

All experiment-related scripts and outputs are under:

virtue/experiments/

See virtue/experiments/README.md for full reproduction instructions.