sfhmm 0.8.0
step-finding-based HMM
Requires Python: >=3.9

# sfHMM

**sfHMM** (Step-Finding based Hidden Markov Model analysis) provides efficient HMM analysis for varieties of biophysical data. Owing to its accurate parameter estimation workflows, sfHMM can be applied to systems with:

- unknown numbers of states
- high noise
- sparse transition

![ex1](assets/animation.gif)

You can also use sfHMM just for step finding or AIC/BIC based Gaussian mixture model selection. Please refer to "example.ipynb" for basic usages.

# Installation

- pip installation

Working in a new environment is highly recommended. For example, if you are using Anaconda:

``` shell
conda create -n myenv python
conda activate myenv
```

then it's ready to install sfHMM.

``` shell
pip install git+https://github.com/hanjinliu/sfHMM
```

- cloning from the source

If you want to clone from the source, you need Rust installed in your local environment.

``` shell
git clone https://github.com/hanjinliu/sfHMM
cd sfHMM
pip install -e .
```

# Contents

### `sfHMM`
This module contains basic classes and functions for **sfHMM data analysis**.
- `sfHMM1` ... sfHMM for single trajectory.
- `sfHMMn` ... sfHMM for multiple trajectories.
- `hmm_sampling` ... sample data generation of smFRET-like data.
- `motor_sampling` ... sample data generation of motor-like data.

### `sfHMM.motor`
This module contains sfHMM classes aiming at analyzing **motor-stepping** or other sparse transition models.
- `sfHMM1Motor` ... sfHMM for single motor-stepping trajectory.
- `sfHMMnMotor` ... sfHMM for multiple motor-stepping trajectories.

### `sfHMM.step`
This module contains several **step finding algorithms** in the same API. My efficient implementation enables analysis of **100,000** data points within **~1 sec**!
- `GaussStep` ... step finding for Gauss distribution [1].
- `PoissonStep` ... step finding for Poisson distribution.
- `SDFixedGaussStep` ... step finding for Gauss distribution with fixed standard deviation.
- `TtestStep` ... step finding using T-test [2].
- `BayesianPoissonStep` ... step finding in Bayesian method [3].

### `sfHMM.gmm`
This module contains classes that inherit `sklearn.mixture.GaussianMixture` while making **Gaussian mixture model clustering** much easier.
- `GMMs` ... Fitting Gaussian mixtures and model selection.

### `sfHMM.io`
This module contains **input/output** functions that are suitable for sfHMM data analysis or other one-dimensional signal processing.
- `read` ... *Not recommended now. Use "read" method in sfHMM classes instead*
- `read_excel` ... Load all the sheets from Excel files.
- `save` ... *Not recommended now. Use "save" method in sfHMM classes instead*

### `sfHMM.viewer`
This module contains **interactive multi-channel viewer** for 1-D data visualization (work in progress).
- `TrajectoryViewer` ... Qt viewer object.

# Common Parameters

All the parameters are optional.

- `sg0` ... The parameter used in denoising process.
- `psf` ... The parameter used in step finding.
- `krange` ... Range of the number of hidden states to test.
- `model` ... Distribution of signal. Gaussian and Poissonian are supported now.
- `name` ... Name of the object.

# Common Methods

- `run_all()` ... Run all the needed algorithm in the most plausible condition.
- `step_finding()` ... Step finding by likelihood maximization.
- `denoising()` ... The standard deviation of noise is cut off to `sg0`.
- `gmmfit()` ... Gaussian mixture model clustering.
- `hmmfit()` ... HMM parameter initialization and optimization.
- `plot()` ... Visualize the results of sfHMM analysis.
- `tdp()` ... Show the results in pseudo transition density plot.
- `read()` ... Load such as csv, txt, dat files, or the first sheet of Excel files.
- `save()` ... Save sfHMM analysis results.

# Use sfHMM in GUI

Since v0.8, sfHMM is now available as a [himena](https://github.com/hanjinliu/himena) plugin, which means that you can run sfHMM algorithms along with the powerful GUI and any other himena plugins.

![himena](assets/himena-window.png)

You can install himena and sfHMM plugin as follows:

``` shell
pip install himena[recommended]
himena --install sfHMM
```

and start himena application:

``` shell
himena
```

Now, you can create sfHMM window from `Tools > sfHMM` menu.

# Citation

If you found sfHMM useful, please consider citing our paper.

    A fast and objective hidden Markov modeling for accurate analysis of biophysical data with numerous states
    Hanjin Liu, Tomohiro Shima
    bioRxiv 2021.05.30.446337; doi: https://doi.org/10.1101/2021.05.30.446337

# References

[1] Kalafut, B., & Visscher, K. (2008). An objective, model-independent method for detection of non-uniform steps in noisy signals. Computer Physics Communications, 179(10), 716-723.

[2] Shuang, B., Cooper, D., Taylor, J. N., Kisley, L., Chen, J., Wang, W., ... & Landes, C. F. (2014). Fast step transition and state identification (STaSI) for discrete single-molecule data analysis. The journal of physical chemistry letters, 5(18), 3157-3161.

[3] Ensign, D. L., & Pande, V. S. (2010). Bayesian detection of intensity changes in  single molecule and molecular dynamics trajectories. Journal of Physical Chemistry B, 114(1), 280–292.