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https://github.com/mancusolab/traceax

Stochastic trace estimation using JAX
https://github.com/mancusolab/traceax

jax machine-learn python3 statistics trace-est

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Stochastic trace estimation using JAX

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README 

        
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# Traceax

``traceax`` is a Python library to perform stochastic trace estimation for linear operators. Namely,

given a square linear operator $\mathbf{A}$, ``traceax`` provides flexible routines that estimate,



$$\text{trace}(\mathbf{A}) = \sum_i \mathbf{A}_{ii},$$



using only matrix-vector products. ``traceax`` is heavily inspired by

[lineax](https://github.com/patrick-kidger/lineax) as well as

[XTrace](https://github.com/eepperly/XTrace).



  [**Installation**](#installation)

  | [**Example**](#get-started-with-example)

  | [**Documentation**](#documentation)

  | [**Notes**](#notes)

  | [**Support**](#support)

  | [**Other Software**](#other-software)



------------------



## Installation



Users can download the latest repository and then use `pip`:



``` bash

git clone https://github.com/mancusolab/traceax.git

cd traceax

pip install .

```



## Get Started with Example



```python

import jax.numpy as jnp

import jax.random as rdm

import lineax as lx



import traceax as tx



# simulate simple symmetric matrix with exponential eigenvalue decay

seed = 0

N = 1000

key = rdm.PRNGKey(seed)

key, xkey = rdm.split(key)



X = rdm.normal(xkey, (N, N))

Q, R = jnp.linalg.qr(X)

U = jnp.power(0.7, jnp.arange(N))

A = (Q * U) @ Q.T



# should be numerically close

print(jnp.trace(A))  # 3.3333323

print(jnp.sum(U))  # 3.3333335



# setup linear operator

operator = lx.MatrixLinearOperator(A)



# number of matrix vector operators

k = 25



# split key for estimators

key, key1, key2, key3, key4 = rdm.split(key, 5)



# Hutchinson estimator; default samples Rademacher {-1,+1}

hutch = tx.HutchinsonEstimator()

print(hutch.estimate(key1, operator, k))  # (Array(3.6007538, dtype=float32), {})



# Hutch++ estimator; default samples Rademacher {-1,+1}

hpp = tx.HutchPlusPlusEstimator()

print(hpp.estimate(key2, operator, k))  # (Array(3.4094956, dtype=float32), {})



# XTrace estimator; default samples uniformly on n-Sphere

xt = tx.XTraceEstimator()

print(xt.estimate(key3, operator, k))  # (Array(3.3030486, dtype=float32), {'std.err': Array(0.01238528, dtype=float32)})



# XNysTrace estimator; Improved performance for NSD/PSD trace estimates

operator = lx.TaggedLinearOperator(operator, lx.positive_semidefinite_tag)

nt = tx.XNysTraceEstimator()

print(nt.estimate(key4, operator, k))  # (Array(3.3314352, dtype=float32), {'std.err': Array(0.0006521, dtype=float32)})

```



## Documentation

Documentation is available at [here](https://mancusolab.github.io/traceax/).



## Notes



-   `traceax` uses [JAX](https://github.com/google/jax) with [Just In

    Time](https://jax.readthedocs.io/en/latest/jax-101/02-jitting.html)

    compilation to achieve high-speed computation. However, there are

    some [issues](https://github.com/google/jax/issues/5501) for JAX

    with Mac M1 chip. To solve this, users need to initiate conda using

    [miniforge](https://github.com/conda-forge/miniforge), and then

    install `traceax` using `pip` in the desired environment.



## Support



Please report any bugs or feature requests in the [Issue

Tracker](https://github.com/mancusolab/traceax/issues). If users have

any questions or comments, please contact Linda Serafin () or

Nicholas Mancuso ().



## Other Software



Feel free to use other software developed by [Mancuso

Lab](https://www.mancusolab.com/):



-   [SuShiE](https://github.com/mancusolab/sushie): a Bayesian

    fine-mapping framework for molecular QTL data across multiple

    ancestries.

-   [MA-FOCUS](https://github.com/mancusolab/ma-focus): a Bayesian

    fine-mapping framework using

    [TWAS](https://www.nature.com/articles/ng.3506) statistics across

    multiple ancestries to identify the causal genes for complex traits.

-   [SuSiE-PCA](https://github.com/mancusolab/susiepca): a scalable

    Bayesian variable selection technique for sparse principal component

    analysis

-   [twas_sim](https://github.com/mancusolab/twas_sim): a Python

    software to simulate [TWAS](https://www.nature.com/articles/ng.3506)

    statistics.

-   [FactorGo](https://github.com/mancusolab/factorgo): a scalable

    variational factor analysis model that learns pleiotropic factors

    from GWAS summary statistics.

-   [HAMSTA](https://github.com/tszfungc/hamsta): a Python software to

    estimate heritability explained by local ancestry data from

    admixture mapping summary statistics.



------------------------------------------------------------------------



``traceax`` is distributed under the terms of the

[Apache-2.0 license](https://spdx.org/licenses/Apache-2.0.html).



------------------------------------------------------------------------



This project has been set up using Hatch. For details and usage

information on Hatch see .