From be3e96fa5624381f177ab111f587b4a7826eef4c Mon Sep 17 00:00:00 2001 From: "W.-C. Xue" <58248583+wcxve@users.noreply.github.com> Date: Sat, 27 Apr 2024 23:26:49 +0800 Subject: [PATCH 1/2] fix: clip the Poisson rate parameter into [1e-30, 1e15] (#42) --- src/elisa/infer/likelihood.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/src/elisa/infer/likelihood.py b/src/elisa/infer/likelihood.py index 7e7ba2de..8078db81 100644 --- a/src/elisa/infer/likelihood.py +++ b/src/elisa/infer/likelihood.py @@ -244,7 +244,8 @@ def likelihood( numpyro.deterministic(name, source_rate / channel_width) source_counts = source_rate * eff_expo spec_data = numpyro.primitives.mutable(f'{name}_Non_data', spec) - spec_model = numpyro.deterministic(f'{name}_Non_model', source_counts) + spec_model = jnp.clip(source_counts, a_min=1e-30, a_max=1e15) + spec_model = numpyro.deterministic(f'{name}_Non_model', spec_model) with numpyro.plate(f'{name}_plate', len(spec)): dist_on = BetterPoisson(spec_model) @@ -289,7 +290,8 @@ def likelihood( numpyro.deterministic(name, source_rate / channel_width) model_counts = source_rate * eff_expo + back_ratio * back spec_data = numpyro.primitives.mutable(f'{name}_Non_data', spec) - spec_model = numpyro.deterministic(f'{name}_Non_model', model_counts) + spec_model = jnp.clip(model_counts, a_min=1e-30, a_max=1e15) + spec_model = numpyro.deterministic(f'{name}_Non_model', spec_model) with numpyro.plate(f'{name}_plate', len(spec_data)): dist_on = BetterPoisson(spec_model) @@ -339,7 +341,8 @@ def likelihood(params: ParamNameValMapping, predictive: bool = False): source_counts, spec_data, back_data, back_error, back_ratio ) model_counts = source_counts + back_ratio * b - spec_model = numpyro.deterministic(f'{name}_Non_model', model_counts) + spec_model = jnp.clip(model_counts, a_min=1e-30, a_max=1e15) + spec_model = numpyro.deterministic(f'{name}_Non_model', spec_model) back_model = numpyro.deterministic(f'{name}_Noff_model', b) with numpyro.plate(f'{name}_plate', len(spec_data)): @@ -398,8 +401,10 @@ def likelihood(params: ParamNameValMapping, predictive: bool = False): source_counts = model_rate * eff_expo b = wstat_background(source_counts, spec_data, back_data, back_ratio) model_counts = source_counts + back_ratio * b - spec_model = numpyro.deterministic(f'{name}_Non_model', model_counts) - back_model = numpyro.deterministic(f'{name}_Noff_model', b) + spec_model = jnp.clip(model_counts, a_min=1e-30, a_max=1e15) + back_model = jnp.clip(b, a_min=1e-30, a_max=1e15) + spec_model = numpyro.deterministic(f'{name}_Non_model', spec_model) + back_model = numpyro.deterministic(f'{name}_Noff_model', back_model) with numpyro.plate(f'{name}_plate', len(spec_data)): dist_on = BetterPoisson(spec_model) From 9f1b0096f70870b865f40df70be14686ec427c84 Mon Sep 17 00:00:00 2001 From: "W.-C. Xue" <58248583+wcxve@users.noreply.github.com> Date: Sun, 28 Apr 2024 04:19:10 +0800 Subject: [PATCH 2/2] Create CODE_OF_CONDUCT.md --- CODE_OF_CONDUCT.md | 128 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 128 insertions(+) create mode 100644 CODE_OF_CONDUCT.md diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..776f3e97 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +wcxuemail@gmail.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations.