BE/Bi 103 b: Statistical Inference in the Biological Sciences
=============================================================

In the `prequel to this course <https://bebi103a.github.io/>`_, we developed tools to build data analysis pieplines, including the organization, preservation, sharing, and display quantitative data. We also learned basic techniques in statistical inference using resampling methods taking a frequentist approach.

In this class, we go deeper into statistical modeling and inference, mostly taking a Bayesian approach. We discuss generative modeling, parameter estimation, model comparison, hierarchical modeling, Markov chain Monte Carlo, graphical display of inference results, and principled workflows. All of these topics are explored through analysis of real biological data sets.

If you are enrolled in the course, please read the :ref:`Course policies<Policies>` below. We will not go over them in detail in class, and it is your responsibility to understand them.


Useful links
-------------

- `Ed <https://us.edstem.org/courses/3198/>`_ (used for course communications)
- `Course Zoom link <http://bebi103.caltech.edu/2021/b/zoom_links/bebi103_main>`_ (password protected)
- `"200 Broad" Gather link <http://bebi103.caltech.edu/2021/b/gather/200_broad/>`_ (password protected)
- `Video recordings <http://bebi103.caltech.edu/2021/b/recordings/google_drive/>`_ (password protected)
- `Google doc for help queue <http://bebi103.caltech.edu/2021/b/help_queue/google_drive/>`_ (password protected)
- `Homework solutions <http://bebi103.caltech.edu/2021b_hw_solutions/hw_solutions.html>`_ (password protected)

During lab and homework help sessions, we will break out into different Zoom sessions headed by various course staff members. Their individual Zoom links are accessible below.


People
------

- Instructor

   + `Justin Bois <http://bois.caltech.edu/>`_ (`bois at caltech dot edu`)

- TAs

   + Rosita Fu (`rfu at caltech dot edu`)
   + Tom Röschinger (`troeschi at caltech dot edu`)
   + Ariana Tribby (`atribby at caltech dot edu`)
   + Julian Wagner (`jwagner2 at caltech dot edu`)


.. toctree::
   :maxdepth: 1
   :caption: Lessons

   lessons/00/setup.ipynb
   lessons/01/index
   lessons/02/plotting_posteriors.ipynb
   lessons/03/marginalization_by_numerical_quadrature.ipynb
   lessons/04/conjugacy.ipynb
   lesson_exercises/exercise_01.ipynb   
   lessons/05/index
   lessons/06/index
   lesson_exercises/exercise_02.ipynb   
   lessons/07/index
   lessons/08/index
   lessons/09/index
   lessons/10/mixture_model_stan.ipynb
   lessons/11/regression_with_stan.ipynb
   lesson_exercises/exercise_03.ipynb   
   lessons/12/index
   lessons/13/prior_predictive_checks.ipynb
   lessons/14/posterior_predictive_checks.ipynb
   lesson_exercises/exercise_04.ipynb   
   lessons/15/box_of_distributions.rst
   lessons/16/mcmc_diagnostics.ipynb
   lessons/17/funnel_of_hell.ipynb
   lesson_exercises/exercise_05.ipynb
   lessons/18/model_comparison.rst
   lessons/19/index
   lesson_exercises/exercise_06.ipynb
   lessons/20/index
   lessons/21/hierarchical_implementation.ipynb
   lesson_exercises/exercise_07.ipynb
   lessons/22/sbc.ipynb
   lessons/23/sbc_in_practice.ipynb
   lesson_exercises/exercise_08.ipynb
   lessons/24/intro_to_gps.ipynb
   lessons/25/index
   lesson_exercises/exercise_09.ipynb
   lessons/26/variational_inference.ipynb
   lessons/27/wrapup


.. toctree::
   :maxdepth: 1
   :caption: Recitations

   recitations/01/review_of_mle.ipynb
   recitations/02/probability_review.rst
   recitations/03/choosing_priors.ipynb
   recitations/04/index
   recitations/05/index
   recitations/06/practice_model_building.ipynb
   recitations/07/hmc.ipynb
   recitations/08/project_proposals.rst
   recitations/09/sampling_discrete_parameters.ipynb


.. toctree::
   :maxdepth: 1
   :caption: Homework

   0. Configuring your team <homework/00/hw0.1>
   homework/01/index
   homework/02/index
   homework/03/index
   homework/04/index
   homework/05/index
   homework/06/index
   homework/07/index
   homework/08/index
   homework/09/index
   homework/10/index
   11. Course feedback <homework/11/hw11.ipynb>


.. toctree::
   :maxdepth: 1
   :caption: Schedule

   schedule


.. toctree::
   :maxdepth: 1
   :caption: Policies

   policies


.. toctree::
   :maxdepth: 1
   :caption: Resources

   resources