uncertainty | Learning with uncertainty for biological discovery | Genomics library
kandi X-RAY | uncertainty Summary
kandi X-RAY | uncertainty Summary
This repository contains the analysis source code used in the paper "Leveraging uncertainty in machine learning accelerates biological discovery and design" by Brian Hie, Bryan Bryson, and Bonnie Berger (Cell Systems, 2020).
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Top functions reviewed by kandi - BETA
- Train the model
- Fit the MLP model
- Predict the Gaussian distribution
- Creates an MLP ensemble
- Compute the GFP PFP structure
- Load embeddings
- Splits the data into training and brightness
- Plots the statistics for each motif
- Plot a scatter plot of a set of models
- Parse iteration log
- Sample from the model
- Predict the covariance
- Fit the GP model
- Explicitly plot the path between two sources
- Acquire perturbations
- Compute the GPFCV for the given model
- Fit Bayesian NN
- Parse the iteration log
- Parse the dgraphdta file
- Predict the covariance of the GP
- Sets up the ProTNN features
- Iterate over the model
- Process sequences and return a list of peptides
- Compute Bayesian NN
- Analyze a regression model
- Plot t test cases
- R Performs perturbation perturbation
- Plots the values for each model
uncertainty Key Features
uncertainty Examples and Code Snippets
Community Discussions
Trending Discussions on uncertainty
QUESTION
ANSWER
Answered 2021-Mar-18 at 15:40You need to define a different surrogate posterior. In Tensorflow's Bayesian linear regression example https://colab.research.google.com/github/tensorflow/probability/blob/master/tensorflow_probability/examples/jupyter_notebooks/Probabilistic_Layers_Regression.ipynb#scrollTo=VwzbWw3_CQ2z
you have the posterior mean field as such
QUESTION
I have the following relationship entity for neo4j Graph Model using Spring data neo4j 6.1.1 to represent relationship like Person-BookedFor->Movie where i can use UUID string for node repositories (Person, Movie) but not for the following relationship Entity BookedFor.
Note: since the neo4j doc describes this neo4j doc ref
...ANSWER
Answered 2021-Jun-10 at 15:17You cannot access relationship properties directly via repositories.
Those classes are just an encapsulation for properties on relationships and are not meant to represent a "physical" relationship or more a relationship entity.
Repositories are for @Node
annotated classes solely.
If you want to access and modify the properties of a relationship, you have to fetch the relationship defining entity. A relationship on its own is always represented by its start and end node.
The lately introduced required @Id
is for internal purposes only.
If you have a special need to persist an id-like property on the relationship, it would be just another property in the @RelationshipProperties
annotated class.
QUESTION
I have a data frame where some of the hours in Time GMT
are missing.
Normally, the hours should be shown in a sequence from 00:00 to 23:00, but sometimes an hour is missed.
Where an hour is missing in the sequence, I would like to insert a new row.
The new row will be a copy of the previous row, but with the following columns changed as follows:
Time GMT
: will contain the next hour of the previous row. i.e, if previous == 5:00, new == 6:00Sample Measurement
: will contain the average between the previous value and the next value in Sample Measurement column.MDL
: will contain the average between the previous value and the next value in column MDL
What have I tried
...ANSWER
Answered 2021-Jun-09 at 21:36You could use tidyverse
:
QUESTION
I was going through Linear and Logistic regression from ISLR and in both cases I found that one of the approaches adopted to increase the flexibility of the model was to use polynomial features - X and X^2 both as features and then apply the regression models as usual while considering X and X^2 as independent features (in sklearn, not the polynomial fit of statsmodel). Does that not increase the collinearity amongst the features though? How does it affect the model performance?
To summarize my thoughts regarding this -
First, X and X^2 have substantial correlation no doubt.
Second, I wrote a blog demonstrating that, at least in Linear regression, collinearity amongst features does not affect the model fit score though it makes the model less interpretable by increasing coefficient uncertainty.
So does the second point have anything to do with this, given that model performance is measured by the fit score.
...ANSWER
Answered 2021-Jun-10 at 04:30Multi-collinearity isn't always a hindrance. It depends from data to data. If your model isn't giving you the best results(high accuracy or low loss), you then remove the outliers or highly correlated features to improve it but is everything is hunky-dory, you don't bother about them.
Same goes with polynomial regression. Yes it adds multi-collinearity in your model by introducing x^2, x^3 features into your model.
To overcome that, you can use orthogonal polynomial regression
which introduces polynomials that are orthogonal to each other.
But it will still introduce higher degree polynomials which can become unstable at the boundaries of your data space.
To overcome this issue, you can use Regression Splines
in which it divides the distribution of the data into separate portions and fit linear or low degree polynomial functions on each of these portions. The points where the division occurs are called Knots
. Functions which we can use for modelling each piece/bin are known as Piecewise functions
. This function has a constraint , suppose, if it is introducing 3 degree of polynomials or cubic features and then the function should be second-order differentiable.
Such a piecewise polynomial of degree m with m-1 continuous derivatives is called a Spline
.
QUESTION
I am inserting data from one table "Tags" from "Recovery" database into another table "Tags" in "R3" database
they all live in my laptop similar SQL Server instance
I have built the insert query and because Recovery..Tags table is around 180M records I decided to break it into smaller sebsets. ( 1 million recs at the time)
Here is my query (Let's call Query A)
...ANSWER
Answered 2021-Jun-10 at 00:06The reason the first query is so much faster is it went parallel. This means the cardinality estimator knew enough about the data it had to handle, and the query was large enough to tip the threshold for parallel execution. Then, the engine passed chunks of data for different processors to handle individually, then report back and repartition the streams.
With the value as a variable, it effectively becomes a scalar function evaluation, and a query cannot go parallel with a scalar function, because the value has to determined before the cardinality estimator can figure out what to do with it. Therefore, it runs in a single thread, and is slower.
Some sort of looping mechanism might help. Create the included indexes to assist the engine in handling this request. You can probably find a better looping mechanism, since you are familiar with the identity ranges you care about, but this should get you in the right direction. Adjust for your needs.
With a loop like this, it commits the changes with each loop, so you aren't locking the table indefinitely.
QUESTION
I'm using ChartJS 2.8.0 and I have the code below:
...ANSWER
Answered 2021-Jun-02 at 22:12You are using V3 syntax for the scales, version 2 used a different syntax, please look at this link for the documentation for the version you are using
Live example with scale min-max:
QUESTION
I got a dictionary with 14 keys.
First Ive created createTableOfRecordsenter
function:
ANSWER
Answered 2021-May-28 at 00:00You've written:
QUESTION
I have several connections to Snowflake issuing SQL commands including adhoc queries I run for debugging/development manually, tasks I run twice a day to make summary tables, and Chartio (a dashboarding application) running interval queries against mostly my summary tables.
I’m using a lot more credits lately primarily due to computational resources. I could segment the different connections to different warehouses in order to isolate which of these distinct users are incurring the most credits, but was hoping to use Snowflake directly to correlate who is making which calls at the hours corresponding to the most credits. It doesn’t have to be a fully automated approach, I can do the legwork, I’m just unsure how to do this without segmenting the warehouses which would take a bit of work and uncertainty since it affects production.
One of the definite steps I took that should help is reducing the size of my warehouse that serves these queries. But I’m unsure how to segment and isolate what’s incurring the most cost here more definitely.
...ANSWER
Answered 2021-May-19 at 18:36It's more a process than a single event or piece of code, but here's a SQL query that can help. To isolate credit consumption cleanly, you need separate warehouses. It is possible, however, to estimate the credit consumption over time by user. It's an estimate because a warehouse is a shared resource, and since two or more users can be using a warehouse simultaneously the best we can do is figure a way to apportion who's responsible for what part of that consumption.
The following query estimates credit consumption by user over time using the following approach:
- Each segment in time that a warehouse runs gets logged as a row in the SNOWFLAKE.ACCOUNT_USAGE.METERING_HISTORY view.
- If only one user is active in the duration of that segment, the query assigns 100% of the usage to that user.
- If more than one user is active in the duration of a segment, the query takes the total query run time for a user and divides it by the total query run time in that segment for all users. This pro-rates the shared warehouse by query runtime.
#3 is the approximation, but it's suitable if you don't use it for chargebacks or billing someone for data share usage.
Be sure to change the warehouse name to your WH name and set the start and end timestamps for the duration you'd like to check usage.
QUESTION
The size of Go's int
datatype is platform dependent but a minimum of 32 bits, according to the documentation.
What's the advantage of having a native datatype which size is platform dependent (considering the uncertainty it introduces)?
Is the native type just faster or are there more advantages?
...ANSWER
Answered 2021-May-05 at 15:39What's the advantage of having a datatype which size is platform dependent [...]?
It is the native (i.e. hardware defined) type of the platform. The underlying hardware has a certain bit width of its integer types (modern hardwares are 64 or 32 bits). It is sensible to have native == hardware types for a language which provides and allows low level optimisations.
QUESTION
I am trying to model an equation that depends on T
and parameters xi
, mu
, sig
.
I have inferred parameters and spread(standard deviation) of those parameters for different durations (1h, 3h, etc). In the example code the parameters are for 1h duration.
I need to create a forloop to create a cloud of zp with the array of xi, mu and sig. The different values T can take are [2, 5, 25, 50, 75, 100]
I also want to show error bars or uncertainty with the standard deviation in line 2. I used Metropolis Hastings Algorithm for exploring the parametric space with 15000 iterations in 3 chains
...ANSWER
Answered 2021-May-04 at 14:53So, you have the (15000,3)
matrix accepted
, where xi=accepted[:,0]
, mu=accepted[:,1]
and sig=accepted[:,2]
.
I will generate some sample data for xi
, mu
and sig
, just to show you the results of plotting.
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Install uncertainty
You can use uncertainty like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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