View source for Non-negative Matrix Factorization for Time-Resolved Raman Spectroscopy Data

PID (if applicable): doi:10.1007/s10910-020-01201-7

== Problem Statement ==

Crystallization of Paracetamol in Ethanol using Raman Spectroscopy

=== Object of Research and Objective ===

Determination of Intermediate States and their Kinetics along the Crystallization of Paracetamol in Ethanol using Raman Spectroscopy.

=== Procedure ===

<b>Data Acquisition:</b><br> Time-resolved Raman Spectroscopy to follow the crystallization of Paracetamol in accoustically-levitated Ethanol droplets. Surface, temperature (22.0 +/- 1.0 °C), and relative humidity (17.5 +/- 2.5 %) of the environment are controlled by Nitrogen stream. <br><br> <b>Data Extraction:</b><br> Extract the spectroscopic measurement matrix <math> \mathbf{M} \in \mathbb{R} _{+}^{n\times m} </math> ( <math>m</math> measurements of <math>n</math> non-negative intensities) from measurement file containing spectroscopic data and metadata. <br><br> <b>Data Analysis:</b><br> Factorize <math> \mathbf{M}</math> such that <math>\mathbf{M} = \mathbf{W} \cdot \mathbf{H}</math> (<math>\mathbf{W} \in \mathbb{R} _{+}^{n\times r},\mathbf{H} \in \mathbb{R} _{+}^{r\times m}</math> with <math>r</math> the rank of factorization or expected number of components) using a novel non-negative matrix factorization (NMF) approach. <br><br> <b>Data Interpretation:</b><br> <math>\mathbf{W_{rec}}</math> contains the spectra of the substances involved in the crystallization process, while <math>\mathbf{H_{rec}}</math> allows an inference on the kinetics. Interpretation of both matrices leads to the identification of intermediate states and the underlying kinetics.

=== Involved Disciplines ===

Chemistry (wikidata:Q2329)<br/> Mathematics (wikidata:Q395)

=== Data Streams ===

Chemistry <math>\Rightarrow</math> Mathematics (.txt File containing measurement matrix <math>\mathbf{M}</math>)<br/> Mathematics <math>\Rightarrow</math> Chemistry (.png Files containing component spectra <math>\mathbf{W}</math> and relative concentration profiles <math>\mathbf {H}</math>)

== Model ==

Non-negative Matrix Factorization

A matrix is factorized into a feature matrix and a weight matrix.

<math>\mathbf{M} = \mathbf{WH}</math>

=== Discretization ===

(if applicable)

* Time: Time-resolution of Raman Spectroscopy
* Space: No

=== Variables ===

{| class="wikitable"
! Name
! Unit
! Symbol
! dependent (measured) / independent (controlled)
|-
| Time
| <math>s</math>
| <math>t</math>
| Independent
|-
| Wavenumber
| <math>cm^{-1}</math>
| <math>\bar{\nu}</math>
| Independent
|-
| Intensity
| -
| <math>I</math>
| Dependent
|-
| Measurement Matrix
| -
| <math>\mathbf{M}</math>
| Dependent
|-
| Substance Matrix
| -
| <math>\mathbf{W}</math>
| Dependent
|-
| Kinetic Matrix
| -
| <math>\mathbf{H}</math>
| Dependent
|}

=== Parameter ===

{| class="wikitable"
! Name
! Unit
! Symbol
|-
| Temperature
| °C
| T
|-
| Relative Humidity
| %
| RH
|-
| rank of factorization
| -
| <math>r</math>
|-
| Number of Singular Values
| -
| <math>k</math>
|-
| Singular Value Tolerance
| -
| <math>tol</math>
|-
| Objective Function Parameter
| -
| <math>\alpha,\beta,\gamma,\delta,\mu</math>
|-
| Maximum Number of Iterations
| -
| MAXITER
|}

== Process Information ==

=== Process Steps ===

{| class="wikitable"
!width="12%"| Name
!width="12%"| Description
!width="12%"| Input
!width="12%"| Output
!width="12%"| Method
!width="12%"| Parameter
!width="12%"| Environment
!width="12%"| Mathematical Area
|-
| Data Acquisition
| Measurement
| -
| Time-resolved Raman Spectra
| Time-resolved Raman Spectroscopy
| T, RH
| RXN1
| -
|-
| Data Extraction
| Extract Spectroscopic Data
| .icraman
| .txt
| -
| -
| IC Raman
| -
|-
| Data Analysis
| Determine Component Spectra &amp; Concentration Profile
| .txt
| .png
| Non-negtaive Matrix Factorization
| <math>r,tol,k,MAXITER,\alpha,\beta,\gamma,\delta,\mu</math>
| Matlab
| Numerical Analysis, Mathematical Optimization, Linear Algebra
|-
| Data Interpretation
| Determine Intermediates and Kinetics
| .png
| -
| -
| -
| -
| -
|}

=== Applied Methods ===

{| class="wikitable"
!width="20%"| ID
!width="20%"| Name
!width="20%"| Process Step
!width="20%"| Parameter
!width="20%"| realised / implemented by
|-
| wikidata:Q420904
| Singular Value Decomposition
| Data Analysis - Pre-Processing
| <math>k</math>
| Matlab R2019a
|-
| wikidata:Q43219517
| Moore-Penrose inverse
| Data Analysis - Initializing
| <math>tol</math>
| Matlab R2019a
|-
| doi:10.1016/j.laa.2004.10.026
| Perron Cluster Cluster Analysis
| Data Analysis - Initializing
| <math>r</math>
| Matlab Script
|-
| wikidata:Q1253278
| Nelder-Mead method
| Data Analysis - Minimizing
| <math>\alpha,\beta,\gamma,\delta,\mu</math>
| Matlab R2019a
|}

=== Software used ===

{| class="wikitable"
!width="11%"| ID
!width="11%"| Name
!width="11%"| Description
!width="11%"| Version
!width="11%"| Programming Language
!width="11%"| Dependencies
!width="11%"| versioned
!width="11%"| published
!width="11%"| documented
|-
|
| IC Raman
| Data Acquisition and Reaction Analysis
| 4.1
| C++ (wikidata:Q2407)<br/> Java (wikidata:Q251)
| Windows
| Yes
| Yes
| Yes
|-
| wikidata:Q169478
| Matlab
| Numerical computing environment for the programming language.
| R2019a
| C++ (wikidata:Q2407)<br/> C (wikidata:Q15777)<br/> Fortran (wikidata:Q83303)<br/> Java (wikidata:Q251)
| Windows, Mac, Linux
| Yes
| Yes
| Yes
|}

=== Experimental Devices/Instruments and Computer-Hardware ===

{| class="wikitable"
! ID
! Name
! Description
! Version
! Part Nr
! Serial Nr
! Location
! Software
|-
|
| Raman RXN1
| Raman Spectrometer
|
|
|
|
|
|-
|
| GenuineIntel
| Intel(R) Core(TM) i7-9700T CPU @ 2.00 GHz
|
|
|
|
|
|}

=== Input Data ===

{| class="wikitable"
!width="10%"| ID
!width="10%"| Name
!width="10%"| Size
!width="10%"| Data Structure
!width="10%"| Format Representation
!width="10%"| Format Exchange
!width="10%"| binary/text
!width="10%"| proprietary
!width="10%"| to publish
!width="10%"| to archive
|-
|
| Time-Resolved Raman Spectroscopy Data
| MB
| Matlab Array
| dense matrix
| .txt
| text
| No
| Yes
| Yes
|}

=== Output Data ===

{| class="wikitable"
!width="10%"| ID
!width="10%"| Name
!width="10%"| Size
!width="10%"| Data Structure
!width="10%"| Format Representation
!width="10%"| Format Exchange
!width="10%"| binary/text
!width="10%"| proprietary
!width="10%"| to publish
!width="10%"| to archive
|-
|
| Component Spectra
| MB
| Matlab Array
| Plot
| .png
| binary
| No
| Yes
| Yes
|-
|
| Concentration Profile
| MB
| Matlab Array
| Plot
| .png
| binary
| No
| Yes
| Yes
|}


== Reproducibility ==

=== Mathematical Reproducibility ===
Yes

=== Runtime Reproducibility ===
Yes

=== Reproducibility of Results ===
Yes

=== Reproducibility on original Hardware ===
Yes

=== Reproducibility on other Hardware ===
Yes

=== Transferability to ===

a) other objects

= Legend =

The following abbreviations are used in the document to indicate/resolve IDs:

doi: DOI / https://dx.doi.org/

sw: swmath / https://swmath.org/software/

wikidata: Wikidata / https://www.wikidata.org/wiki/

mardi: MaRDI / https://portal.mardi4nfdi.de/wiki/

[[Category:MaRDMO workflows]]