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

Data Acquisition:
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.

Data Extraction:
Extract the spectroscopic measurement matrix $\mathbf {M} \in \mathbb {R} _{+}^{n\times m}$ ( $m$ measurements of $n$ non-negative intensities) from measurement file containing spectroscopic data and metadata.

Data Analysis:
Factorize $\mathbf {M}$ such that $\mathbf {M} =\mathbf {W} \cdot \mathbf {H}$ ($\mathbf {W} \in \mathbb {R} _{+}^{n\times r},\mathbf {H} \in \mathbb {R} _{+}^{r\times m}$ with $r$ the rank of factorization or expected number of components) using a novel non-negative matrix factorization (NMF) approach.

Data Interpretation:
$\mathbf {W_{rec}}$ contains the spectra of the substances involved in the crystallization process, while $\mathbf {H_{rec}}$ 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)
Mathematics (wikidata:Q395)

Data Streams

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

Model

Non-negative Matrix Factorization

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

$\mathbf {M} =\mathbf {WH}$

Discretization

(if applicable)

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

Variables

Name	Unit	Symbol	dependent (measured) / independent (controlled)
Time	$s$	$t$	Independent
Wavenumber	$cm^{-1}$	${\bar {\nu }}$	Independent
Intensity	-	$I$	Dependent
Measurement Matrix	-	$\mathbf {M}$	Dependent
Substance Matrix	-	$\mathbf {W}$	Dependent
Kinetic Matrix	-	$\mathbf {H}$	Dependent

Parameter

Name	Unit	Symbol
Temperature	°C	T
Relative Humidity	%	RH
rank of factorization	-	$r$
Number of Singular Values	-	$k$
Singular Value Tolerance	-	$tol$
Objective Function Parameter	-	$\alpha ,\beta ,\gamma ,\delta ,\mu$
Maximum Number of Iterations	-	MAXITER

Process Information

Process Steps

Name	Description	Input	Output	Method	Parameter	Environment	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 & Concentration Profile	.txt	.png	Non-negtaive Matrix Factorization	$r,tol,k,MAXITER,\alpha ,\beta ,\gamma ,\delta ,\mu$	Matlab	Numerical Analysis, Mathematical Optimization, Linear Algebra
Data Interpretation	Determine Intermediates and Kinetics	.png	-	-	-	-	-

Applied Methods

ID	Name	Process Step	Parameter	realised / implemented by
wikidata:Q420904	Singular Value Decomposition	Data Analysis - Pre-Processing	$k$	Matlab R2019a
wikidata:Q43219517	Moore-Penrose inverse	Data Analysis - Initializing	$tol$	Matlab R2019a
doi:10.1016/j.laa.2004.10.026	Perron Cluster Cluster Analysis	Data Analysis - Initializing	$r$	Matlab Script
wikidata:Q1253278	Nelder-Mead method	Data Analysis - Minimizing	$\alpha ,\beta ,\gamma ,\delta ,\mu$	Matlab R2019a

Software used

ID	Name	Description	Version	Programming Language	Dependencies	versioned	published	documented
	IC Raman	Data Acquisition and Reaction Analysis	4.1	C++ (wikidata:Q2407) Java (wikidata:Q251)	Windows	Yes	Yes	Yes
wikidata:Q169478	Matlab	Numerical computing environment for the programming language.	R2019a	C++ (wikidata:Q2407) C (wikidata:Q15777) Fortran (wikidata:Q83303) Java (wikidata:Q251)	Windows, Mac, Linux	Yes	Yes	Yes

Experimental Devices/Instruments and Computer-Hardware

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

ID	Name	Size	Data Structure	Format Representation	Format Exchange	binary/text	proprietary	to publish	to archive
	Time-Resolved Raman Spectroscopy Data	MB	Matlab Array