1/n
Our pre-print is finally out!
Here's my first #paperthread 🧵
In this work, co-authors and I clustered ischaemic stroke patients profiles, and recovered common patterns of cognitive, sensorimotor damage.

...Historically many focal lesions to specific cortical areas were associated with specific distinction, but most strokes involve subcortical regions and bring multivariate patterns of deficits.
To characterize those patterns, many studies have turned to correlation analysis, factor analysis, PCA, focusing on the relations among variables==domains of impairments...

https://www.medrxiv.org/content/10.1101/2023.11.08.23297808

#stroke #neuroscience #machinelearning #clustering

Behavior Clusters in Ischemic Stroke using NIHSS

BACKGROUND Stroke is one of the leading causes of death and disability. The resulting behavioral deficits can be measured with clinical scales of motor, sensory, and cognitive impairment. The most common of such scales is the National Institutes of Health Stroke Scale, or NIHSS. Computerized tomography (CT) and magnetic resonance imaging (MRI) scans show predominantly subcortical or subcortical-cortical lesions, with pure cortical lesions occurring less frequently. While many experimental studies have correlated specific deficits (e.g. motor or language impairment) with stroke lesion locations, the mapping between symptoms and lesions is not straightforward in clinical practice. The advancement of machine learning and data science in recent years has shown unprecedented opportunities even in the biomedical domain. Nevertheless, their application to medicine is not simple, and the development of data driven methods to learn general mathematical models of diseases from healthcare data is still an unsolved challenge. METHODS In this paper we measure statistical similarities of stroke patients based on their NIHSS scores, and we aggregate symptoms profiles through two different unsupervised machine learning techniques: spectral clustering and affinity propagation. RESULTS We identify clusters of patients with largely overlapping, coherent lesions, based on the similarity of behavioral profiles. CONCLUSIONS Overall, we show that an unsupervised learning workflow, open source and transferable to other conditions, can identify coherent mathematical representations of stroke lesions based only on NIHSS data. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the Department of excellence 2018-2022 initiative of the Italian Ministry of education (MIUR) awarded to the Department of Neuroscience-University of Padua. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: For data of patients of the Saint Louis cohort: the Internal Review Board of Washington University School of Medicine (WUSM) gave ethical approval for this work. For data of patients of the Padua cohort: the Ethics Committee of the Azienda Ospedale Universit&agrave Padova (AOUP) gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data can be made available upon reasonable request to Maurizio Corbettta at maurizio.corbetta{at}unipd.it. * AP : Affinity Propagation. GDM : General Distance Measure. GSM : General Similarity Measure. NIHSS : National Institutes of Health Stroke Scale. RSC : Repeated Spectral Clustering.

medRxiv

2/n

Our approach was instead from the other point of view!
We tried to understand recurring damage patterns by grouping similar patients and analysing their profiles.
How to compute similarities?
The subjects were evaluated on the NIH Stroke Scale, a 15 items battery to test sensorimotor and cognitive function, which is an ordinal scale with different range on different items

#nihss #stroke #neurology

3/n

We thus decided to use the General Distance Measure to compute pairwise similarities between our 172 subjects, and obtained a matrix, which as math savy people know, is also the description of a network (an "adjacency matrix" for a "weighted undirected graph").
The problem was then to find cliques, communities or clusters of similar patients in such a network, and we used spectral clustering.
Spectral clustering is a family of techniques that use spectra of matrices describing networks, i.e. use eigenvalues of matrices to understand the structure of those networks.

#spectralanalysis #spectralclustering #clustering #neuroscience

4/n

Reverting our General Distance matrix into the General Similarity matrix yields an ambiguous spectrum, whose eigenvalues do not help to determine the number of clusters in the data.
But repeating clustering and tracing which subjects consistently get clustered together, actually yields the right information, encoded in a co-occurrence matrix.
This latter is quite evidently composed of 5 main clusters.
Our second approach, affinity propagation, found autonomously 7 clusters, that are mainly finer grained partitions of the former 5.

#machinelearning #clustering

5/5

Our dataset comprises also CT and MRI scans with patients lesions segmented by an expert.
This allowed us to look at the distribution of lesions cluster-wise, and validate the associations between symptoms and lesions.

Check our pre-print and comment, make questions, offer suggestions!
Although it is not simple to share data, we will release code soon, as a means to replicate the approach on similar data and more.
The link is already in the paper!
And let us know if you have data you'd like to share and analyse with our developing methods👨🏾‍💻

We are deciding on the best match for a journal to review and possibly publish this work, of which I am super proud and thankful to co-authors Andrea Zanola, Antonio Bisogno, Silvia Facchini, Lorenzo Pini, Manfredo Atzori, and Maurizio Corbetta!

#scicomm #paperthread #preprints #neuroscience #machinelearning #mri #stroke #clustering

I mean, it looks cool, but it is even cooler if you consider that this network plot is the result of projecting another network's node into a multidimensional sphere and cluster it a thousand times to discover who is akin to whom!
And the radar charts+brain scans show what this kinship concretely is.
@fabrice13 that is cool. What did you make the network plot in?

@gpollara the network plot is made with the Python package "networkx".
It might not be the most intuitive tool at first, but overall is fine (and I am also open to suggestions).
In this case the nodes have names (labels, for the package) that are their anonymous codes, and colors reflecting the cluster label. The edges are colored and weighted by the adjacency matrix of the graph, and act like springs (high weight=high attraction force, Fruchterman Reingolg algorithm, package built-in💻).

We will publish code, likely before journal publication, with utils functions and #JupyterNotebook !

#networkscience #BrainScience