update pages

docs/_data/alumni_members.yml

@@ -1,3 +1,46 @@
+- name: Daniel M. Low
+  photo: ../images/daniel_low_lo_fi.png
+  info: PhD Student
+  email: [email protected]
+  duration: 2019 - 2024
+  number_educ: 2
+  education1: MA Language & Communication Technologies, University of Groningen
+  education2: MS Cognitive Science, CIMeC, University of Trento
+
+- name: Gasser Elbanna
+  photo: ../images/Gasser.png
+  info: PhD Student
+  email: [email protected]
+  duration: 2022 - 2024
+  number_educ: 2
+  education1: M.Sc. in Neuroscience and Neuroengineering, EPFL
+  education2: B.Sc. in Systems and Biomedical Engineering, Cairo University
+
+- name: Sabeen Lohawala
+  photo: ../images/sabeen.png
+  info: MEng Student, MIT
+  email: [email protected]
+  duration: 2023 - 2024
+  number_educ: 2
+  education1: MEng in Computer Science, MIT
+  education2: B.S. in Computer Science, MIT
+
+- name: Ahmed Zain
+  photo: ../images/ahmed_zain.jpeg
+  info: Undergraduate Researcher
+  email: [email protected]
+  duration: 2023 - 2024
+  number_educ: 1
+  education1: B.S. in Computer Science and Engineering, MIT
+
+- name: Agathe Tournant
+  photo: //scholar.googleusercontent.com/citations?view_op=view_photo&user=cwcd3BIAAAAJ&citpid=2
+  info: Visiting M.S. student from ETH Zurich
+  email: [email protected]
+  duration: 2023 - 2024
+  number_educ: 1
+  education1: B.S. in Physics, EPFL
+
 - name: Alicia Zhang
   photo: ../images/alicia_zhang_photo.jpg
   info: Undergraduate Researcher

docs/_data/news.yml

@@ -1,3 +1,39 @@
+- date: 2024 05 30
+  headline: >
+    A paper published on detecting vocal fold paralysis from acousting recordings and 
+    understanding sources of bias in recordings. 
+    <a href="https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0000516">Paper link</a>
+
+- date: 2024 05 01
+  headline: > 
+    Welcome Jordan Wilke.
+
+- date: 2024 05 17
+  headline: > 
+    Congrats to Sabeen for successfully submitting her thesis.
+    
+- date: 2024 04 30
+  headline: > 
+    Congrats to Daniel for successfully defending his 
+    <a href="https://drive.google.com/file/d/1R-u9r-47doN5w6t058K46GEPvKAG4_D-/view?usp=sharing">thesis</a>.
+
+- date: 2024 04 12
+  headline: > 
+    Congrats to Agathe for successfully presenting her 
+    <a href="https://drive.google.com/file/d/173hwVU2LQf3pqaXti9ynsi1UOIxa_Kyh/view?usp=sharing">thesis</a>.
+
+- date: 2024 04 01
+  headline: > 
+    Welcome Isaac Bevers.
+
+- date: 2024 03 16
+  headline: > 
+    Welcome Tek Raj Chhetri.
+
+- date: 2024 02 05
+  headline: > 
+    Welcome Miles Silva.
+
 - date: 2024 01 16
   headline: > 
     Welcome Chaitanya Kapoor.

docs/_data/projects.yml

@@ -10,6 +10,21 @@
   highlight: 1
   news2: <a href="https://github.com/dandi" target="_blank">DANDI on GitHub</a>
 
+- title: "BICAN Knowledgebase for neuroscience"
+  image: https://static.wixstatic.com/media/c57c96_fa6f08e1e79240838d786b6b1b8d5842~mv2.png/v1/fill/w_576,h_324,al_c,lg_1,q_85,enc_auto/Image-empty-state.png
+  description: >
+    Develop an extensible Brain Cell Knowledge Base (BCKB) to ingest and standardize c
+    omprehensive cell type information from BICAN's development of a multimodal, 
+    multi-species brain cell atlas and disseminate that atlas as an open and interactive 
+    community resource for advancing knowledge of the brain. Supported by NIMH 1U24MH130918
+     (PI: Mufti, Hawrylycz, Ng, and Ghosh).
+  authors: BICAN team (Allen Institute for Brain Science, MIT)
+  link:
+    url: https://beta.brainkb.org
+    display:  Project website.
+  highlight: 1
+  news2: <a href="https://github.com/brain-bican" target="_blank">BICAN on GitHub</a>
+
 - title: "Nobrainer: A Robust And Validated Neural Netwrok Tool Suite For Imagers"
   image: https://github.com/neuronets/trained-models/raw/master/images/brain-extraction/unet-best-prediction.png
   description: >
@@ -23,18 +38,6 @@
   highlight: 1
   news2: <a href="https://github.com/neuronets" target="_blank">Neuronets on GitHub</a>
 
-- title: "Nipype: Dataflows for Reproducible Biomedical Research"
-  image: //miykael.github.io/nipype_tutorial/static/images/nipype_architecture.png
-  description: >
-    A Python-based platform for scalable scientific workflow design and execution.
-    Supported by NIBIB R01 EB020740.
-  authors: Nipype team
-  link:
-    url: https://nipype.readthedocs.io/en/latest/
-    display:  Read more about Nipype
-  highlight: 1
-  news2: <a href="https://github.com/nipy/nipype" target="_blank">Nipype on GitHub</a>
-
 - title: "ReproNim: A Center for Reproducible Neuroimaging Computation"
   image: http://www.repronim.org/flow.svg
   description: >
@@ -50,18 +53,6 @@
   highlight: 1
   news2: <a href="https://github.com/repronim" target="_blank">ReproNim on GitHub</a>
 
-- title: "Neuroscout: A cloud-based platform for rapid re-analysis of naturalistic fMRI datasets"
-  image: https://neuroscout.org/static/Neuroscout_Simple_Wide.svg
-  description: >
-    A platform for fast and flexible re-analysis of (naturalistic) fMRI studies.
-    Supported by NIMH R01 MH109682 (PI: Tal Yarkoni, UTexas, Austin).
-  authors: Neuroscout team
-  link:
-    url: https://neuroscout.org/
-    display:  Neuroscout Website
-  highlight: 0
-  news2: <a href="https://github.com/neuroscout" target="_blank">Neuroscout on GitHub</a>
-
 - title: "Naturalistic Parcellation and audiovisual integration"
   image: ../images/brain_parcellation.png
   description: >
@@ -73,120 +64,22 @@
   highlight: 1
   news2:
 
-- title: Voice and language biomarkers of mental health
+- title: Voice and language biomarkers of health
   image: ../images/review_figure3_heatmap.jpeg
   description: >
-    The goal of this project is to observe and analyze speech variations in psychiatric disorders by analyzing different types of data including ecological momentary assessments, recordings of clinical interviews, and social media posts.
-    Key questions we hope to answer are: 1) Is speech a good longitudinal biomarker? 2) How much speech information is needed for stable tracking? 3) Can linguistic information augment voice models? 4) Can we create a neurocomputational model of such systems?
-  authors: Daniel Low
+    The goal of this project is to observe and analyze speech variations in 
+    across disorders by analyzing different types of data including ecological 
+    momentary assessments, recordings of clinical interviews, and social media posts.
+    Key questions we hope to answer are: 1) Is speech a good longitudinal biomarker? 
+    2) How much speech information is needed for stable tracking? 3) Can linguistic 
+    information augment voice models?
+  authors: Isaac Bevers, Kaley Jenny, Rahul Brito, Jordan Wilke, Miles Silva, Fabio Catania
   link:
     url: ../speech_biomarkers
     display:  Project details
   highlight: 1
   news2:
 
-
-- title: Detecting unilateral vocal fold paralysis
-  image: ../images/fig_speech_schematic_cropped.png
-  description: >
-    The aim of this project was to develop a model to detect unilateral vocal
-    fold paralysis from audio recording of voice.
-  authors: D Low, P Song, G Randolph, V Rao
-  link:
-    url: https://doi.org/10.1101/2020.11.23.20235945
-    display:  Preprint
-  highlight: 1
-  news2:
-
-- title: Subcortical anatomy of the auditory system
-  image: https://ndownloader.figshare.com/files/14418503/preview/14418503/preview.jpg
-  description: >
-    The aim of this project is to identify brainstem structures and their
-    connectivity. This is Kevin Sitek's NIH F31 project involving high resolution
-    imaging and analysis of _post mortem_ and _in vivo_ data.
-  authors: K Sitek, OF Gulban, F de Martino, GA Johnson, E Calabrese
-  link:
-    url: https://docs.google.com/presentation/d/1HeepU82sskD2VL62vcktGBSE5nl35toq9k47gKefBqc/edit#slide=id.p
-    display:  Poster from OHBM 2019
-  highlight: 0
-  news2: <a href="https://www.biorxiv.org/content/10.1101/568139v2">Article preprint</a>
-
-- title: Imaging genetics analysis of schizophrenia
-  image: ../images/OHBM_poster_model.png
-  description: >
-   This is a collaboration with the <a href="http://genus.mgh.harvard.edu/">Genus
-   Consortium</a> to apply multivariate data mining and visualizatin tools to
-   the GENUS dataset. An additional target is to support data harmonization in
-   multi-site studies. Key questions are: 1) Do multivariate deterministic and
-   probabilistic tools provide a more sensitive approach to detecting genetic
-   markers of brain structure and cognitive variation? 2) Can a common
-   vocabulary help organize and analyze multi-site data?
-  authors: D Burdinski, Y Sanchez-Araujo, K Batmanghelich, G Blokland, T Petryshen
-  link:
-    url: https://docs.google.com/presentation/d/14wvviEmK9FYyex6y8GqT-5w5wDdq02pjAF6wP5kSyvQ/edit
-    display:  OHBM 2019 presentation
-  highlight: 1
-  news2: <a href="https://github.com/YSanchezAraujo/variational_lsrc">Analysis code</a>
-
-- title: Using neurofeedback to reduce auditory hallucination in schizophrenia
-  image: https://cos.northeastern.edu/penlab/wp-content/uploads/2018/12/rtfMRI_update_final-1024x908.png
-  description: >
-   This is a collaboration with the <a href="https://cos.northeastern.edu/penlab/"
-   target="_blank">PEN Lab</a> to use realtime fMRI biofeedback to to increase
-   the positive diametric activity in patients with schizophrenia.
-  authors: >
-    S Whitfield-Gabrieli, C Bauer, K Okano, M Niznikiewicz, A van der Kouwe,
-    P Wighton
-  link:
-    url: https://cos.northeastern.edu/penlab/projects/real-time-fmri-neurofeedback/
-    display:  Description at PEN Lab
-  highlight: 0
-  news2:
-
-- title: Mental well-being platform
-  image: https://images.unsplash.com/photo-1588775841450-fc1aaefe1836?ixlib=rb-1.2.1&ixid=MXwxMjA3fDB8MHxwaG90by1wYWdlfHx8fGVufDB8fHw%3D&auto=format&fit=crop&w=708&q=80
-  description: >
-   The aim of this project is to create a platform outlining tasks that have been shown to improve well-being with the option of input by the user community.
-   The platform includes an optional study protocol to monitor the effects of performing the tasks over time. 
-   The website will serve as the basis for future well-being studies.
-  authors: >
-    D Low, D Burdinski, A Dulski, K Wang
-  link:
-    url: https://mentalwellbeing.us/
-    display:  Mentalwellbeing.us
-  highlight: 1
-  news2:
-
-- title: Disease risk prediction from imaging genetics
-  image: ../images/undraw_medicine.png
-  description: >
-   The aim of this project is to harness both genetic and brain imaging data from the Adolescent Brain Cognitive Development Study 
-   and the UK Biobank in order to design models that predict disease risk from genes and brain endophenotypes. 
-   The project will explore to what extent incorporating intermediate phenotypes that are more closely tied to biology 
-   and may capture environmental effects increases predictive ability compared to polygenic risk scores alone, 
-   and what additional insights can be gained with this method (eg. new loci discovery, better mechanistic understanding, delineation of new disease subtypes).
-  authors: >
-    D Burdinski
-  link:
-    url:
-    display:  
-  highlight: 1
-  news2:
-
-- title: "Vocallect: Detecting Speech Biomarkers of Communication Disorders"
-  image: ../images/Vocallect Image.png
-  description: >
-    The purpose of this study is to understand and classify the impacts that communication disorders may have on speech production and acoustic quality. Subjects
-    will respond to questions regarding their current health, and provide sample voice recordings and free and read speech through a smartphone application and/or 
-    web browser. By collecting and correlating self-reported symptoms with audio features, we intend to develop and validate a voice-based technology using signal
-    processing and machine learning that can be used for in-hospital and in-home monitoring of communication disorders, treatment, and recovery.
-  authors: K Nguyen
-  link:
-    url: ../vocallect
-    display:  Project details
-  highlight: 1
-  news2:
-
 - title: "Mumble Melody: Musically Modulated Auditory Feedback to Increase Fluency for People Who Stutter"
   image: ../images/Mumble_Melody_logo.jpg
   description: >

docs/_data/team_members.yml

@@ -23,14 +23,6 @@
   number_educ: 1
   education1: PhD Cognitive and Neural Systems, Boston University
 
-- name: Daniel M. Low
-  photo: ../images/daniel_low_lo_fi.png
-  info: PhD Student
-  email: [email protected]
-  number_educ: 2
-  education1: MA Language & Communication Technologies, University of Groningen
-  education2: MS Cognitive Science, CIMeC, University of Trento
-
 - name: Debbie Burdinski
   photo: ../images/debbie.jpeg
   info: MD-PhD Student, Harvard Medical School and MIT
@@ -53,14 +45,6 @@
   number_educ: 1
   education1: BS Bioengineering, University of Washington
 
-- name: Gasser Elbanna
-  photo: ../images/Gasser.png
-  info: PhD Student
-  email: [email protected]
-  number_educ: 2
-  education1: M.Sc. in Neuroscience and Neuroengineering, EPFL
-  education2: B.Sc. in Systems and Biomedical Engineering, Cairo University
-
 - name: Fabio Catania
   photo: ../images/fabio_catania_photo.jpg
   info: Postdoctoral research fellow, MIT
@@ -99,14 +83,6 @@
   number_educ: 1
   education1: B.S. in Neuroscience, Emmanuel College
 
-- name: Sabeen Lohawala
-  photo: ../images/sabeen.png
-  info: MEng Student, MIT
-  email: [email protected]
-  number_educ: 2
-  education1: MEng in Computer Science, MIT
-  education2: B.S. in Computer Science, MIT
-
 - name: Harsha Gazula
   photo: ../images/non_descript_photo.png
   info: Research Scientist
@@ -135,20 +111,6 @@
   number_educ: 1
   education1: Ph.D. in Electrical Engineering and Computer Science, KAIST, Korea
 
-- name: Ahmed Zain
-  photo: ../images/ahmed_zain.jpeg
-  info: Undergraduate Researcher
-  email: [email protected]
-  number_educ: 1
-  education1: B.S. in Computer Science and Engineering, MIT
-
-- name: Agathe Tournant
-  photo: //scholar.googleusercontent.com/citations?view_op=view_photo&user=cwcd3BIAAAAJ&citpid=2
-  info: Visiting M.S. student from ETH Zurich
-  email: [email protected]
-  number_educ: 1
-  education1: B.S. in Physics, EPFL
-
 - name: Aaron Kanzer
   photo: ../images/Aaron_Kanzer.png
   info: Software Engineer

docs/_pages/speech_biomakers.md

@@ -1,20 +1,32 @@
 ---
-title: "Voice and Language Biomarkers for Mental Health"
+title: "Voice and Language Biomarkers for Health"
 layout: textlay
 excerpt: "Speech biomarkers"
 sitemap: false
 permalink: /speech_biomarkers/
 ---
 
-# Voice and Language Biomarkers for Mental Health
+# Voice and Language Biomarkers for Health
 
 <img src="{{ "/images/reddit_figure1_covid19_boolean.png" | prepend: site.baseurl | prepend: site.url}}" class="img-responsive" width="25%" style="float: right; margin: 0.8%; min-width: 350px" />
 
 <br />
 
-**Overall Aim:** To detect mental health symptoms from voice and language data
+**Overall Aim:** To detect health symptoms from voice, language, and other sensor data
 
-**Team Members:** Daniel Low, Debbie Burdinski, Satra Ghosh
+**Team Members:** Isaac Bevers, Kaley Jenny, Rahul Brito, Jordan Wilke, Miles Silva, Fabio Catania
+
+<br />
+
+**Prior work:**
+
+#### Detecting vocal fold paralysis and biases in voice data collection
+Analyzing sustained vowel and read speech to detect unilateral vocal fold paralysis. Also exploring biases
+in recording and comparing ML performance to that of clinician's ability to detect diagnosis from voice.
+
+[Link to publication](https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0000516)
+
+**Collaborators:** Phil Song
 
 <br />
 
@@ -47,13 +59,3 @@ Featured in [MIT News](https://news.mit.edu/2020/covid-19-impact-mental-health-1
 **Collaborators:** Matt Nock, Walter Dempsey, Kelly Zuromski, Daniel Kessler, RallyPoint 
 
 <br />
-
-#### Tracking longitudinal changes in voice and language using ecological momentary assessments
-**Collaborators:** Kate Bentley, Joe Maimone, Daniel Coppersmith, Rebecca Fortrang, Alex Millner, Matt Nock 
-
-<br />
-
-#### Tracking changes in speech during transcranial magnetic stimulation trials
-**Collaborators:** Joan Camprodon
-
- <br />