Performance of cell and velocity embeddings on simulated data, compared to ground truth principal curve.

Denis Bucher (352807)
Barry J. Grant (19471)
Phineus R. Markwick (352808)
J. Andrew McCammon (12411)

February 2013

(a) Interdomain angles shown here for one set of AMBER simulations (sim1, sim2, sim5). The horizo...

GPA performed on trajectories shapes using the PC values interpolated as explained above and treated as homologous landmarks.

Paolo Piras (489773)
Antonietta Evangelista (513509)
Stefano Gabriele (513510)
Paola Nardinocchi (513511)
Luciano Teresi (513512)
Concetta Torromeo (513513)
Michele Schiariti (513514)
Valerio Varano (513515)
Paolo Emilio Puddu (513516)

January 2014

Median points were excluded during Procrustes Distance minimization process and were passively ap...

Smoothed κ-velo projection of velocities in the pancreas endocrinogenesis dataset.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

The two UMAPs compare (A) smoothed κ-velo velocities projected by Nyström projection and (B) smoothe...

Performance of cell and velocity embeddings on simulated data, compared to ground truth velocity directions.

Gennady Gorin (8466255)
Meichen Fang (13775419)
Tara Chari (13775422)
Lior Pachter (54416)

September 2022

a. Linear PCA embedding of ground truth velocities. b. Linear PCA embedding of inferred velocities. ...

Performance of cell and velocity embeddings on the forebrain data.

Gennady Gorin (8466255)
Meichen Fang (13775419)
Tara Chari (13775422)
Lior Pachter (54416)

September 2022

Top: PCA embedding with linear baseline and nonlinear aggregated velocity directions. Bottom: UMAP a...

Visualisation of simulated velocities with linear and nonlinear projection methods.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

A. Velocities projected on PCA embedding. The blue outline highlights a region of high velocity vari...

Comparison of velocities recovered by κ-velo and scVelo on simulation projected on 2D-PCA embedding of spliced counts.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

(A) Norm of the errors: with the true 2D velocity vector on PCA and the recovered vector. (B) Cha...

Comparison of velocities recovered by κ-velo and scVelo on simulation projected on PCA embedding of spliced counts.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

(A) Real simulated velocities (B) velocities recovered by κ-velo and (C) velocities recovered by scV...

Projection of the velocity arrows (test set data points) onto existing embedding of initial cell positions (training set).

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

We compare our projection approach (left column) to scVelo’s [2] (right column) projection for t-SNE...

PCA and nMDS embedded representation of Trajectory 1 applied to internal coordinate space.

Aruna Rajan (365473)
Peter L. Freddolino (161904)
Klaus Schulten (102849)

February 2013

Two panels showing the embedding of trajectory 1 from the internal coordinate space (described in...

PCA projection of velocities in the pancreas endocrinogenesis dataset.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

(A) Velocities returned by κ-velo projected on PCA embedding of spliced counts. (B) Velocities retur...

Quantitative comparison of low-dimensional projection of velocities.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

We compare κ-velo velocities projected by Nyström-projection v1 to eco-velo velocities projected ont...

Projection of the velocity arrows (test set data points) onto existing diffusion map embedding of initial cell positions (training set).

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

We compare our projection approach in A to scVelo’s [2]’s projection in B. (TIFF)</p

PCA and nMDS embedded representation of trajectory 1 applied to dihedral angle space.

Aruna Rajan (365473)
Peter L. Freddolino (161904)
Klaus Schulten (102849)

February 2013

Two panels showing the embedding of trajectory 1 from the dihedral angle space to a 2D space obta...

Simulation results representing contoured velocity fields at φ = 0.2 for PBS, Fluid 1, Fluid 2.

Hyeonji Hong (4524382)
Jae Min Song (365629)
Eunseop Yeom (825693)

January 2019

Simulation results representing contoured velocity fields at φ = 0.2 for PBS, Fluid 1, Fluid 2.</p

Accelerated MD trajectories.

Denis Bucher (352807)
Barry J. Grant (19471)
Phineus R. Markwick (352808)
J. Andrew McCammon (12411)

February 2013

(a) Interdomain angles shown here for one set of AMBER simulations (sim1, sim2, sim5). The horizo...

GPA performed on trajectories shapes using the PC values interpolated as explained above and treated as homologous landmarks.

Paolo Piras (489773)
Antonietta Evangelista (513509)
Stefano Gabriele (513510)
Paola Nardinocchi (513511)
Luciano Teresi (513512)
Concetta Torromeo (513513)
Michele Schiariti (513514)
Valerio Varano (513515)
Paolo Emilio Puddu (513516)

January 2014

Median points were excluded during Procrustes Distance minimization process and were passively ap...

Smoothed κ-velo projection of velocities in the pancreas endocrinogenesis dataset.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

The two UMAPs compare (A) smoothed κ-velo velocities projected by Nyström projection and (B) smoothe...

Performance of cell and velocity embeddings on simulated data, compared to ground truth velocity directions.

Gennady Gorin (8466255)
Meichen Fang (13775419)
Tara Chari (13775422)
Lior Pachter (54416)

September 2022

a. Linear PCA embedding of ground truth velocities. b. Linear PCA embedding of inferred velocities. ...

Performance of cell and velocity embeddings on the forebrain data.

Gennady Gorin (8466255)
Meichen Fang (13775419)
Tara Chari (13775422)
Lior Pachter (54416)

September 2022

Top: PCA embedding with linear baseline and nonlinear aggregated velocity directions. Bottom: UMAP a...

Visualisation of simulated velocities with linear and nonlinear projection methods.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

A. Velocities projected on PCA embedding. The blue outline highlights a region of high velocity vari...

Comparison of velocities recovered by κ-velo and scVelo on simulation projected on 2D-PCA embedding of spliced counts.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

(A) Norm of the errors: with the true 2D velocity vector on PCA and the recovered vector. (B) Cha...

Comparison of velocities recovered by κ-velo and scVelo on simulation projected on PCA embedding of spliced counts.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

(A) Real simulated velocities (B) velocities recovered by κ-velo and (C) velocities recovered by scV...

Projection of the velocity arrows (test set data points) onto existing embedding of initial cell positions (training set).

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

We compare our projection approach (left column) to scVelo’s [2] (right column) projection for t-SNE...

PCA and nMDS embedded representation of Trajectory 1 applied to internal coordinate space.

Aruna Rajan (365473)
Peter L. Freddolino (161904)
Klaus Schulten (102849)

February 2013

Two panels showing the embedding of trajectory 1 from the internal coordinate space (described in...

PCA projection of velocities in the pancreas endocrinogenesis dataset.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

(A) Velocities returned by κ-velo projected on PCA embedding of spliced counts. (B) Velocities retur...

Quantitative comparison of low-dimensional projection of velocities.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

We compare κ-velo velocities projected by Nyström-projection v1 to eco-velo velocities projected ont...

Projection of the velocity arrows (test set data points) onto existing diffusion map embedding of initial cell positions (training set).

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

We compare our projection approach in A to scVelo’s [2]’s projection in B. (TIFF)</p

PCA and nMDS embedded representation of trajectory 1 applied to dihedral angle space.

Aruna Rajan (365473)
Peter L. Freddolino (161904)
Klaus Schulten (102849)

February 2013

Two panels showing the embedding of trajectory 1 from the dihedral angle space to a 2D space obta...

Simulation results representing contoured velocity fields at φ = 0.2 for PBS, Fluid 1, Fluid 2.

Hyeonji Hong (4524382)
Jae Min Song (365629)
Eunseop Yeom (825693)

January 2019

Simulation results representing contoured velocity fields at φ = 0.2 for PBS, Fluid 1, Fluid 2.</p

Accelerated MD trajectories.

Denis Bucher (352807)
Barry J. Grant (19471)
Phineus R. Markwick (352808)
J. Andrew McCammon (12411)

February 2013

(a) Interdomain angles shown here for one set of AMBER simulations (sim1, sim2, sim5). The horizo...

GPA performed on trajectories shapes using the PC values interpolated as explained above and treated as homologous landmarks.

Paolo Piras (489773)
Antonietta Evangelista (513509)
Stefano Gabriele (513510)
Paola Nardinocchi (513511)
Luciano Teresi (513512)
Concetta Torromeo (513513)
Michele Schiariti (513514)
Valerio Varano (513515)
Paolo Emilio Puddu (513516)

January 2014

Median points were excluded during Procrustes Distance minimization process and were passively ap...

Smoothed κ-velo projection of velocities in the pancreas endocrinogenesis dataset.

Valérie Marot-Lassauzaie (13876700)
Brigitte Joanne Bouman (13876703)
Fearghal Declan Donaghy (13876706)
Yasmin Demerdash (13876709)
Marieke Alida Gertruda Essers (13876712)
Laleh Haghverdi (13770395)

September 2022

The two UMAPs compare (A) smoothed κ-velo velocities projected by Nyström projection and (B) smoothe...

Performance of cell and velocity embeddings on simulated data, compared to ground truth principal curve.

Abstract

Extracted data

Performance of cell and velocity embeddings on simulated data, compared to ground truth principal curve.

Abstract

Extracted data

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