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Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Elements of the cover design.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
data visualization + art

Science Advances Cover

6 January 2023, Issue 9, Volume 1

1 · The cover

Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.

The cover depicts three sets of 672 bases of barcode sequences, which are encoded onto 7-dimensional cubes. Three overlapping cubes are shown, one for each of the three sequencing platforms: 10X Chromium v3 scRNA-seq, Quartz-seq2, and Drop-seq.

Individual bases are encoded by oriented triangles on each of the 2-dimensional faces of the cube (of which there are 672). I created various designs and in the one chosen by Science Advances, the triangles are 7.5% of their full size (more details).

Science Advances caption: DNA sequencing read translation in high-dimensional space. The cover image was created when 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes. Kijima et al. have developed a software tool that interprets DNA sequences to extract encoded information for additional biological analysis. The tool called, INTERSTELLAR, will facilitate development of sequencing-based experiments and sharing of data analysis pipelines.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A Rosetta Stone for DNA sequencing read translation in high-dimensional space: 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms are encoded as oriented triangles on the faces of three 7-dimensional cubes. Cubes encode DNA barcodes from 10X Chromium v3 scRNA-seq, Quartz-seq2 v3.1, and Drop-seq.
Discover all the things that are not trying to make you stronger.
I've encoded DNA in other ways — such as paths.

2 · Inspiration

We wanted to create some kind of high-dimensional encoding of sequences. For this, I looked back to my collaboration with Max Cooper's for his Ascent video from his Unspoken Words album.

My animation of 5 dimensions sets the stage for Max Cooper's track Ascent from his new album Unspoken Words.

In ascent, we animated multiple 5-dimensional cubes to create a flurries of lines and shapes — a promising direction for encoding sequences.

3 · Other covers

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)
news + thoughts

Convolutional neural networks

Thu 17-08-2023

Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry. – Richard Feynman

Following up on our Neural network primer column, this month we explore a different kind of network architecture: a convolutional network.

The convolutional network replaces the hidden layer of a fully connected network (FCN) with one or more filters (a kind of neuron that looks at the input within a narrow window).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Convolutional neural networks. (read)

Even through convolutional networks have far fewer neurons that an FCN, they can perform substantially better for certain kinds of problems, such as sequence motif detection.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Convolutional neural networks. Nature Methods 20:.

Background reading

Derry, A., Krzywinski, M. & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

Neural network primer

Tue 10-01-2023

Nature is often hidden, sometimes overcome, seldom extinguished. —Francis Bacon

In the first of a series of columns about neural networks, we introduce them with an intuitive approach that draws from our discussion about logistic regression.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Neural network primer. (read)

Simple neural networks are just a chain of linear regressions. And, although neural network models can get very complicated, their essence can be understood in terms of relatively basic principles.

We show how neural network components (neurons) can be arranged in the network and discuss the ideas of hidden layers. Using a simple data set we show how even a 3-neuron neural network can already model relatively complicated data patterns.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.

Background reading

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

Cell Genomics cover

Mon 16-01-2023

Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.

Designed in collaboration with with Carlos Urzua.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Our Cell Genomics cover depicts parent-of-origin assignment as a circuit (volume 3, issue 1, 11 January 2023). (more)

Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Science Advances cover

Thu 05-01-2023

My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes.

More details about the design.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Science Advances cover that encodes sequence onto hypercubes (volume 9, issue 1, 6 January 2023). (more)

Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Regression modeling of time-to-event data with censoring

Thu 17-08-2023

If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber

In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.

We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Regression modeling of time-to-event data with censoring. (read)

Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19:1513–1515.


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