Lior Pachter
@lpachter
Followers
47K
Following
21K
Media
3K
Statuses
26K
Bren Professor of Computational Biology @caltech. Blog at https://t.co/FFQzhEsmhi. Tweets represent my views, not my employer's. #methodsmatter
Pasadena, CA
Joined April 2009
In principle I support swindling money from idiot tech bros, but the eugenics company doing embryo selection for IQ is bad. It's bad that they achieve their outlandish predictive power by statistical trickery with assumed latent factors. It's bad that they control for...
6
6
64
Calling on all scientists to call out hype, grift & BS when u see it. If u don't, u risk anti-science grifters leveraging overhyped & underdelivered promises & shoddy science to destroy public trust in the enterprise. Keep science & science comm grounded & truthful.
18
37
392
tl:dr this is an excerpt from a physics textbook.
"Dad ‘Embarrassed’ To Be Struggling With Daughter’s Third-Grade Math Problem"
3
0
24
This performance art piece that calls itself a conference must be a gold mine for hallucinated citations. First paper I looked at, for example, and first citation I checked (citation 14). Just totally made up authors
#Agents4Science received over 300 submissions and accepted 48 papers. Check them out here: https://t.co/mpp2rxEOC7 Many of these AI agent-written papers are quite interesting! The online conference will be on Oct 22; you can register for free at https://t.co/dD3sNnLBHT
9
10
139
I listened to the Soundcloud and FWIW I think Pythagoras would have preferred Bach.
0
0
3
My article on AI for science, in which I characterize a deviant notion of scientific objectivity rooted in the impossible ideal of theory-free inference, is available now open-access in Erkenntnis
link.springer.com
Erkenntnis - This paper contends with the notion that the methods of machine learning (ML) are unique among the tools of science in enabling a form of theory-free inductive inference. I challenge...
1
35
190
Strange that the MIT AI BIO Frontiers Forum has no women in their lineup, especially considering that many of the top people in the field right now are women. 👀
8
25
239
I recently visited the town of Zbąszyń in Poland. I took some time there to reflect on the plight of refugees and to bear witness for the dead and the living. This led me to write something up about its history. https://t.co/hVeAtI15o6
liorpachter.wordpress.com
The mathematician Carl Friedrich Gauss invented the heliotrope for long-distance surveying in 1821. Just a year later, he proved that least squares regression provided the BLUE estimator for data w…
0
0
8
Brilliant work by @Josephmrich & Conrad Oakes working out the math and implementing wompwomp. It has been submitted to @Bioconductor and in the future we may also implement it in Python to facilitate usage with single-cell genomics packages. Any feedback will be appreciated. Thx!
0
0
3
🚨 60 Degrees Pharmaceuticals $SXTP: Advancing Breakthrough Tick-Borne Disease Treatment Tick-borne infections like babesiosis are rising rapidly, and 60 Degrees Pharmaceuticals is at the forefront of developing a first-in-class therapy with major market potential. Tafenoquine
0
0
7
The underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and @HusonDaniel's NeighborNet as a good heuristic, but there is certainly room for improvement.
1
0
2
The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros
1
0
0
The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.
1
0
2
The underlying optimization questions turned out to be really interesting. The methods underlying wompwomp are described in the accompanying preprint on @arxiv:
arxiv.org
Alluvial plots can be effective for visualization of multivariate data, but rely on ordering of alluvia that can be non-trivial to arrange. We formulate two optimization problems that formalize...
1
0
1
Work on wompwomp was motivated by plots made for this paper, where we first implemented a naïve approach to optimizing an alluvial plot (panel D)
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In https://t.co/rVOiR847CY w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
1
0
1
wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.
1
0
1
In a new work with @Josephmrich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: https://t.co/njQRkjYHNh
2
19
64
I got notified of a spike of viewers on this post from 11 years ago https://t.co/AytO5LaSfW Indeed the study I critiqued didn't replicate https://t.co/Z3HRbzTqIM "The press may not cite studies that do not find sensational effects, but these studies are still extremely important"
0
0
11