Reliably transmitting data over noisy channels with linear codes

Messages transmitted over noisy channels are liable to be corrupted by errors, which may by corrected by including extra information at the cost of increased complexity of decoding. We’ll learn about the class of linear error-correcting codes, which make use of linear relations among codewords to correct errors efficiently and automatically. These codes provide a powerful mathematical framework for combinatorial experimental design, wherein large numbers of biological specimens are pooled according to the rules of a code and assayed in aggregate.

MIA Meeting – https://youtu.be/WoCyfCm_kGM?t=2680
Yaniv Erlich
Columbia University (Computer Science), New York Genome Center

Compressed Experiments

Molecular biology increasingly relies on large screens where enormous numbers of specimens are systematically assayed in the search for a particular, rare outcome. These screens include the systematic testing of small molecules for potential drugs and testing the association between genetic variation and a phenotype of interest. While these screens are “hypothesis-free,” they can be wasteful; pooling the specimens and then testing the pools is more efficient. We articulate in precise mathematical ways the type of structures useful in combinatorial pooling designs so as to eliminate waste, to provide light weight, flexible, and modular designs. We show that Reed-Solomon codes, and more generally linear codes, satisfy all of these mathematical properties. We further demonstrate the power of this technique with Reed-Solomon-based biological experiments. We provide general purpose tools for experimentalists to construct and carry out practical pooling designs with rigorous guarantees for large screens.

Source: MIA Primer: Ryan Peckner / Seminar: Yaniv Erlich (2016) – YouTube

The PostgreSQL Global Development Group announces today that the first beta release of PostgreSQL 9.6 is available for download. This release contains previews of all of the features which will be available in the final release of version 9.6, although some details will change before then. Users are encouraged to begin testing their applications against this latest release.

Major Features of 9.6

Version 9.6 includes significant changes and exciting enhancements including:

• Parallel sequential scans, joins and aggregates
• Support for consistent, read-scaling clusters through multiple synchronous standbys and “remote_apply” synchronous commit.
• Full text search for phrases
• postgres_fdw can now execute sorts, joins, UPDATEs and DELETEs on the remote server
• Decreased autovacuum impact on big tables by avoiding “refreezing” old data.

In particular, parallel execution should bring a noticeable increase in performance to supported queries.

Source: PostgreSQL: PostgreSQL 9.6 Beta 1 Released

by RICHARD P. FEYNMAN

Some remarks on science, pseudoscience, and learning how to not fool yourself. Caltech’s 1974 commencement address.

During the Middle Ages there were all kinds of crazy ideas, such as that a piece of rhinoceros horn would increase potency. (Another crazy idea of the Middle Ages is these hats we have on today—which is too loose in my case.)  Then a method was discovered for separating the ideas—which was to try one to see if it worked, and if it didn’t work, to eliminate it.  This method became organized, of course, into science.  And it developed very well, so that we are now in the scientific age.  It is such a scientific age, in fact, that we have difficulty in understanding how­ witch doctors could ever have existed, when nothing that they proposed ever really worked—or very little of it did.

But even today I meet lots of people who sooner or later get me into a conversation about UFO’s, or astrology, or some form of mysticism, expanded consciousness, new types of awareness, ESP, and so forth.  And I’ve concluded that it’s not a scientific world.

Most people believe so many wonderful things that I decided to investigate why they did.  And what has been referred to as my curiosity for investigation has landed me in a difficulty where I found so much junk to talk about that I can’t do it in this talk. I’m overwhelmed.  First I started out by investigating various ideas of mysticism, and mystic experiences.  I went into isolation tanks (they’re dark and quiet and you float in Epsom salts) and got many hours of hallucinations, so I know something about that.  Then I went to Esalen, which is a hotbed of this kind of thought (it’s a wonderful place; you should go visit there). Then I became overwhelmed. I didn’t realize how much there was.

Source: Cargo Cult Science

For two years, Electron has lowered the barrier to developing desktop applications—making it possible for developers to build cross-platform apps using HTML, CSS, and JavaScript. Now we’re excited to share a major milestone for Electron and for the community behind it. The release of Electron 1.0 is now available from electron.atom.io.

New to Electron? Electron is an open source framework that can help you build apps for Mac, Windows, and Linux. See how:

Source: Electron 1.0 is here

The genomic era arrives. And this time it’s probably real

WHEN the DNA sequence of the human genome was revealed in 2000, many people expected it to start a revolution. Researchers would be able to discover the genes that caused or influenced diseases. And drug companies would be able to use that knowledge to create better medicines. Until recently, though, it has been a case of “revolution postponed”. The flood of promised discoveries has been more like a trickle.

Much of the reason for the unfulfilled promises was naivity about how straightforward the link between different versions of genes and particular diseases would be. But that naivity has gone, and the fact that complex illnesses often have contributions from large numbers of genes is now recognised. This recognition, plus better computing and sequencing power, mean researchers are indeed beginning to pick the relationships between genes and disease apart.

In January, for example, a group at the Broad Institute in Cambridge, Massachusetts said they had homed in on most of the genes involved in schizophrenia, and thus had a hypothesis for a mechanism that might be causing it. This week it is the turn of breast cancer, as the most comprehensive analysis yet of mutations related to this condition is published in Nature.

The team that did the analysis, led by Serena Nik-Zainal of the Sanger Institute in Cambridge, England, sequenced the genomes of cells from 560 tumours. These, says Dr Nik-Zainal, proved vastly different from the genomes of healthy cells from the patients involved, for they had generally acquired thousands of mutations. That is not surprising. Early mutations in the development of a tumour often involve genes involved in DNA repair. Once this has happened other mutations accumulate. But all these secondary mutations make it hard to sift out the ones which are clinically relevant. To do so you need to compare lots of samples from different people, and thus see which mutations some of them have in common.

Source: Encore une fois | The Economist

Cancer is a leading cause of death worldwide, with over 14 million new cases per year and over 8 million deaths annually. Cancer incidence is expected to increase more than 70% over the next 20 years. At least half of all cancers in the United States are diagnosed in Stage III and Stage IV, leading to lower survival rates. Detecting cancer at the earliest stages dramatically increases the probability of a cure and long-term survival.The mission of Grail is to enable the early detection of cancer in asymptomatic individuals through a blood screen – with the goal of massively decreasing global cancer mortality by detection at a curable stage. Grail will leverage the power of “ultra-deep” sequencing technology, the best talent in the field and the passion of its leadership to deliver on that promise.Ultra-deep sequencing to detect circulating tumor DNA has the potential to be the holy grail for early cancer detection in asymptomatic individuals. Most tumors shed nucleic acids into the blood. Circulating tumor DNA is a direct measurement of cancer DNA, rather than an indirect measure of the effects of cancer.

Source: Grail | Pan-cancer blood screening test for circulating tumor DNA

A critical medical equipment crashed during a heart procedure due to a timely scan triggered by the antivirus software installed on the PC to which the said device was sending data for logging and monitoring.

The device in question is Merge Hemo, a complex medical equipment used to supervise heart catheterization procedures, during which doctors insert a catheter inside veins and arteries in order to diagnose various types of heart diseases.

The incident happened in February 2016

Merge Hemo consists of two main modules. The main component is the actual medical device, connected to the catheters, through which data acquisition takes place. This component is connected to a local PC or tablets via a serial port.

The second component is a software package that runs on the doctor’s computer or tablet and takes recorded data and logs it or displays it on the screen via simple-to-read charts.

Just like any other software package, Merge Hemo is subject to the same limitations and dangers that other applications face, and sometimes may crash. When something like this happens, and doctors report the event, the software vendor must investigate and file an Adverse Event Report with the FDA (US Food and Drug Administration).

According to one such report filed by Merge Healthcare in February, Merge Hemo suffered a mysterious crash right in the middle of a heart procedure when the screen went black and doctors had to reboot their computer.

Fortunately, the patient was sedated, and the doctors had five minutes at their disposal to wait for the computer to finish rebooting, start the Merge Hemo application again, and complete their procedure without any health risks for the patient.

Source: Medical Equipment Crashes During Heart Procedure Because of Antivirus Scan

These are slide-synchronized video recordings from the ICML’15 Deep Learning Workshop I organized with Kyunghyun Cho, Yann LeCun, Max Welling, Geoffrey Hinton and Yoshua Bengio. It took a while before we got permission from all involved parties, but here they are! For the recordings without slides, please see this YouTube playlist.
Source: Video Recordings of the ICML’15 Deep Learning Workshop | Durk Kingma