Sunday, November 17, 2019

Thoughts on O'Neil's Weapons of Math Destruction: What happens when learning for machines makes judgements on people

We read Cathy O’Neil’s book, Weapons of Math Destruction, with great interest. O’Neil discusses many of the biases and unfair situations that arise in the modern data science world based on mathematical models or algorithms. An avid mathematician and former academic who moved to industry to “carry mathematics from abstract theory into practice,” O’Neil realized that her favorite science field was part of a cycle of co-production with society: design of numerous mathematical models reflected and exacerbated social problems.

In a sense, it is obvious that an algorithm trained with biased data will be biased. While an algorithm can be efficient in the sense of optimizing and minimizing the number of false positives and false negatives, each of the “mistakes” might still lead to unjust and unfair outcomes if applied to an individual person or a group. The book makes this point with many clear case studies. Whether they are for loan approval, college ranking, law enforcement, or business optimization, models aimed at improving efficiency or boosting profits backfired. Such models created feedback loops that widened gaps within society because their limited designs proved to be oblivious to broader professional and social contexts.

A few recurring themes stand out from the book. The two most important of which, we think, are the emphases on balanced objectives and heightened awareness needed before building a “Big Data” model. O’Neil strongly makes the case for broadening a model’s objective, understanding its strengths and limitations, and being fully aware of how human biases can diffuse to collected (and uncollected) data. We particularly like the discussion of the widespread worry about the fall in standardized test performance in the United States, and how this turned out to be totally erroneous. In reality, SAT scores in each subgroup were actually increasing, but more disadvantaged kids were taking the test – a mistake due to the famous statistical error known as Simpson's paradox.

The book also touches on the proprietary nature of many commercial algorithms. In this regard, the book praises the well-known FICO score, which is viewed as a model of transparency compared to more closed types of rating systems. We also like the way the book goes through a lot of the jargon of modern commercial data sciences, such as proxies (which are often features that stand-in for a different feature that can’t be as easily measured or is not appropriate to measure) and micro-targeting. Pointing out the limitations of proxies is especially resonant today in light of several studies that followed the book’s publication in 2016, the most recent of which appeared in Science last month on the inherent bias in a widely used algorithm that inaccurately used health costs as a proxy to health needs.

The book is human-centered, no doubt. O’Neil calls for measures in favor of the protection and collective betterment of everyone’s lives. She acknowledges the potential utility of “Big Data,” thoroughly demonstrates that good intentions are not enough, and chooses to raise alarming issues at the heart of this rapidly unfolding field. Altogether, we found this book to be a fun read that we would recommend to anyone interested in large-scale data science that involves actual people as opposed to inanimate objects.

M Gerstein & H Mohsen

Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy
by Cathy O’Neil

Sunday, October 27, 2019

Thoughts on Tara's Secret Life of Fat: Scientific facts, practical tips & interesting personalities, related to the cells around your waist

I read Sylvia Tara’s The Secret Life of Fat with great interest. Similar in spirit to Justin and Erica Sonnenburg’s The Good Gut, this book combines hardcore science with practical pointers for daily life. Scientifically, Tara discusses the different types of fat – such as brown, visceral, subcutaneous – and how fat can essentially act as a regulating and self-regulated organ by interacting with the endocrine system. Practically, Tara notes how it is good to fast as long as possible each day to increase fat burning and how it is important to monitor one’s daily fat intake. The Secret Life of Fat also includes interesting profiles of leading scientists, such as those involved in the discovery of leptin, and patients’ who suffer from a variety of ailments associated with obesity and dysregulated fat regulation. Overall, I found this book a good read and a complement to the Good Gut.

The Secret Life of Fat: The Science Behind the Body's Least Understood Organ and What It Means for You
by Sylvia Tara


Saturday, October 05, 2019

Thoughts on Pollan's Cooked: Explains the science & history of the most commonplace of things - really learned a lot about fermentation

I read Michael Pollan's masterwork Cooked with great interest. This book takes a simple thing – food and how we prepare it – and delves deep into the underlying science and history of this subject.

The book first discusses using fire and water for cooking. It covers topics such as the Maillard reaction, which gives food flavor, and the way a stewpot acts as a second stomach, in a sense, predigesting foods and opening up their nutritional value.

I found the final section of the book, on fermentation, the most interesting. Fermentation ("cold fire") uses microorganisms to digest foods partially and to create flavors. The book highlights several key fermented foods – in particular, bread, wine, and cheese – and discusses various aspects of the fermentation process.

First, considering bread, fermentation allows us to readily use grasses for food and reclaim much more solar energy. The book suggests that ~90 percent of the energy in food is lost at each step of the food pyramid; thus, being able to eat grass directly is a major triumph of the agricultural revolution. Of course, nowadays, we have taken this fantastic process even further and essentially industrialized grass in the form of white bread -- taking out much of the original nutrients, including fiber, and then putting different nutrients back in. Another exciting aspect of baking bread is what Pollan describes as an emergent phenomenon. Most other forms of cooking, for instance, heating by fire or warming in a pot, involve a simple extrapolation of the preparation conditions. Baking bread is different. It is a "system property," where one combines various ingredients and makes something completely different than the original constituents. Pollan also describes how gluten acts almost like an elastic to create cavities in bread that can fill with gas and facilitate rising.

The next fermented food Pollan discusses is wine. To make it clear how easy it is to achieve fermentation, he shares humorous stories from his childhood of fermenting grape juice and having the vessel burst. He also brings up a philosophical question of whether we have domesticated Saccharomyces cerevisiae or whether it has domesticated us: alcohol itself, which is the product of many fermentations, is toxic to most organisms, yet we have evolved enzymes and pathways in our liver to break it down. Pollan also talks about how one can understand the different flavors of wine in terms of the various microorganisms available. Humans, in a sense, have co-evolved with wine and can benefit from having a glass a day based on a variety of health indicators.

The final section on fermentation talks about cheese. Cheese represents the product of rotting or decay in its extreme. Pollan describes cheese fermentation as a multistep process where, initially, microorganisms aerobically colonize the center of a bit of milk, digesting it partially and raising its pH, but eventually, the increasing acidity fouls the microbes' nest. Then, there is effectively an ecological succession where other species of bacteria replace the initial microbes; this continues to raise the pH. What I found most interesting is that a secondary fermentation then occurs from the outside of the cheese, where yeasts – which are aerobic – send in their hyphae and partially neutralize the increasing pH. The competition between these different fermentations gives rise to new chemistries, flavors, and compounds.

Cheese is also unusual in that it represents the nexus for competition between two current groups of people: the fermentos, those who believe in the importance of microorganisms for health and for giving food its flavors, and the Pasteurians, those who want to purge all foods of microbes. Their differences are evident when choosing a vessel for making cheese: should it be made out of old rotten, moldy wood or modern stainless steel?

The overall discussion of fermented foods points to the legacy of the agricultural revolution and the great importance of microbes in day-to-day life.

Altogether, I highly recommend this book. I find myself revisiting many of the book's points when I enjoy various meals and purchase things at the grocery store.

Cooked: A Natural History of Transformation – April 23, 2013
by Michael Pollan


Monday, September 23, 2019

Thoughts on Dittrich’s Patient HM: Strong personalities bring the science of memory to life

I enjoyed reading Luke Dittrich's book entitled "Patient H.M.: A Story of Memory, Madness, and Family Secrets." This book combines a great story about the celebrated patient Henry Molaison with factual knowledge about the brain. The personalities involved in the story were intriguing, from a great surgeon and his grandson to recent scientists battling over control of tissue samples and data. I found reading about the personal struggles helpful to understand the scientific road taken. I also enjoyed the interspersed facts about brain anatomy and some of the peculiarities of the approaches and lives of neurosurgeons and neuroscientists, such as how we somewhat haphazardly get at the seat of memory and how we disentangle key concepts such as semantic memory.

Despite being an overall interesting book, I definitely felt Dittrich took it "to the edge" with some of his points about Suzanne Corkin's treatment of Henry Molaison's brain, his famous grandmother, and the operations he performed. I wonder whether these highly controversial points are backed up by robust factual research. Nonetheless, the book was thought-provoking and enjoyable to read.

Patient H.M.: A Story of Memory, Madness, and Family Secrets
by Luke Dittrich


Sunday, September 15, 2019

Thoughts on Carreyrou's Bad Blood: Riveting tale, contrasting the tech & biotech worlds

We thoroughly enjoyed reading John Carreyrou's book, Bad Blood, about the Theranos debacle. Overall, it is a gripping story about the fall of a poster-child company operating at the intersection of computer tech and biotech.

We were struck by a number of points in the book.

First of all, it was amazing that Elizabeth Holmes was able to recruit and fool such an eminent board of directors. Her ability to control the narrative and grow the company in spite of some early warning signs and skepticism was interesting. This was most evident in the family conflict amongst the Shultzes, and the huge personal and financial burden on Tyler Schultz in this conflict was amazing.

We also found the book's indictment of the “fake it until you make it” culture in Silicon Valley quite telling. What can work for software might not work so well in the regulated world of health devices -- where bugs or incorrect results can have life-altering consequences. This cautionary tale continues to demonstrate its relevance in light of recent accusations at the microbiome sequencing company uBiome. DNA sequencing technology and many of the companies seeking to commercialize its use as a tool or diagnostic similarly spans the tech and biotech worlds. The tale of Theranos illustrates what can go wrong when these two worlds collide and highlights the need for care and attention when merging tech and biotech in order to realize the promise of advances in digital health.

Finally, we were struck by how Theranos managed to keep its secrets for so long, perhaps through such tight legal regulation and surveillance. It's amazing that they could keep so many people from talking for so long.

All together a gripping, great read that we highly recommend.

Mark Gerstein (with Paul Muir)

Bad Blood: Secrets and Lies in a Silicon Valley Startup
by John Carreyrou

Wednesday, August 28, 2019

Thoughts on Soni & Goodman's A Mind at Play - A portrait of one of the few great American mathematicians, Has an interesting interplay of practical tinkering & abstract thought

I enjoyed reading “A Mind at Play: How Claude Shannon Invented the Information Age,” by Jimmy Soni and Rob Goodman. Shannon was one of the great American scientists and mathematicians and deserves tremendous praise for his ideas that underlie the Computer Age.

What I found most appealing about the book was the mixture of Shannon’s life in historical context with technical knowledge about information theory. The book interweaves Shannon’s early learning on electrical switches and wires at Bell labs with his later development of information theory. I found this conjunction between Shannon’s practical hands-on tinkering and the abstract mathematical work, for which he is famous, quite interesting and inspirational in terms of developing mathematical ideas.

The book also makes clear how much Shannon was impacted by his early training. Shannon benefited greatly from his initial experiences at MIT and his mentorship by the great scientific administrator Vannevar Bush. In a sense, Shannon embodied many of MIT’s characteristics when he returned to the institution. It is also interesting that while Shannon is famous for his work in communication theory, the substance of his PhD was actually related to genetics. Only now, many years later, do people realize the connection between genomics and information theory.

Overall, I found this book to be a great read that I would highly recommend to people interested in mathematical sciences and American scientists in general.

A Mind at Play: How Claude Shannon Invented the Information Age Hardcover – July 18, 2017
by Jimmy Soni (Author), Rob Goodman (Author)

Friday, August 23, 2019

Thoughts on Dehaene's Consciousness & the Brain: Nice overview of the higher functions of the brain, Describing measurement approaches & theories of consciousness

Consciousness and the Brain by Stanislas Dehaene is a great introduction for anyone interested in learning about key ideas in neuroscience. Consciousness is a fascinating natural phenomenon, although it is not yet completely understood. Dehaene provides a solid overview of the many disparate fields that probe this concept.

On a psychological level, Dehaene talks about specific phenomena, such as subliminal priming and the Wheatstone stereoscope related to binocular perception, and how they give clues into the conscious mind. He also underscores the importance of subliminal thinking for much of what we do. In terms of brain physiology, Dehaene describes the different areas of the brain and the importance of the prefrontal cortex and the large pyramidal neurons it has in maintaining conscious thought.

On a more basic chemical and physical level, Dehaene describes many of the techniques that scientists use to learn about the brain, such as EEG and fMRI. He touches upon some of the key underlying phenomena such as the P300 wave, thought to be a signal of consciousness. Dehaene also describes a number of grand, but speculative, theories of consciousness. For example, he discusses the workspace theory of the mind, as well as an “applause” concept that posits that conscious ideas are amplified and step above all the other things on one's mind.

Overall, I found this an excellent read for someone wanting to learn about the mind, and I would recommend it heartily.

Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts
Stanislas Dehaene: 9780670025435: Books