Aether... or how I learned to love Supersymmetric String Theory
Monday, October 17, 2022
Aether... or how I learned to love Supersymmetric String Theory
Monday, July 25, 2022
Philosophical Implications of Entropy
Preliminary readings:
https://thestandupphilosophers.co.uk/the-trump-card-of-modern-nihilism-entropy/
https://www.life.illinois.edu/crofts/papers/Life_information_entropy_and_time.html
https://thestandupphilosophers.co.uk/what-is-entropy/
and if you got this far....
https://www.hindawi.com/journals/complexity/2020/8769060/
Musing
The concept of entropy is broad and deep, with both physical and intellectual interpretations. In our physical universe, entropy is a quantity never less than zero, first introduced by a German physicist in 1850, Rudolf Clausius, that evolved into the second law of thermodynamics, primarily through the rigors of Boltzmann and his approach to estimating the most probable state in statistical mechanics. By linking to probability, Boltzmann describes entropy as not an existing mode and state of the general mass and energy of the system but the mode and state of the organization, matching, and distribution of these mass and energy. Since entropy is an estimate of the distribution of this mass in energy at any given state, the change in entropy suggests a change in how mass or energy represents itself. As the laws of physics would tell us, that change in entropy is never negative. The change in the mass organization is unidirectional by virtue of how one defines a change.
Almost 100 years later, Shannon delves into what “information” means in his study of information theory. He postulates non-randomness as “information”: a set system(s) that can generate random messages or signs with their own probabilities.
These two ideas have profound interpretations in a metaphysical sense.
From the Boltzmann perspective, entropy is never less than zero (at least in the physical universe we experience). As far as I can tell, evidence that dS> 0 requires an increment of time to measure a change. So, does this mean that when dS~0, the state of a system is what it is when there is no corresponding change in time? Missing bits of DNA after millions of replications would think so.
Second: What is “information theory” anyway, and what does randomness have to do with information? Shannon entropy quantifies this in a purely mathematical way. Perhaps this is really just a relative argument since one doesn’t have information in a vacuum; rather, information is put into context with other information (which supports my general theory that mackintosh apples, with their colorful skin, is way more informative than plane old golden delicious apples… and yes, I will fight you on this).
Is the universe just another victim of entropy?
What also needs to be discussed are these loosie-goosey interpretations of entropy and how they connect with philosophy in our modern-day lives. These are broad generalized statements: "… well things just fall apart so … [insert waxing poetry]”. But underneath all these sentiments is the realization that adopting a worldview that “nothing has meaning” because
A) of the inevitable collapsing of the universe.
B) my brain and neurons are two different things, so I give up.
C) my pastor told me so.
D) etc.,
Of particular note, A), has some (physical) legitimacy since the universe will tend to a state with lower energy (Quick cut to the “Entropy is justification for Nihilism memes”) … because it’s physics! Things break down, and we just must deal with the consequences.
Random topics of query:
1. The YouTube video purports that “we create order -and progress- at the expense of disorder elsewhere.” Do you agree with this assertion?
2. Is entropy really nihilism's trump card?
3. Does thinking of a universe with negative entropy makes sense?
4. What is the fascination with humans trying to create order anyway?
Wednesday, March 31, 2021
Seimens Medical Systums releases new modification for KD-era linacs
For immediate release: March 32, 2021
Seimens Medical Systums releases new modification for KD-era linacs
We are proud to provide a new method of permitting existing Siemens KD-eral linacs with an novel option of significantly improving the quality of care of patients with our new Digital Optimizer for Radiotherapy via Klystron Synchronization, or DORKS. DORKS provides a means of delivering a tumorcidal dose while greatly sparing normal tissues from the harmful side effects from radiation therapy. Dr. Lee Van Cleef, head engineer and part-time gun slinger:
DORKS allow us to be in new markets and open new opportunities for research. We expect great things from DORKS. DORKS will help pave the way for our future here in Seimens Medical Systums.
Friday, August 28, 2020
Medical Physics Games
Medical Physics Games in Education
Radiation Oncology Game - Intended Learners
Counterfactual learning systems
Separating causation and correlation in AI systems is a challenge because most machine learning systems look for trends, but not 'counterfactual' information, which is more like the way we, humans, and doctors think.
People, like doctors, make decision based on what they know to be true and untrue, and build causal reasoning into a diagnosis. Most #machinelearning systems don't build causality: they are built on associations / correlations. We don't care the sky is probably blue when we get a cold, but we do care your T-cell count is low when you get a cold (causation vs. correlation). Counterfactual data? "Lets get a chest x-ray / ultrasound / CBC ..." i.e., some data that rules out other possibilities to see how symptom relates to disorder (directly or indirectly). But what rules can you build for machine learning? (Un)surprisingly this paper shows it can be simple, (because thats how *our* brains probably work): disease should be consistent with diagnosis, rule out stuff that isn't possible, and keep it simple: 1 Dx fitting M symptoms is better than N Dx fitting M symptoms. They go on to define things called "expected disablement" and "expected sufficiency". The former is obvious, but the latter is like "sufficient cause", and state theorems, one of which is that disablement and sufficiency are sufficient conditions for the rules above. But real data is noisy and murks the variables and so there needs to be a way to account for noise. (insert mathy stuff here). Thats all fine, but the litmus test is "How does this compare to actual clinical decisions?" In short, a physician achieves higher accuracy in diagnosing a disorder for simpler problems, and the algorithm outperforms for more complex problems. Thats good for rare disease classification. That makes sense as the story of #machinelearning and #AI in medical diagnoses suggests utility in a role as a 'decision support tool', but not a fully autonomous one. The difference here is that the model behaves more like a clinician would. For you Bayesians ... when you first learned Bayes' Theorem I bet you pondered "Why can't we do counterfactual inference in medical diagnosis? ...policy making? ... court decisions?". This article is a nice progression of how we can use AI based on causation - not just correlation. Don't believe me? Read for yourself.Extracellular vesicle and particle biomarkers and AI
A very interesting article on
extracellular vesicle and particle biomarkers and how they might be used in
cancer detection.
https://www.sciencedirect.com/science/article/pii/S0092867420308746?via%3Dihub
There are gazillion authors from a bajillion institutions on this paper.
Collaboration!
The gold standard to confirm cancer and other aliments is a tissue biopsy,
where a small sample of tissue is extracted from the suspicious growth. But
extracting a tissue sample isn’t possible in many situations, especially when
there are other co-morbidities where the biopsy can introduce more problems
than it attempts to solve.
So ‘liquid’ biopsies is another
approach: stuff like drawing blood, lymphatic/bile, etc., which is not as
difficult. But that stuff isn’t where the tumor is… its stuff floating around
the body. Some of the gunk that floats around outside the cell are EVPs...or ‘extracellular
vesicles and particles’. Basically they’re goops of stuff that float outside
the cell, originating from ‘sorters of things’ in your cells. I (probably
mistakenly) think of them as recipe pages floating outside the bookstore that
sells recipe books. Except there are gazillion (actually billions of EVPs)
recipes, and a gazillion books: trying to figure out what page came from what
book would seem an impossible task, right? Well… this is where the story gets
interesting!
This team used machine learning
techniques to sort through all the EVPs based on sizes and other subcategories
(mice/human, cancers). They found that the relationship between +10K EVPs and
tumors in mice and humans were not the same (interesting since mouse models are
used in so much research). They then sifted through all these possible markers
to see if they could be used as a cancer detector.
How do you sort through literally 10s
of thousands of markers for trends? Reliably? #Machinelearning, of course. They
found the presence/absence of 13 common EVPs could be used to classify both
lung and pancreatic cancers. But are those little floaters actually associated
with tumors? In other words, is there a relationship between biopsy findings
and the floaters?
While their dataset was kinda small, they could verify the biopsy findings with the floaters to +90% sensitivity / specificity (sensitivity is how well you can detect something (like how likely you are to stop at a sign that looks like a stop sign), and specificity is how well you can rule all other possibilities out (like how well you ignore the sign that looks like a stop sign but really isn’t). They then attempted to ensure that what they saw wasn’t just stuff you’d seen normally... not a trivial task.
What does it all mean? Maybe *earlier* cancer detection? Increased precision cancer detection? Dunno… but it is super cool that floaters in the blood could be so precise in detecting disease. These EVPs may be echoes of the body saying ‘something ain’t right’. We didn’t have the tools to be able to appreciate this signal until we developed the technology to detect the echoes.
Super cool.
Meet RoboBEER
Meet RoboBEER, a robotic beer pourer.
As you know, the demand for high quality beers worldwide has exploded over the last few decades. What drives quality? Well one way to discern quality is to objectively characterize features within the beer.
What features you may ask? Some of them are visual, like the color and foam-ability, such as maximum volume of foam, total lifetime of foam, foam drainage, size of the bubbles in the foam. But not just any idiot can pour the beer, as a Guinness lover will tell you, since a good pour is crucial. Fortunately RoboBEER can pull the ‘perfect’ pint: RoboBEER pulls 80 mL (+/- 10 mL) while monitoring the liquid temperature, assessing the alcohol and CO2 levels, all through your kids Arduino control board and a Matlab interface (yeay Matlab!).
But what about more important features like taste? Surely no robot could do that right? No way. But… maybe you could predict things like mouthfeel from all the features obtained in by RoboBEER? You could capture descriptions of taste from experts through a questionnaire: 10 basic categories: bitter, sweet, sour, aroma in grains, aroma in hops, aroma in yeast, viscosity, astringency, carbonation mouthfeel, and flavor hops. Then, have them sample twenty-two beers. (What I would do to be a part of this study!)
Could you train a neural network to predict what the beer would taste like just based off the data from RoboBEER?
A ‘feedforward’ neural network was designed where, essentially, you take all the inputs from the RoboBEER (head size, color, etc), and the outputs from the tasters (bitterness, sweetness, mouthfeel) and see if a neural network can predict the taste based on those inputs. You do some fun math like principal component analysis to help with sorting all the data and patterns, pump them into the network for AI training and what do you get?
For the independent testing data, the AI system from RoboBEER data could predict what it a beer would taste like with an accuracy of 86%. What does this mean? Well… very likely, RoboBEER is a better judge of beer than you are. And it doesn’t even have to taste the beer.
Don’t believe me? Read for yourself.
https://onlinelibrary.wiley.com/doi/epdf/10.1111/1750-3841.14114
Thursday, September 19, 2019
What is your best workplace productivity hack?
I am a big fan of the "GTD" workflow. If you haven't read it and want to learn some tips on improving workplace productivity, you really should pick up the book. But once you have, you then really ought to check out Luc Beaulieus' blog, particularly his digital GTD series. So after connecting with Luc and Thor Bjarnason (and the antithesis of Luc's love for Macs!) we cobbled up a proposal for a workshop.
Productivity implies the ability to yield a high degree of 'output' without expending too much energy. This assumes you have quality inputs and an efficient process which yields, ideally, high quality outputs. The metrics of outputs are important (e.g., number of publications, number of quality assurance checks performed, % increase in salary, etc.,) but also important are the inputs. The old saying "Garbage In = Garbage Out" applies... but generally, when it comes to Medical Physics tasks, we are good at conditioning the inputs (i.e., taking good measurements, or filtering important queries from colleagues, etc.). And often we have good strategies in processing those inputs and yielding good outputs. But can we do that processing more efficiently (i.e., improve your 'workflow')? One of the goals of this workshop is to shed some light on some optimal workflow strategies for different types of inputs.
But digging deeper into the topic got me on to something: One of the things we may not appreciate when we think "productivity" is the influence inputs have on things outside of the process itself. What I mean by this is that even the basic human needs, such as shelter, sustenance, the need for belonging, and friendships can have a huge impact on your professional productivity. Furthermore, while you may have great strategies for dealing with a barrage of e-mails and QA tasks, those 'inputs' could affect your well-being. Strategies like closing your door for an hour a day, or (one of my favorite techniques) having a 'personal time-out', can not only help you process things efficiently, they can improve overall well being.
I'm really looking forward to sharing some of our strategies for improving workplace productivity with our Medical Physics community, and, more importantly, learning from participants of their challenges and strategies in managing life as a Clinical, Research, and/or Administrative Medical Physicist.
Here is the link to the workshop details.
After the workshop, maybe Luc, Thor and I will cobble together an article for the COMP Newsletter or something.
See you in Kelowna!
Friday, July 27, 2018
My latest paper on Computing Science
We have elected to publish this work anonymously, under the pseudonyms of DUNE characterless.
The paper is accessible here:
https://drive.google.com/open?id=1O-VTvM0i4ZzAgWxAtQPAmuky5ktOLvkp
(seriously... https://pdos.csail.mit.edu/archive/scigen/#about )
Monday, November 6, 2017
International Day of Medical Physics Crossword Puzzle - 2017
Here is a harder crossword puzzle for this year... last year was too easy: this one will test the limits of medical physics knowledge (or perhaps your googlifying skills!).
If you're interested, I used this online tool to create the crossword which can neatly create a word or pdf of your puzzle. Enjoy!
Thursday, March 2, 2017
My venture into Wikipedia
Backstory
Long ago when I was the Editor of the COMP InterACTIONS Newsletter I wrote an article about (among other things) Wikipedia (see here for the publication). Back in 2007, Wikipedia was still relatively new and there was good reason to be skeptical of the published content. Relevant excerpts from that article are reproduced below (with post notes and inserted links):"...Out of curiosity, I typed in the words ‘Medical Physics’ in Wikipedia. After following a few links, I came across web pages that had the words ‘EDIT’ alongside each of the written texts. I clicked it and started to feel like a blind, thumbless plumber stumbling towards a CT with the gantry covers off (incompetent). After stopping myself from inflicting damage, I pondered: who are the contributors of these rather finely crafted words?
After seeing some rather anonymous contributors, I noticed that characters by the names of ‘kungfuadam’ and ‘Bobo the Ninja’ appeared to be editing some of the pages. It turns out that Bobo is a self-proclaimed expert in chemistry who attends Rock Bridge High School in Missouri. I don’t know what kind of journals you are reading, but I haven’t cited or read many works from Bobo yet. [Post note: Bobo is gone! or has changed identities!]
Some interesting facts about Wikipedia:
• Wikipedia is a free internet encyclopedia that anyone can edit
• There is a entry of ‘Wikipedia’ on Wikipedia
• According to a peer reviewed study published in Nature, Wikipedia is as reliable as an encyclopedia in the accuracy of information provided (something the traveling Britannica salesman failed to mention).
To me, Wikipedia is a shining example of how good -and bad- things can get when you mix science and everyday life. Theoretically, if you wait long enough, any falsehoods, or ‘graffiti’, would be replaced with a majority consensus opinion on the “correct” description. Interesting concept. I just hope those volunteers adding to the website are competent. Sounds like digital Darwinism. Stephen Colbert, a comedian/political satirist calls it “bringing democracy to knowledge”, which I found particularly funny, and scary. [Post note: Stephen Colbert performed a hilarious experiment with Wikipedia]"
"The problem, most researchers and Wikipedia stewards seem to agree, is that the core community of Wikipedians are too hostile to newcomers, scaring them off with intractable guidelines and a general defensiveness. One detailed study from 2012 found that new editors often find that their first contributions to the site are quickly rejected by more experienced users, which directly correlates with a drop in the likelihood that they will continue to contribute to the site. "I found this particularly worrisome after realizing that someone needed to create an entry for Jack Cunningham somewhere on the internet.
My venture
If you don't know Jack Cunningham, well... you can now read his profile on Wikipedia. My motivation for creating an entry was based on the few times I searched him through various search engines. Too frequently I'd be disappointed with the results. So I figured why not enter him into Wikipedia? It is citable and a probably a good thing to do. Plus I could add some of my medical physics competency into this massive digital-Darwin experiment.The steps were quite easy.
- Create a profile in Wikipedia
- Read what you need to do to create your first article
- Follow all the suggestions in that article
- And write it up in your draft-space!
- Get all your references lined up
- Write and edit.
- Edit some more
- Then submit it for review
Now that the page is created, anyone can edit it. And that kind of scares me a bit. Maybe Bobo The Ninja is hammering away at the page at this second (probably not). Now that I am an editor of a page, I can receive a message / flag if any changes are made. And I still have some more work to do (see the 'warnings' on the front page... that I will likely remove soon).
I have to say that the process was a lot easier than I expected. Even enough for me to consider submitting more articles or editing others.
I'd love to hear your thoughts on this.
Wednesday, December 14, 2016
BC proposes new college for diagnostic and health professions
Background
While "Health" is a Federal Ministry in Canada (and have 'Acts'), healthcare is administered and executed at the provincial level. This means that the bulk of health care legislation resides in provincial Acts and, subsequently, legal provisions for administering health care (insurance plans), funding for hospitals and other facilities, and administering and paying for services are through the province. In so doing, each province has a variety of healthcare-related Acts to follow through with these obligations, including a Health Professions Act that defines who can deliver healthcare services.Here is a simple search on CANLII on 'health professsions acts'. As you'll see, some provinces have a single Act and make changes when new 'professions' of import and need are defined, whereas other Acts are more complex. Often coupled with such Acts are reference to some type of body (organization, college, etc) that has an authority -independent of the government- to determine if an individual has the academic and/or clinical background to be a healthcare professional. Through legislation, the provincial government can empower an organization to regulate a profession. This simple framework exists for most professions in healthcare.
But today's delivery of healthcare requires many different types of skills and knowledge sets, and often healthcare needs outpace the speed of legislation. This phase difference can result in medical errors. Take for example, a recent series of incidents related to pathologists in Canada. An inquiry into those errors suggested that more work needs to be done in establishing credentials, national standards, quality assurance procedures and processes, and accountability. Much of this can be accomplished through sound organizations which are firmly committed to patient safety. Such organizations may be empowered through legislation to be 'self-regulating' such that they, among other things, are 'gate-keepers' of the profession that can regulate entry into the profession. These colleges exist for many health professionals. Regulation, often through the mechanism of a college, helps define accountability, which is the bond of trust between healthcare professionals.
Medical Physicist as a Profession in Canada
At the time of writing this post, outside of Quebec, the phrase 'Medical Physicist' does not exist in any provincial legislation. And even within Quebec, the phrase 'Medical Physicist' is only used in the context of the Hospital Insurance Act and in reference to collective bargaining units (i.e., how they get paid). There are some important radiation safety documents published by provincial and federal agencies that specifically refer to a "Medical Physicist", often preceded by "qualified", and followed by "cerftied by [CCPM/ABR/etc]".At the Federal level, the most commonly cited example of the use of "Medical Physicist" is Safety Code 35 : Safety Procedures for Installation, Use and Control of X-ray Equipment in Large Medical Radiological Facilities:
"There must be a Medical Physicist or Radiation Safety Officer to act as an advisor on all radiation protection aspects during the initial stages of construction of the facility, installation of the equipment, and during subsequent operations. Medical physicists are health care professionals with specialized training in the medical applications of physics."and that individual must have achieved a measure of competency.
"The medical physicist /radiation safety officer must:
- possess qualifications required by any applicable federal, provincial, or territorial regulations or statutes and be certified according to a recognized standard, such as for medical physicists, the Canadian College of Physicists in Medicine;"
And at the provincial level, one example in the use of "Medical Physicist" is in BC's Diagnostic Accreditation Program (www.dap.org) which spells out who can perform acceptance testing and quality assurance on various diagnostic imaging technologies.
While such mentions are important for ensuring quality in patient care, the profession itself is not "protected". Traditionally, the profession of 'Medical Physicist', if only by name, is regulated by the 'employer'. While the situation in Canada does not render itself to misjudgements in hiring a 'qualified' Medical Physicist, a gap in regulating the profession exists, and as evidenced for Pathologists mistakes can happen.
I don't want to get into a detailed conversation over whether the profession of Medical Physicist should -or should not- be regulated in Canada. There is an excellent post in the COMP Point-CounterPoint (see April 2015, page 53) that discusses the pros and cons of this at length. The goal of this blog is to take a snapshot of the status today, particularly in BC.
Medical Physicist as a Profession in British Columbia
So where are we today? Since inception, the British Columbia Association of Medical Physicists (BCAMP) purposes are:Since 2012 there has been more rigour directed at including "Medical Physicist" within the BC "Health Professions Act" (it's a quick read... don't be scared!). As you'd guess, many professions are not included in this (rather old) legislation. In order to be included on this list, the Minister of Health needs to be convinced that the practice of that profession may involve risk of physical, mental or emotional harm to the health, safety or well-being of the public, particularly -in the case of Medical Physicists- in regard to technology, including instruments and materials, used by practitioners of the health profession. Within the Act, the Minister has the authority to determine if the public would benefit from regulating that profession.
The Coalition College of Diagnostic and Health Professions
Of notable omission as a Health Care Profession are Medical Radiation Technologists. For a decades' long effort, the BCAMRT has been working towards creating a regulated college. During that time, other organizations, such as the BC Society of Laboratory Science (www.bcsls.net), have equally been working towards this goal. Rather than introducing professions into the Act one-at-a-time (and ensuring there was proper framework for a regulatory college if needed) the Ministry of Health opted for a different approach. Basically, the steps for any profession could follow a standardized trajectory:- Determine the type of profession it is. This might mean looking at the specifics of the qualifications (education and training) of the profession.
- Determine if the profession fits within the context of the Health Professions Act.
- Spell out what specific restricted activities *to the patient* the professional undertakes. Note, we're not talking about activities like QA'ing a machine, but rather those activities done to the patient, that only health professionals should do.
"...proposing to establish a new college of diagnostic and therapeutic health professions to enhance patient safety and quality of care in British Columbia.
The new college would initially oversee four types of health-care professionals: respiratory therapists, radiation therapists, clinical perfusionists and medical laboratory technologists."
"Once the new college has been substantially implemented, the ministry will continue its work on regulatory options for a number of other diagnostic and therapeutic health-care occupations, including nuclear medicine technologists, medical radiography technologists, magnetic resonance imaging technologists, medical laboratory assistants, cardiology technologists, diagnostic medical sonographers and medical physicists."*
Medical Physicists as a Regulated Profession in BC
Medical Physicists are health professionals responsible for assuring the safe and effective delivery of radiation to achieve a diagnostic or therapeutic result by overseeing and managing technical aspects of the use of radiation in medical applications; implementing and overseeing quality assurance programs for accurate patient dosimetry and quality imaging; and, assuring compliance with relevant legislation and regulations.
