nhaliday + graphs   122

Ask HN: Favorite note-taking software? | Hacker News
Ask HN: What is your ideal note-taking software and/or hardware?: https://news.ycombinator.com/item?id=13221158

my wishlist as of 2019:
- web + desktop macOS + mobile iOS (at least viewing on the last but ideally also editing)
- sync across all those
- open-source data format that's easy to manipulate for scripting purposes
- flexible organization: mostly tree hierarchical (subsuming linear/unorganized) but with the option for directed (acyclic) graph (possibly a second layer of structure/linking)
- can store plain text, LaTeX, diagrams, and raster/vector images (video prob not necessary except as links to elsewhere)
- full-text search
- somehow digest/import data from Pinboard, Workflowy, Papers 3/Bookends, and Skim, ideally absorbing most of their functionality
- so, eg, track notes/annotations side-by-side w/ original PDF/DjVu/ePub documents (to replace Papers3/Bookends/Skim), and maybe web pages too (to replace Pinboard)
- OCR of handwritten notes (how to handle equations/diagrams?)
- various forms of NLP analysis of everything (topic models, clustering, etc)
- maybe version control (less important than export)

candidates?:
- Evernote prob ruled out do to heavy use of proprietary data formats (unless I can find some way to export with tolerably clean output)
- Workflowy/Dynalist are good but only cover a subset of functionality I want
- org-mode doesn't interact w/ mobile well (and I haven't evaluated it in detail otherwise)
- TiddlyWiki/Zim are in the running, but not sure about mobile
- idk about vimwiki but I'm not that wedded to vim and it seems less widely used than org-mode/TiddlyWiki/Zim so prob pass on that
- Quiver/Joplin/Inkdrop look similar and cover a lot of bases, TODO: evaluate more
- Trilium looks especially promising, tho read-only mobile and for macOS desktop look at this: https://github.com/zadam/trilium/issues/511
- RocketBook is interesting scanning/OCR solution but prob not sufficient due to proprietary data format
- TODO: many more candidates, eg, TreeSheets, Gingko, OneNote (macOS?...), Notion (proprietary data format...), Zotero, Nodebook (https://nodebook.io/landing), Polar (https://getpolarized.io), Roam (looks very promising)

Ask HN: What do you use for you personal note taking activity?: https://news.ycombinator.com/item?id=15736102

Ask HN: What are your note-taking techniques?: https://news.ycombinator.com/item?id=9976751

Ask HN: How do you take notes (useful note-taking strategies)?: https://news.ycombinator.com/item?id=13064215

Ask HN: How to get better at taking notes?: https://news.ycombinator.com/item?id=21419478

Ask HN: How did you build up your personal knowledge base?: https://news.ycombinator.com/item?id=21332957
nice comment from math guy on structure and difference between math and CS: https://news.ycombinator.com/item?id=21338628
useful comment collating related discussions: https://news.ycombinator.com/item?id=21333383
highlights:
Designing a Personal Knowledge base: https://news.ycombinator.com/item?id=8270759
Ask HN: How to organize personal knowledge?: https://news.ycombinator.com/item?id=17892731
Do you use a personal 'knowledge base'?: https://news.ycombinator.com/item?id=21108527
Ask HN: How do you share/organize knowledge at work and life?: https://news.ycombinator.com/item?id=21310030

other stuff:
plain text: https://news.ycombinator.com/item?id=21685660

https://www.getdnote.com/blog/how-i-built-personal-knowledge-base-for-myself/
Tiago Forte: https://www.buildingasecondbrain.com

hn search: https://hn.algolia.com/?query=notetaking&type=story

Slant comparison commentary: https://news.ycombinator.com/item?id=7011281

good comparison of options here in comments here (and Trilium itself looks good): https://news.ycombinator.com/item?id=18840990

https://en.wikipedia.org/wiki/Comparison_of_note-taking_software

wikis:
https://www.slant.co/versus/5116/8768/~tiddlywiki_vs_zim
https://www.wikimatrix.org/compare/tiddlywiki+zim
http://tiddlymap.org/
https://www.zim-wiki.org/manual/Plugins/BackLinks_Pane.html
https://zim-wiki.org/manual/Plugins/Link_Map.html

apps:
Roam: https://news.ycombinator.com/item?id=21440289

intriguing but probably not appropriate for my needs: https://www.sophya.ai/

Inkdrop: https://news.ycombinator.com/item?id=20103589

Joplin: https://news.ycombinator.com/item?id=15815040
https://news.ycombinator.com/item?id=21555238

https://wreeto.com/

Leo Editor (combines tree outlining w/ literate programming/scripting, I think?): https://news.ycombinator.com/item?id=17769892

Frame: https://news.ycombinator.com/item?id=18760079

https://www.reddit.com/r/TheMotte/comments/cb18sy/anyone_use_a_personal_wiki_software_to_catalog/
https://archive.is/xViTY
Notion: https://news.ycombinator.com/item?id=18904648

https://www.reddit.com/r/slatestarcodex/comments/ap437v/modified_cornell_method_the_optimal_notetaking/
https://archive.is/e9oHu
https://www.reddit.com/r/slatestarcodex/comments/bt8a1r/im_about_to_start_a_one_month_journaling_test/
https://www.reddit.com/r/slatestarcodex/comments/9cot3m/question_how_do_you_guys_learn_things/
https://archive.is/HUH8V
https://www.reddit.com/r/slatestarcodex/comments/d7bvcp/how_to_read_a_book_for_understanding/
https://archive.is/VL2mi

Anki:
https://www.reddit.com/r/Anki/comments/as8i4t/use_anki_for_technical_books/
https://www.freecodecamp.org/news/how-anki-saved-my-engineering-career-293a90f70a73/
https://www.reddit.com/r/slatestarcodex/comments/ch24q9/anki_is_it_inferior_to_the_3x5_index_card_an/
https://archive.is/OaGc5
maybe not the best source for a review/advice

interesting comment(s) about tree outliners and spreadsheets: https://news.ycombinator.com/item?id=21170434

tablet:
https://www.inkandswitch.com/muse-studio-for-ideas.html
https://www.inkandswitch.com/capstone-manuscript.html
https://news.ycombinator.com/item?id=20255457
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7 weeks ago by nhaliday
Zettelkästen? | Hacker News
Here’s a LessWrong post that describes it (including the insight “I honestly didn’t think Zettelkasten sounded like a good idea before I tried it” which I also felt).

yeah doesn't sound like a good idea to me either. idk
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7 weeks ago by nhaliday
CppCon 2015: Chandler Carruth "Tuning C++: Benchmarks, and CPUs, and Compilers! Oh My!" - YouTube
- very basics of benchmarking
- Q: why does preemptive reserve speed up push_back by 10x?
- favorite tool is Linux perf
- callgraph profiling
- important option: -fomit-frame-pointer
- perf has nice interface ('a' = "annotate") for reading assembly (good display of branches/jumps)
- A: optimized to no-op
- how to turn off optimizer
- profilers aren't infallible. a lot of the time samples are misattributed to neighboring ops
- fast mod example
- branch prediction hints (#define UNLIKELY(x), __builtin_expected, etc)
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7 weeks ago by nhaliday
Parallel Computing: Theory and Practice
by Umut Acar who also co-authored a different book on parallel algorithms w/ Guy Blelloch from a more high-level and functional perspective
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11 weeks ago by nhaliday
Call graph - Wikipedia
I've found both static and dynamic versions useful (former mostly when I don't want to go thru pain of compiling something)

best options AFAICT:

C/C++ and maybe Go: https://github.com/gperftools/gperftools
https://gperftools.github.io/gperftools/cpuprofile.html

static: https://github.com/Vermeille/clang-callgraph
https://stackoverflow.com/questions/5373714/how-to-generate-a-calling-graph-for-c-code
I had to go through some extra pain to get this to work:
- if you use Homebrew LLVM (that's slightly incompatible w/ macOS c++filt, make sure to pass -n flag)
- similarly macOS sed needs two extra backslashes for each escape of the angle brackets

another option: doxygen

Go: https://stackoverflow.com/questions/31362332/creating-call-graph-in-golang
both static and dynamic in one tool

Java: https://github.com/gousiosg/java-callgraph
both static and dynamic in one tool

Python:
https://github.com/gak/pycallgraph
more up-to-date forks: https://github.com/daneads/pycallgraph2 and https://github.com/YannLuo/pycallgraph
old docs: https://pycallgraph.readthedocs.io/en/master/
I've had some trouble getting nice output from this (even just getting the right set of nodes displayed, not even taking into account layout and formatting).
- Argument parsing syntax is idiosyncratic. Just read `pycallgraph --help`.
- Options -i and -e take glob patterns (see pycallgraph2/{tracer,globbing_filter}.py), which are applied the function names qualified w/ module paths.
- Functions defined in the script you are running receive no module path. There is no easy way to filter for them using the -i and -e options.
- The --debug option gives you the graphviz for your own use instead of just writing the final image produced.

static: https://github.com/davidfraser/pyan
more up-to-date fork: https://github.com/itsayellow/pyan/
one way to good results: `pyan -dea --format yed $MODULE_FILES > output.graphml`, then open up in yEd and use hierarchical layout

various: https://github.com/jrfonseca/gprof2dot

I believe all the dynamic tools listed here support weighting nodes and edges by CPU time/samples (inclusive and exclusive of descendants) and discrete calls. In the case of the gperftools and the Java option you probably have to parse the output to get the latter, tho.

IIRC Dtrace has probes for function entry/exit. So that's an option as well.

old pin: https://github.com/nst/objc_dep
Graph the import dependancies in an Objective-C project
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july 2019 by nhaliday
Amazon Products Visualization - YASIV
based off a single test run, this works really well, at least for popular books (all I was interested in at the time)
tools  search  recommendations  consumerism  books  aggregator  exploratory  let-me-see  network-structure  amazon  similarity  graphs  visualization 
july 2019 by nhaliday
Frama-C
Frama-C is organized with a plug-in architecture (comparable to that of the Gimp or Eclipse). A common kernel centralizes information and conducts the analysis. Plug-ins interact with each other through interfaces defined by the kernel. This makes for robustness in the development of Frama-C while allowing a wide functionality spectrum.

...

Three heavyweight plug-ins that are used by the other plug-ins:

- Eva (Evolved Value analysis)
This plug-in computes variation domains for variables. It is quite automatic, although the user may guide the analysis in places. It handles a wide spectrum of C constructs. This plug-in uses abstract interpretation techniques.
- Jessie and Wp, two deductive verification plug-ins
These plug-ins are based on weakest precondition computation techniques. They allow to prove that C functions satisfy their specification as expressed in ACSL. These proofs are modular: the specifications of the called functions are used to establish the proof without looking at their code.

For browsing unfamiliar code:
- Impact analysis
This plug-in highlights the locations in the source code that are impacted by a modification.
- Scope & Data-flow browsing
This plug-in allows the user to navigate the dataflow of the program, from definition to use or from use to definition.
- Variable occurrence browsing
Also provided as a simple example for new plug-in development, this plug-in allows the user to reach the statements where a given variable is used.
- Metrics calculation
This plug-in allows the user to compute various metrics from the source code.

For code transformation:
- Semantic constant folding
This plug-in makes use of the results of the evolved value analysis plug-in to replace, in the source code, the constant expressions by their values. Because it relies on EVA, it is able to do more of these simplifications than a syntactic analysis would.
- Slicing
This plug-in slices the code according to a user-provided criterion: it creates a copy of the program, but keeps only those parts which are necessary with respect to the given criterion.
- Spare code: remove "spare code", code that does not contribute to the final results of the program.
- E-ACSL: translate annotations into C code for runtime assertion checking.
For verifying functional specifications:

- Aoraï: verify specifications expressed as LTL (Linear Temporal Logic) formulas
Other functionalities documented together with the EVA plug-in can be considered as verifying low-level functional specifications (inputs, outputs, dependencies,…)
For test-case generation:

- PathCrawler automatically finds test-case inputs to ensure coverage of a C function. It can be used for structural unit testing, as a complement to static analysis or to study the feasible execution paths of the function.
For concurrent programs:

- Mthread
This plug-in automatically analyzes concurrent C programs, using the EVA plug-in, taking into account all possible thread interactions. At the end of its execution, the concurrent behavior of each thread is over-approximated, resulting in precise information about shared variables, which mutex protects a part of the code, etc.
Front-end for other languages

- Frama-Clang
This plug-in provides a C++ front-end to Frama-C, based on the clang compiler. It transforms C++ code into a Frama-C AST, which can then be analyzed by the plug-ins above. Note however that it is very experimental and only supports a subset of C++11
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may 2019 by nhaliday
Continuous Code Quality | SonarSource
they have cyclomatic complexity rule
$150/year for dev edition (needed for C++ but not Java/Python)
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may 2019 by nhaliday
Lateralization of brain function - Wikipedia
Language
Language functions such as grammar, vocabulary and literal meaning are typically lateralized to the left hemisphere, especially in right handed individuals.[3] While language production is left-lateralized in up to 90% of right-handers, it is more bilateral, or even right-lateralized, in approximately 50% of left-handers.[4]

Broca's area and Wernicke's area, two areas associated with the production of speech, are located in the left cerebral hemisphere for about 95% of right-handers, but about 70% of left-handers.[5]:69

Auditory and visual processing
The processing of visual and auditory stimuli, spatial manipulation, facial perception, and artistic ability are represented bilaterally.[4] Numerical estimation, comparison and online calculation depend on bilateral parietal regions[6][7] while exact calculation and fact retrieval are associated with left parietal regions, perhaps due to their ties to linguistic processing.[6][7]

...

Depression is linked with a hyperactive right hemisphere, with evidence of selective involvement in "processing negative emotions, pessimistic thoughts and unconstructive thinking styles", as well as vigilance, arousal and self-reflection, and a relatively hypoactive left hemisphere, "specifically involved in processing pleasurable experiences" and "relatively more involved in decision-making processes".

Chaos and Order; the right and left hemispheres: https://orthosphere.wordpress.com/2018/05/23/chaos-and-order-the-right-and-left-hemispheres/
In The Master and His Emissary, Iain McGilchrist writes that a creature like a bird needs two types of consciousness simultaneously. It needs to be able to focus on something specific, such as pecking at food, while it also needs to keep an eye out for predators which requires a more general awareness of environment.

These are quite different activities. The Left Hemisphere (LH) is adapted for a narrow focus. The Right Hemisphere (RH) for the broad. The brains of human beings have the same division of function.

The LH governs the right side of the body, the RH, the left side. With birds, the left eye (RH) looks for predators, the right eye (LH) focuses on food and specifics. Since danger can take many forms and is unpredictable, the RH has to be very open-minded.

The LH is for narrow focus, the explicit, the familiar, the literal, tools, mechanism/machines and the man-made. The broad focus of the RH is necessarily more vague and intuitive and handles the anomalous, novel, metaphorical, the living and organic. The LH is high resolution but narrow, the RH low resolution but broad.

The LH exhibits unrealistic optimism and self-belief. The RH has a tendency towards depression and is much more realistic about a person’s own abilities. LH has trouble following narratives because it has a poor sense of “wholes.” In art it favors flatness, abstract and conceptual art, black and white rather than color, simple geometric shapes and multiple perspectives all shoved together, e.g., cubism. Particularly RH paintings emphasize vistas with great depth of field and thus space and time,[1] emotion, figurative painting and scenes related to the life world. In music, LH likes simple, repetitive rhythms. The RH favors melody, harmony and complex rhythms.

...

Schizophrenia is a disease of extreme LH emphasis. Since empathy is RH and the ability to notice emotional nuance facially, vocally and bodily expressed, schizophrenics tend to be paranoid and are often convinced that the real people they know have been replaced by robotic imposters. This is at least partly because they lose the ability to intuit what other people are thinking and feeling – hence they seem robotic and suspicious.

Oswald Spengler’s The Decline of the West as well as McGilchrist characterize the West as awash in phenomena associated with an extreme LH emphasis. Spengler argues that Western civilization was originally much more RH (to use McGilchrist’s categories) and that all its most significant artistic (in the broadest sense) achievements were triumphs of RH accentuation.

The RH is where novel experiences and the anomalous are processed and where mathematical, and other, problems are solved. The RH is involved with the natural, the unfamiliar, the unique, emotions, the embodied, music, humor, understanding intonation and emotional nuance of speech, the metaphorical, nuance, and social relations. It has very little speech, but the RH is necessary for processing all the nonlinguistic aspects of speaking, including body language. Understanding what someone means by vocal inflection and facial expressions is an intuitive RH process rather than explicit.

...

RH is very much the center of lived experience; of the life world with all its depth and richness. The RH is “the master” from the title of McGilchrist’s book. The LH ought to be no more than the emissary; the valued servant of the RH. However, in the last few centuries, the LH, which has tyrannical tendencies, has tried to become the master. The LH is where the ego is predominantly located. In split brain patients where the LH and the RH are surgically divided (this is done sometimes in the case of epileptic patients) one hand will sometimes fight with the other. In one man’s case, one hand would reach out to hug his wife while the other pushed her away. One hand reached for one shirt, the other another shirt. Or a patient will be driving a car and one hand will try to turn the steering wheel in the opposite direction. In these cases, the “naughty” hand is usually the left hand (RH), while the patient tends to identify herself with the right hand governed by the LH. The two hemispheres have quite different personalities.

The connection between LH and ego can also be seen in the fact that the LH is competitive, contentious, and agonistic. It wants to win. It is the part of you that hates to lose arguments.

Using the metaphor of Chaos and Order, the RH deals with Chaos – the unknown, the unfamiliar, the implicit, the emotional, the dark, danger, mystery. The LH is connected with Order – the known, the familiar, the rule-driven, the explicit, and light of day. Learning something means to take something unfamiliar and making it familiar. Since the RH deals with the novel, it is the problem-solving part. Once understood, the results are dealt with by the LH. When learning a new piece on the piano, the RH is involved. Once mastered, the result becomes a LH affair. The muscle memory developed by repetition is processed by the LH. If errors are made, the activity returns to the RH to figure out what went wrong; the activity is repeated until the correct muscle memory is developed in which case it becomes part of the familiar LH.

Science is an attempt to find Order. It would not be necessary if people lived in an entirely orderly, explicit, known world. The lived context of science implies Chaos. Theories are reductive and simplifying and help to pick out salient features of a phenomenon. They are always partial truths, though some are more partial than others. The alternative to a certain level of reductionism or partialness would be to simply reproduce the world which of course would be both impossible and unproductive. The test for whether a theory is sufficiently non-partial is whether it is fit for purpose and whether it contributes to human flourishing.

...

Analytic philosophers pride themselves on trying to do away with vagueness. To do so, they tend to jettison context which cannot be brought into fine focus. However, in order to understand things and discern their meaning, it is necessary to have the big picture, the overview, as well as the details. There is no point in having details if the subject does not know what they are details of. Such philosophers also tend to leave themselves out of the picture even when what they are thinking about has reflexive implications. John Locke, for instance, tried to banish the RH from reality. All phenomena having to do with subjective experience he deemed unreal and once remarked about metaphors, a RH phenomenon, that they are “perfect cheats.” Analytic philosophers tend to check the logic of the words on the page and not to think about what those words might say about them. The trick is for them to recognize that they and their theories, which exist in minds, are part of reality too.

The RH test for whether someone actually believes something can be found by examining his actions. If he finds that he must regard his own actions as free, and, in order to get along with other people, must also attribute free will to them and treat them as free agents, then he effectively believes in free will – no matter his LH theoretical commitments.

...

We do not know the origin of life. We do not know how or even if consciousness can emerge from matter. We do not know the nature of 96% of the matter of the universe. Clearly all these things exist. They can provide the subject matter of theories but they continue to exist as theorizing ceases or theories change. Not knowing how something is possible is irrelevant to its actual existence. An inability to explain something is ultimately neither here nor there.

If thought begins and ends with the LH, then thinking has no content – content being provided by experience (RH), and skepticism and nihilism ensue. The LH spins its wheels self-referentially, never referring back to experience. Theory assumes such primacy that it will simply outlaw experiences and data inconsistent with it; a profoundly wrong-headed approach.

...

Gödel’s Theorem proves that not everything true can be proven to be true. This means there is an ineradicable role for faith, hope and intuition in every moderately complex human intellectual endeavor. There is no one set of consistent axioms from which all other truths can be derived.

Alan Turing’s proof of the halting problem proves that there is no effective procedure for finding effective procedures. Without a mechanical decision procedure, (LH), when it comes to … [more]
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september 2018 by nhaliday
Society of Mind - Wikipedia
A core tenet of Minsky's philosophy is that "minds are what brains do". The society of mind theory views the human mind and any other naturally evolved cognitive systems as a vast society of individually simple processes known as agents. These processes are the fundamental thinking entities from which minds are built, and together produce the many abilities we attribute to minds. The great power in viewing a mind as a society of agents, as opposed to the consequence of some basic principle or some simple formal system, is that different agents can be based on different types of processes with different purposes, ways of representing knowledge, and methods for producing results.

This idea is perhaps best summarized by the following quote:

What magical trick makes us intelligent? The trick is that there is no trick. The power of intelligence stems from our vast diversity, not from any single, perfect principle. —Marvin Minsky, The Society of Mind, p. 308

https://en.wikipedia.org/wiki/Modularity_of_mind

The modular organization of human anatomical
brain networks: Accounting for the cost of wiring: https://www.mitpressjournals.org/doi/pdfplus/10.1162/NETN_a_00002
Brain networks are expected to be modular. However, existing techniques for estimating a network’s modules make it difficult to assess the influence of organizational principles such as wiring cost reduction on the detected modules. Here we present a modification of an existing module detection algorithm that allowed us to focus on connections that are unexpected under a cost-reduction wiring rule and to identify modules from among these connections. We applied this technique to anatomical brain networks and showed that the modules we detected differ from those detected using the standard technique. We demonstrated that these novel modules are spatially distributed, exhibit unique functional fingerprints, and overlap considerably with rich clubs, giving rise to an alternative and complementary interpretation of the functional roles of specific brain regions. Finally, we demonstrated that, using the modified module detection approach, we can detect modules in a developmental dataset that track normative patterns of maturation. Collectively, these findings support the hypothesis that brain networks are composed of modules and provide additional insight into the function of those modules.
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april 2018 by nhaliday
Antinomia Imediata – experiments in a reaction from the left
https://antinomiaimediata.wordpress.com/lrx/
So, what is the Left Reaction? First of all, it’s reaction: opposition to the modern rationalist establishment, the Cathedral. It opposes the universalist Jacobin program of global government, favoring a fractured geopolitics organized through long-evolved complex systems. It’s profoundly anti-socialist and anti-communist, favoring market economy and individualism. It abhors tribalism and seeks a realistic plan for dismantling it (primarily informed by HBD and HBE). It looks at modernity as a degenerative ratchet, whose only way out is intensification (hence clinging to crypto-marxist market-driven acceleration).

How come can any of this still be in the *Left*? It defends equality of power, i.e. freedom. This radical understanding of liberty is deeply rooted in leftist tradition and has been consistently abhored by the Right. LRx is not democrat, is not socialist, is not progressist and is not even liberal (in its current, American use). But it defends equality of power. It’s utopia is individual sovereignty. It’s method is paleo-agorism. The anti-hierarchy of hunter-gatherer nomads is its understanding of the only realistic objective of equality.

...

In more cosmic terms, it seeks only to fulfill the Revolution’s side in the left-right intelligence pump: mutation or creation of paths. Proudhon’s antinomy is essentially about this: the collective force of the socius, evinced in moral standards and social organization vs the creative force of the individuals, that constantly revolutionize and disrupt the social body. The interplay of these forces create reality (it’s a metaphysics indeed): the Absolute (socius) builds so that the (individualistic) Revolution can destroy so that the Absolute may adapt, and then repeat. The good old formula of ‘solve et coagula’.

Ultimately, if the Neoreaction promises eternal hell, the LRx sneers “but Satan is with us”.

https://antinomiaimediata.wordpress.com/2016/12/16/a-statement-of-principles/
Liberty is to be understood as the ability and right of all sentient beings to dispose of their persons and the fruits of their labor, and nothing else, as they see fit. This stems from their self-awareness and their ability to control and choose the content of their actions.

...

Equality is to be understood as the state of no imbalance of power, that is, of no subjection to another sentient being. This stems from their universal ability for empathy, and from their equal ability for reason.

...

It is important to notice that, contrary to usual statements of these two principles, my standpoint is that Liberty and Equality here are not merely compatible, meaning they could coexist in some possible universe, but rather they are two sides of the same coin, complementary and interdependent. There can be NO Liberty where there is no Equality, for the imbalance of power, the state of subjection, will render sentient beings unable to dispose of their persons and the fruits of their labor[1], and it will limit their ability to choose over their rightful jurisdiction. Likewise, there can be NO Equality without Liberty, for restraining sentient beings’ ability to choose and dispose of their persons and fruits of labor will render some more powerful than the rest, and establish a state of subjection.

https://antinomiaimediata.wordpress.com/2017/04/18/flatness/
equality is the founding principle (and ultimately indistinguishable from) freedom. of course, it’s only in one specific sense of “equality” that this sentence is true.

to try and eliminate the bullshit, let’s turn to networks again:

any nodes’ degrees of freedom is the number of nodes they are connected to in a network. freedom is maximum when the network is symmetrically connected, i. e., when all nodes are connected to each other and thus there is no topographical hierarchy (middlemen) – in other words, flatness.

in this understanding, the maximization of freedom is the maximization of entropy production, that is, of intelligence. As Land puts it:

https://antinomiaimediata.wordpress.com/category/philosophy/mutualism/
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march 2018 by nhaliday
Fitting a Structural Equation Model
seems rather unrigorous: nonlinear optimization, possibility of nonconvergence, doesn't even mention local vs. global optimality...
pdf  slides  lectures  acm  stats  hypothesis-testing  graphs  graphical-models  latent-variables  model-class  optimization  nonlinearity  gotchas  nibble  ML-MAP-E  iteration-recursion  convergence 
november 2017 by nhaliday
What are the Laws of Biology?
The core finding of systems biology is that only a very small subset of possible network motifs is actually used and that these motifs recur in all kinds of different systems, from transcriptional to biochemical to neural networks. This is because only those arrangements of interactions effectively perform some useful operation, which underlies some necessary function at a cellular or organismal level. There are different arrangements for input summation, input comparison, integration over time, high-pass or low-pass filtering, negative auto-regulation, coincidence detection, periodic oscillation, bistability, rapid onset response, rapid offset response, turning a graded signal into a sharp pulse or boundary, and so on, and so on.

These are all familiar concepts and designs in engineering and computing, with well-known properties. In living organisms there is one other general property that the designs must satisfy: robustness. They have to work with noisy components, at a scale that’s highly susceptible to thermal noise and environmental perturbations. Of the subset of designs that perform some operation, only a much smaller subset will do it robustly enough to be useful in a living organism. That is, they can still perform their particular functions in the face of noisy or fluctuating inputs or variation in the number of components constituting the elements of the network itself.
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november 2017 by nhaliday
Homebrew: List only installed top level formulas - Stack Overflow
Use brew leaves: show installed formulae that are not dependencies of another installed formula.
q-n-a  stackex  howto  yak-shaving  programming  osx  terminal  network-structure  graphs  trivia  tip-of-tongue  workflow  build-packaging 
november 2017 by nhaliday
Does Learning to Read Improve Intelligence? A Longitudinal Multivariate Analysis in Identical Twins From Age 7 to 16
Stuart Richie, Bates, Plomin

SEM: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354297/figure/fig03/

The variance explained by each path in the diagrams included here can be calculated by squaring its path weight. To take one example, reading differences at age 12 in the model shown in Figure​Figure33 explain 7% of intelligence differences at age 16 (.262). However, since our measures are of differences, they are likely to include substantial amounts of noise: Measurement error may produce spurious differences. To remove this error variance, we can take an estimate of the reliability of the measures (generally high, since our measures are normed, standardized tests), which indicates the variance expected purely by the reliability of the measure, and subtract it from the observed variance between twins in our sample. Correcting for reliability in this way, the effect size estimates are somewhat larger; to take the above example, the reliability-corrected effect size of age 12 reading differences on age 16 intelligence differences is around 13% of the “signal” variance. It should be noted that the age 12 reading differences themselves are influenced by many previous paths from both reading and intelligence, as illustrated in Figure​Figure33.

...

The present study provided compelling evidence that improvements in reading ability, themselves caused purely by the nonshared environment, may result in improvements in both verbal and nonverbal cognitive ability, and may thus be a factor increasing cognitive diversity within families (Plomin, 2011). These associations are present at least as early as age 7, and are not—to the extent we were able to test this possibility—driven by differences in reading exposure. Since reading is a potentially remediable ability, these findings have implications for reading instruction: Early remediation of reading problems might not only aid in the growth of literacy, but may also improve more general cognitive abilities that are of critical importance across the life span.

Does Reading Cause Later Intelligence? Accounting for Stability in Models of Change: http://sci-hub.tw/10.1111/cdev.12669
Results from a state–trait model suggest that reported effects of reading ability on later intelligence may be artifacts of previously uncontrolled factors, both environmental in origin and stable during this developmental period, influencing both constructs throughout development.
study  albion  scitariat  spearhead  psychology  cog-psych  psychometrics  iq  intelligence  eden  language  psych-architecture  longitudinal  twin-study  developmental  environmental-effects  studying  🌞  retrofit  signal-noise  intervention  causation  graphs  graphical-models  flexibility  britain  neuro-nitgrit  effect-size  variance-components  measurement  multi  sequential  time  composition-decomposition  biodet  behavioral-gen  direct-indirect  systematic-ad-hoc  debate  hmm  pdf  piracy  flux-stasis 
september 2017 by nhaliday
Rank aggregation basics: Local Kemeny optimisation | David R. MacIver
This turns our problem from a global search to a local one: Basically we can start from any point in the search space and search locally by swapping adjacent pairs until we hit a minimum. This turns out to be quite easy to do. _We basically run insertion sort_: At step n we have the first n items in a locally Kemeny optimal order. Swap the n+1th item backwards until the majority think its predecessor is < it. This ensures all adjacent pairs are in the majority order, so swapping them would result in a greater than or equal K. This is of course an O(n^2) algorithm. In fact, the problem of merely finding a locally Kemeny optimal solution can be done in O(n log(n)) (for much the same reason as you can sort better than insertion sort). You just take the directed graph of majority votes and find a Hamiltonian Path. The nice thing about the above version of the algorithm is that it gives you a lot of control over where you start your search.
techtariat  liner-notes  papers  tcs  algorithms  machine-learning  acm  optimization  approximation  local-global  orders  graphs  graph-theory  explanation  iteration-recursion  time-complexity  nibble 
september 2017 by nhaliday
PsycARTICLES - Is education associated with improvements in general cognitive ability, or in specific skills?
Results indicated that the association of education with improved cognitive test scores is not mediated by g, but consists of direct effects on specific cognitive skills. These results suggest a decoupling of educational gains from increases in general intellectual capacity.

look at Model C for the coefficients

How much does education improve intelligence? A meta-analysis: https://psyarxiv.com/kymhp
Intelligence test scores and educational duration are positively correlated. This correlation can be interpreted in two ways: students with greater propensity for intelligence go on to complete more education, or a longer education increases intelligence. We meta-analysed three categories of quasi-experimental studies of educational effects on intelligence: those estimating education-intelligence associations after controlling for earlier intelligence, those using compulsory schooling policy changes as instrumental variables, and those using regression-discontinuity designs on school-entry age cutoffs. Across 142 effect sizes from 42 datasets involving over 600,000 participants, we found consistent evidence for beneficial effects of education on cognitive abilities, of approximately 1 to 5 IQ points for an additional year of education. Moderator analyses indicated that the effects persisted across the lifespan, and were present on all broad categories of cognitive ability studied. Education appears to be the most consistent, robust, and durable method yet to be identified for raising intelligence.

three study designs: control for prior IQ, exogenous policy change, and school age cutoff regression discontinuity

https://westhunt.wordpress.com/2017/11/07/skoptsys/#comment-97601
It’s surprising that there isn’t much of a fadeout (p11) – half of the effect size is still there by age 70 (?!). That wasn’t what I expected. Maybe they’re being pulled upwards by smaller outlier studies – most of the bigger ones tend towards the lower end.

https://twitter.com/gwern/status/928308706370052098
https://archive.is/v98bd
These gains are hollow, as they acknowledge in the discussion. Examples:
albion  spearhead  scitariat  study  psychology  cog-psych  iq  large-factor  education  intervention  null-result  longitudinal  britain  anglo  psychometrics  psych-architecture  graphs  graphical-models  causation  neuro-nitgrit  effect-size  stylized-facts  direct-indirect  flexibility  input-output  evidence-based  preprint  multi  optimism  meta-analysis  west-hunter  poast  commentary  aging  marginal  europe  nordic  shift  twitter  social  backup  ratty  gwern  links  flynn  environmental-effects  debate  roots 
march 2017 by nhaliday
Main Page - Competitive Programming Algorithms: E-Maxx Algorithms in English
original russian version: http://e-maxx.ru/algo/

some notable stuff:
- O(N) factorization sieve
- discrete logarithm
- factorial N! (mod P) in O(P log N)
- flow algorithms
- enumerating submasks
- bridges, articulation points
- Ukkonen algorithm
- sqrt(N) trick, eg, for range mode query
explanation  programming  algorithms  russia  foreign-lang  oly  oly-programming  problem-solving  accretion  math.NT  graphs  graph-theory  optimization  data-structures  yoga  tidbits  multi  anglo  language  arrows  strings 
february 2017 by nhaliday
Lecture 11
In which we prove that the Edmonds-Karp algorithm for maximum flow is a strongly polynomial time algorithm, and we begin to talk about the push-relabel approach.
pdf  lecture-notes  exposition  optimization  algorithms  linear-programming  graphs  stanford  luca-trevisan  nibble  direction  stock-flow  tcs  constraint-satisfaction  tcstariat 
january 2017 by nhaliday
Lecture 16
In which we define a multi-commodity flow problem, and we see that its dual is the relaxation of a useful graph partitioning problem. The relaxation can be rounded to yield an approximate graph partitioning algorithm.
pdf  lecture-notes  exposition  optimization  linear-programming  graphs  graph-theory  algorithms  duality  rounding  stanford  approximation  rand-approx  luca-trevisan  relaxation  nibble  stock-flow  constraint-satisfaction  tcs  tcstariat 
january 2017 by nhaliday
CS 731 Advanced Artificial Intelligence - Spring 2011
- statistical machine learning
- sparsity in regression
- graphical models
- exponential families
- variational methods
- MCMC
- dimensionality reduction, eg, PCA
- Bayesian nonparametrics
- compressive sensing, matrix completion, and Johnson-Lindenstrauss
course  lecture-notes  yoga  acm  stats  machine-learning  graphical-models  graphs  model-class  bayesian  learning-theory  sparsity  embeddings  markov  monte-carlo  norms  unit  nonparametric  compressed-sensing  matrix-factorization  features 
january 2017 by nhaliday
D-separation
collider C = A->C<-B
A, B d-connected (resp. conditioned on Z) iff path A~>B or B~>A w/o colliders (resp. path excluding vertices in Z)
A,B d-separated conditioned on Z iff not d-connected conditioned on Z

http://bayes.cs.ucla.edu/BOOK-2K/d-sep.html
concept  explanation  causation  bayesian  graphical-models  cmu  org:edu  stats  methodology  tutorial  jargon  graphs  hypothesis-testing  confounding  🔬  direct-indirect  philosophy  definition  volo-avolo  multi  org:junk 
january 2017 by nhaliday
Dgsh – Directed graph shell | Hacker News
I've worked with and looked at a lot of data processing helpers. Tools, that try to help you build data pipelines, for the sake of performance, reproducibility or simply code uniformity.
What I found so far: Most tools, that invent a new language or try to cram complex processes into lesser suited syntactical environments are not loved too much.

...

I'll give dgsh a try. The tool reuse approach and the UNIX spirit seems nice. But my initial impression of the "C code metrics" example from the site is mixed: It reminds me of awk, about which one of the authors said, that it's a beautiful language, but if your programs getting longer than hundred lines, you might want to switch to something else.

Two libraries which have a great grip at the plumbing aspect of data processing systems are airflow and luigi. They are python libraries and with it you have a concise syntax and basically all python libraries plus non-python tools with a command line interface at you fingertips.

I am curious, what kind of process orchestration tools people use and can recommend?

--

Exactly our experience too, from complex machine learning workflows in various aspects of drug discovery.
We basically did not really find any of the popular DSL-based bioinformatics pipeline tools (snakemake, bpipe etc) to fit the bill. Nextflow came close, but in fact allows quite some custom code too.

What worked for us was to use Spotify's Luigi, which is a python library rather than DSL.

The only thing was that we had to develop a flow-based inspired API on top of Luigi's more functional programming based one, in order to make defining dependencies fluent and easy enough to specify for our complex workflows.

Our flow-based inspired Luigi API (SciLuigi) for complex workflows, is available at:

https://github.com/pharmbio/sciluigi

--

We have measured many of the examples against the use of temporary files and the web report one against (single-threaded) implementations in Perl and Java. In almost all cases dgsh takes less wall clock time, but often consumes more CPU resources.
commentary  project  programming  terminal  worrydream  pls  plt  unix  hn  graphs  tools  devtools  let-me-see  composition-decomposition  yak-shaving  workflow  exocortex  hmm  cool  software  desktop  sci-comp  stock-flow  performance  comparison  links  libraries  python 
january 2017 by nhaliday
Shtetl-Optimized » Blog Archive » Why I Am Not An Integrated Information Theorist (or, The Unconscious Expander)
In my opinion, how to construct a theory that tells us which physical systems are conscious and which aren’t—giving answers that agree with “common sense” whenever the latter renders a verdict—is one of the deepest, most fascinating problems in all of science. Since I don’t know a standard name for the problem, I hereby call it the Pretty-Hard Problem of Consciousness. Unlike with the Hard Hard Problem, I don’t know of any philosophical reason why the Pretty-Hard Problem should be inherently unsolvable; but on the other hand, humans seem nowhere close to solving it (if we had solved it, then we could reduce the abortion, animal rights, and strong AI debates to “gentlemen, let us calculate!”).

Now, I regard IIT as a serious, honorable attempt to grapple with the Pretty-Hard Problem of Consciousness: something concrete enough to move the discussion forward. But I also regard IIT as a failed attempt on the problem. And I wish people would recognize its failure, learn from it, and move on.

In my view, IIT fails to solve the Pretty-Hard Problem because it unavoidably predicts vast amounts of consciousness in physical systems that no sane person would regard as particularly “conscious” at all: indeed, systems that do nothing but apply a low-density parity-check code, or other simple transformations of their input data. Moreover, IIT predicts not merely that these systems are “slightly” conscious (which would be fine), but that they can be unboundedly more conscious than humans are.

To justify that claim, I first need to define Φ. Strikingly, despite the large literature about Φ, I had a hard time finding a clear mathematical definition of it—one that not only listed formulas but fully defined the structures that the formulas were talking about. Complicating matters further, there are several competing definitions of Φ in the literature, including ΦDM (discrete memoryless), ΦE (empirical), and ΦAR (autoregressive), which apply in different contexts (e.g., some take time evolution into account and others don’t). Nevertheless, I think I can define Φ in a way that will make sense to theoretical computer scientists. And crucially, the broad point I want to make about Φ won’t depend much on the details of its formalization anyway.

We consider a discrete system in a state x=(x1,…,xn)∈Sn, where S is a finite alphabet (the simplest case is S={0,1}). We imagine that the system evolves via an “updating function” f:Sn→Sn. Then the question that interests us is whether the xi‘s can be partitioned into two sets A and B, of roughly comparable size, such that the updates to the variables in A don’t depend very much on the variables in B and vice versa. If such a partition exists, then we say that the computation of f does not involve “global integration of information,” which on Tononi’s theory is a defining aspect of consciousness.
aaronson  tcstariat  philosophy  dennett  interdisciplinary  critique  nibble  org:bleg  within-without  the-self  neuro  psychology  cog-psych  metrics  nitty-gritty  composition-decomposition  complex-systems  cybernetics  bits  information-theory  entropy-like  forms-instances  empirical  walls  arrows  math.DS  structure  causation  quantitative-qualitative  number  extrema  optimization  abstraction  explanation  summary  degrees-of-freedom  whole-partial-many  network-structure  systematic-ad-hoc  tcs  complexity  hardness  no-go  computation  measurement  intricacy  examples  counterexample  coding-theory  linear-algebra  fields  graphs  graph-theory  expanders  math  math.CO  properties  local-global  intuition  error  definition  coupling-cohesion 
january 2017 by nhaliday
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