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ROGER PENROSE: THE ROAD to REALITY

We (not royal we here) intend to read this over the next 2 years in installments of 20ish pages every 2nd week. I think it will do wonders for our understanding of physics and if not, we will write an angry letter to Sir Roger Penrose and The Times.

Since one of us have standard working hours we will do it before work – probably like 6.30AM to 8.00 AM – per Skype. A good start of the day and your breakfast will taste better. If somebody want to join, please contact me. We will start in January.

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Summary of “Mathematical Chemistry and Chemoinformatics” page 399-417

Last time we made the following comment: “An interesting point is that if it was possible to exclude the possibility that the molecule had a ring, then the correct result would jump from position 16 to position 2.”
This time we are doing exactly that sort of thing. Based on the theory in chapter 8.

The structure criteria (either that something is present or absent) with probability over 95% is used to restrict the set of possibilities. In the example, this reduces the set of candidates from around 30 to around 3.

A comparison between MOLGEN-MS and two competitors; ACD MS Fragmenter and MetFrag, is made. It seems that they are about the same in quality. Some have better percentwise ranking (RRP) but also more candidates.

Mass spectrometry yields more than just a spiky digram. It also produces the diagram in real time. To take the time element into account, we look at retention time.
Retention properties – retention is the time it takes from insertion to observation and is used in chomtography. (There are to rentention indices, but they build on the same idea)
There is some error when measuring the retention time, so one approach is to allow a molecule if it is within 2 standard deviation of a retention measurement.

2 other properties can be used similarly to retention time to exclude unlikely candidates:
Partitioning properties – A measure for how the molecule partitions related to retention time.
Steric energy – molecules with too high steric energy that are so weird, that they cannot exist.

An alternative to the above approach is Consensus scoring. The idea is to give a combined rank for candidates instead of eliminating unlikely ones for each criterion. This requires a formula for combining the different criteria, which is provided. The formula has some disadvantages, but overall this seems like a more promising approach.

The example used tries to find the molecules present in contaminated groundwater in Germany.

The chapter concludes with naming some ways to improve CASE studies I the future. It mentions that there is a long way to go before it is automated.

The second conclusion is about CASE with high accuracy data. It is not efficient in practice, since the databases are in their infant stages, but people are working on it.

General comments:
The workflow on figure 9.9 is not guilty of the same lack of details as the previous ones.
Chapter 7,8 also seemed like case-studies.

Next up is a talk on Monday 14-16 in the department of statistics. We discuss the contents of the entire book. Interested people are welcome.

Summary: Cook (1971) The Complexity of Theorem-Proving Procedures

[Summary written by Carlo Maria Scandolo]

A decision or recognition problem concerns the issue of determining if an element (input string) is in a given set (language).
We want to study the complexity of such problems. We can do this by considering ordinary (multi-tape) Turing machines as well as
non-deterministic Turing machines. There are two main results in the paper concerning propositional logic:


The first states that every problem that can be solved in polynomial time by a non-deterministic Turing machine can be reduced to checking whether a given logical proposition expressed in disjunctive normal form is a tautology. In more modern terminology, we would say that checking if a logical proposition in the disjunctive normal form is a tautology is NP-complete. In other words, if we solve the tautology problem, we also solve also all problems in the NP class, namely all problems that can be
solved in polynomial time by a non-deterministic Turing machine.

The second result establishes that checking whether a logical proposition is a tautology in its disjunctive normal form has the same degree of difficulty of the following problems:

  1. checking whether a proposition (expressed in any form) is a
    tautology;
  2. checking whether a proposition in disjunctive normal form where each disjunct has at most three conjunctions is a tautology;
  3. given two finite undirected graphs, checking whether the former is isomorphic to a subgraph of the latter.

To sum up, in general, it is a hard problem to determine if a given
logical proposition is a tautology even if it is expressed in disjunctive normal forms. Another consequence is that it is fruitless to develop a polynomial algorithm for solving the subgraph isomorphism decision problem on a deterministic Turing machine: it is isomorphic to the tautology problem.

Bibliography
S. A. Cook, The Complexity of Theorem-Proving Procedures, Proceedings
of the third annual ACM symposium on theory of computing, 1971

Keynes: General Theory, chapters 10-12

[Summary by Ulla S. Koch]

Chapter 10: The marginal propensity to consume and the multiplier

The MPC is based on the psychological assumption that tendency to increase/decrease consumption in sync with real income. MPC is defined as the change in comsumtion divided by the change in income. (If I earn an extra 100 kr and spend 80 – my MPC is 0.8). An increase in production means increase in income means increase in spending means increase in production etc. This benign circle gives the multiplier = 1/1-MPC in this example it would 1/0.2 = 5. So every extra kr. I earn generates 5 kr extra income in Denmark – if I only buy Danish stuff. Spending on imoprts adversely affects the multiplier effect.
MPC is subject to psychological and political influences, and is liable to decrease as incomes and employment levels rise.
In situations with underemployment the benificient effect of public works is largest, since the MPC and the multiplier at the margin is very large. If politics are against public invest ment, even burying bottles with money and leasing the right to excavate for them would have positive effect on employment. Gold mining and wars are example of private/public futile investments that fuel the economy. Building pyramids thus a paramount example of good public works, they do not “stale with abundance”. (Sounds like the mechanism of service economy?)

Chapter 11: The marginal efficiency of capital

Seems to me to be investment theory.
The marginal efficiency (MEC) is “equal to that rate of discount which would make the present value of the series of annuities given by the return expected from the capital asset during its life just equal to its supply.” I.e. the expected rate of profit. In other words, the marginal efficiency of a capital asset is the rate at which the prospective yield expected from one additional unit (marginal unit) of the asset must be discounted if it is just equal to the cost, that is, the supply price of that asset.
So, you invest, if the percentage you earn from an investment (calculating its present day value) is higher that what you would earn by the discount rate.
The MEC is the factor through which “the expectation of the future influences the present” through the demand price for surable equipment.

Chapter 12: The state of long-term expectations.

An excursion into psychology. MJK distinguishes between short-term (day to day, ch. 5) and long term expectations. He describes the function of the state of confidence, a psychological factor which influence investment. Cold calculation is not in itself enough to make people invest, without an element of gambling and pride of achievement no pyramids would be built. Historically, an investment was hard to reevaluate or change after being made. The introduction of the stock market changed that. The investment for the individual is based on reliance on the convention that changes are not drastic and that the future can be extrapolated from the present, with only minor, often foreseeable, changes. However, in the stock market investment is made by people who have no actual knowledge of the businesses they invest in, i.e. the general evaluation of prospects is unreliable. Stock markets are prey to ephemeral phenomena (e.g. ice in summer) which cause fluctuations, just as it is prey to moods (“psychology”), which means long term evaluation is unreliable.
JMK compares the expert trading the stock market with someone playing musical chairs. Or with a contest for picking the six pretiest faces, which does not entail choosing the ones you yourself fancy, but those you second guess others will. (Is there some element of game theory here? In effect this means no long term expectations?)
Speculation is forecasting the psychology of the market. Speculators invest not for “income”, but for a rise in popular evaluation of the investment – they are interested in what “average opinion expects average opinion to be”. Speculation is the evil of modern investment markets – an investment should have the permanency of a marriage. A cure for crisis of confidence would be to compel people to either consume or order production of specific capital asset.
MJK points out that our decision making is often based on “animal spirits” rather than calculation of quantitative probabilities (yup – cognitive illusions, Kahnemann). He advises the state take more responsibility for organising invest ment, since it has better information at its disposal.

(Note: Since I read the Gutenberg free PDF, my page numbers do not correspond to the printed edition used by the rest of the reading group)

Summarizing a Lecture by Von Neumann given in 1948 on the theory of Automata

[Summary written by Patrick Gemmell]

We read The General and Logical Theory of Automata, a lecture given by John Von Neumann at the Hixon Symposium, Pasadena, in September, 1948. (At about 40 pages, we can only assume the talk finished some time in 1949.)

In actual fact, the lecture was fairly entertaining from a historical perspective, and gives some sort of idea of the direction people thought computing, neuroscience, and AI might have been going in 1948.

First off, JVN (John Von Neumann) was keen to argue for an axiomatic black box approach to understanding biology and brains. In particular, he saw brains as collections of about 10 billion black boxes that emitted pulses and behaved in an essentially digital fashion. (The figure for the number of neurons is, as far as we know, roughly correct, though it must be said that neurons are often modelled in more detail, e.g. using the Hodgkin-Huxley model, for which the Nobel Prize was awarded in ‘63.) Amusingly, JVN described the computer as smaller than the brain “in the sense which really matters,” i.e. switching complexity. Today the computer is smaller in both senses (a modern A8 chip from an iPhone has about 1 billion switches) though tomorrow it may be the brain which will be smaller in the “only sense that matters.”

JVN also took time to contrast analogous machines (analogue computers, where numbers are represented by physical quantities such as current, rotation, or fluid) with digital ones. According to JVN, the main advantage of digital machines is that they can conduct calculations to whatever precision we design them to, while the analogous machines always have, in practice, a fairly limited signal to noise ratio. On the other hand, JVN pointed out that each step involved in a digital calculation must be correct or else errors can be very large: interestingly, JVN could think of no other human endeavour where the result essentially depends on a sequence of a billion steps. Nor could we, can you? Today most people seem to have forgotten about both of these interesting characteristics of digital computers and merely take them for granted.

In the talk, JVN was prescient about future developments in some ways but missed the mark in others. For example, JVN was clear that it is important to determine the number of steps needed in a computing procedure (a la computational complexity theory) rather than just whether a procedure can be computed in principle (a la computability theory/Turing ‘36). On the other hand, JVN though that an equally important development would be to take account of the non-zero probability of errors at intermediate steps in a computation. Today, algorithms are usually accompanied by descriptions of their complexity but no one really worries about the probability of failure, as this is taken account of using coding layers, transmission protocols, and hardware redundancy. JVN also thought that there was “no doubt” that one can design self repairing machines though today self-healing computers remain a daydream so that, again, we tend to rely on redundancy more than anything more organically inspired.

Towards the end of his talk, JVN discussed self reproducing automata and neuroscience. This was perhaps the most interesting part of the reading because JVN was opinionated, and may yet be proved right. [JVN’s stance seems to reflect his interest in natural science and appears in contrast to Turing’s, as well as the major thread of AI that dominated the post-cybernetics/ pre-connectionist eras.] First, JVN thought it unfortunate that computation was so closely connected to formal logic, which he thought of as a rigid, combinatorial field, divorced from the more cultivated area of number and analysis. Second, JVN though that, given biology’s success at dealing with abstract concepts, logic and computing would eventually borrow more from neuroscience than neuroscience would from formal logic. While there have been many advances on the logical side of computing since 1948, it does seem that today more excitement is being generated by deep learning or hierarchical Bayesian modelling than is being generated by symbolic AI; certainly, if an undergraduate were asked to solve JVN’s example problem of recognising triangles, they would be much more likely to train up a neural network than they would be to think about how to describe the attributes of geometric objects in logical terms. On the other hand, the majority of computing is not (yet!) AI, and logical/discrete techniques developed since JVN’s talk support the bulk of the big ideas in the computer science curriculum such as languages, automata, compilers, formal verification, database theory, operating systems, and so on.

JVN’s talk finished with a discussion of self replicating machines. Here JVN explained that all one needs to make self replicating machines is (a) a machine that fabricates the machine described on a blueprint, (b) a machine that duplicates blueprints, and (c) a machine that takes a blueprint, feeds it to a manufacturing machine (a), copies it in copying machine (b), and then shoves the newly copied blueprint into the newly minted machine. Here we were finally a little incredulous, and decided that JVN’s black box thinking had gone a little too far: now everything interesting was happening inside the black box. Perhaps we should read about the Universal Constructor next