Given its status as a classic problem and its importance to both theoreticians and practitioners, edit distance provides an excellent lens through which to understand how the theoretical analysis of algorithms impacts practical implementations. From an applied perspective, the goals of theoretical analysis are to predict the empirical performance of an algorithm and to serve as a yardstick to design novel algorithms that perform well in practice. In this paper, we systematically survey the types of theoretical analysis techniques that have been applied to edit distance and evaluate the extent to which each one has achieved these two goals. These techniques include traditional worst-case analysis, worst-case analysis parametrized by edit distance or entropy or compressibility, average-case analysis, semi-random models, and advice-based models. We find that the track record is mixed. On one hand, two algorithms widely used in practice have been born out of theoretical analysis and their empirical performance is captured well by theoretical predictions. On the other hand, all the algorithms developed using theoretical analysis as a yardstick since then have not had any practical relevance. We conclude by discussing the remaining open problems and how they can be tackled.

The approximate uniform sampling of graph realizations with a given degree sequence is an everyday task in several social science, computer science, engineering etc. projects. One approach is using Markov chains. The best available current result about the well-studied switch Markov chain is that it is rapidly mixing on P-stable degree sequences (see DOI:10.1016/j.ejc.2021.103421). The switch Markov chain does not change any degree sequence. However, there are cases where degree intervals are specified rather than a single degree sequence. (A natural scenario where this problem arises is in hypothesis testing on social networks that are only partially observed.) Rechner, Strowick, and M\"uller-Hannemann introduced in 2018 the notion of degree interval Markov chain which uses three (separately well-studied) local operations (switch, hinge-flip and toggle), and employing on degree sequence realizations where any two sequences under scrutiny have very small coordinate-wise distance. Recently Amanatidis and Kleer published a beautiful paper (arXiv:2110.09068), showing that the degree interval Markov chain is rapidly mixing if the sequences are coming from a system of very thin intervals which are centered not far from a regular degree sequence. In this paper we extend substantially their result, showing that the degree interval Markov chain is rapidly mixing if the intervals are centred at P-stable degree sequences.

In this paper we introduce a new approach to discrete-time semi-Markov decision processes based on the sojourn time process. Different characterizations of discrete-time semi-Markov processes are exploited and decision processes are constructed by their means. With this new approach, the agent is allowed to consider different actions depending also on the sojourn time of the process in the current state. A numerical method based on $Q$-learning algorithms for finite horizon reinforcement learning and stochastic recursive relations is investigated. Finally, we consider two toy examples: one in which the reward depends on the sojourn-time, according to the gambler's fallacy; the other in which the environment is semi-Markov even if the reward function does not depend on the sojourn time. These are used to carry on some numerical evaluations on the previously presented $Q$-learning algorithm and on a different naive method based on deep reinforcement learning.

Common tasks encountered in epidemiology, including disease incidence estimation and causal inference, rely on predictive modeling. Constructing a predictive model can be thought of as learning a prediction function, i.e., a function that takes as input covariate data and outputs a predicted value. Many strategies for learning these functions from data are available, from parametric regressions to machine learning algorithms. It can be challenging to choose an approach, as it is impossible to know in advance which one is the most suitable for a particular dataset and prediction task at hand. The super learner (SL) is an algorithm that alleviates concerns over selecting the one "right" strategy while providing the freedom to consider many of them, such as those recommended by collaborators, used in related research, or specified by subject-matter experts. It is an entirely pre-specified and data-adaptive strategy for predictive modeling. To ensure the SL is well-specified for learning the prediction function, the analyst does need to make a few important choices. In this Education Corner article, we provide step-by-step guidelines for making these choices, walking the reader through each of them and providing intuition along the way. In doing so, we aim to empower the analyst to tailor the SL specification to their prediction task, thereby ensuring their SL performs as well as possible. A flowchart provides a concise, easy-to-follow summary of key suggestions and heuristics, based on our accumulated experience, and guided by theory.

Tokenization is an important text preprocessing step to prepare input tokens for deep language models. WordPiece and BPE are de facto methods employed by important models, such as BERT and GPT. However, the impact of tokenization can be different for morphologically rich languages, such as Turkic languages, where many words can be generated by adding prefixes and suffixes. We compare five tokenizers at different granularity levels, i.e. their outputs vary from smallest pieces of characters to the surface form of words, including a Morphological-level tokenizer. We train these tokenizers and pretrain medium-sized language models using RoBERTa pretraining procedure on the Turkish split of the OSCAR corpus. We then fine-tune our models on six downstream tasks. Our experiments, supported by statistical tests, reveal that Morphological-level tokenizer has challenging performance with de facto tokenizers. Furthermore, we find that increasing the vocabulary size improves the performance of Morphological and Word-level tokenizers more than that of de facto tokenizers. The ratio of the number of vocabulary parameters to the total number of model parameters can be empirically chosen as 20% for de facto tokenizers and 40% for other tokenizers to obtain a reasonable trade-off between model size and performance.

Reinforcement learning (RL) has shown promise as a tool for engineering safe, ethical, or legal behaviour in autonomous agents. Its use typically relies on assigning punishments to state-action pairs that constitute unsafe or unethical choices. Despite this assignment being a crucial step in this approach, however, there has been limited discussion on generalizing the process of selecting punishments and deciding where to apply them. In this paper, we adopt an approach that leverages an existing framework -- the normative supervisor of (Neufeld et al., 2021) -- during training. This normative supervisor is used to dynamically translate states and the applicable normative system into defeasible deontic logic theories, feed these theories to a theorem prover, and use the conclusions derived to decide whether or not to assign a punishment to the agent. We use multi-objective RL (MORL) to balance the ethical objective of avoiding violations with a non-ethical objective; we will demonstrate that our approach works for a multiplicity of MORL techniques, and show that it is effective regardless of the magnitude of the punishment we assign.

In this paper we get error bounds for fully discrete approximations of infinite horizon problems via the dynamic programming approach. It is well known that considering a time discretization with a positive step size $h$ an error bound of size $h$ can be proved for the difference between the value function (viscosity solution of the Hamilton-Jacobi-Bellman equation corresponding to the infinite horizon) and the value function of the discrete time problem. However, including also a spatial discretization based on elements of size $k$ an error bound of size $O(k/h)$ can be found in the literature for the error between the value functions of the continuous problem and the fully discrete problem. In this paper we revise the error bound of the fully discrete method and prove, under similar assumptions to those of the time discrete case, that the error of the fully discrete case is in fact $O(h+k)$ which gives first order in time and space for the method. This error bound matches the numerical experiments of many papers in the literature in which the behaviour $1/h$ from the bound $O(k/h)$ have not been observed.

Many forms of dependence manifest themselves over time, with behavior of variables in dynamical systems as a paradigmatic example. This paper studies temporal dependence in dynamical systems from a logical perspective, by extending a minimal modal base logic of static functional dependencies. We define a logic for dynamical systems with single time steps, provide a complete axiomatic proof calculus, and show the decidability of the satisfiability problem for a substantial fragment. The system comes in two guises: modal and first-order, that naturally complement each other. Next, we consider a timed semantics for our logic, as an intermediate between state spaces and temporal universes for the unfoldings of a dynamical system. We prove completeness and decidability by combining techniques from dynamic-epistemic logic and modal logic of functional dependencies with complex terms for objects. Also, we extend these results to the timed logic with functional symbols and term identity. Finally, we conclude with a brief outlook on how the system proposed here connects with richer temporal logics of system behavior, and with dynamic topological logic.

Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use the variational approach to conformation dynamics to discover the slowest dynamical modes of the simulations. This allows the different metastable states of the system to be located and organized hierarchically. The physical descriptors that characterize metastable states are discovered by means of a machine learning method. We show in the cases of two proteins, Chignolin and Bovine Pancreatic Trypsin Inhibitor, how such analysis can be effortlessly performed in a matter of seconds. Another strength of our approach is that it can be applied to the analysis of both unbiased and biased simulations.

We recall some of the history of the information-theoretic approach to deriving core results in probability theory and indicate parts of the recent resurgence of interest in this area with current progress along several interesting directions. Then we give a new information-theoretic proof of a finite version of de Finetti's classical representation theorem for finite-valued random variables. We derive an upper bound on the relative entropy between the distribution of the first $k$ in a sequence of $n$ exchangeable random variables, and an appropriate mixture over product distributions. The mixing measure is characterised as the law of the empirical measure of the original sequence, and de Finetti's result is recovered as a corollary. The proof is nicely motivated by the Gibbs conditioning principle in connection with statistical mechanics, and it follows along an appealing sequence of steps. The technical estimates required for these steps are obtained via the use of a collection of combinatorial tools known within information theory as `the method of types.'

Given its status as a classic problem and its importance to both theoreticians and practitioners, edit distance provides an excellent lens through which to understand how the theoretical analysis of algorithms impacts practical implementations. From an applied perspective, the goals of theoretical analysis are to predict the empirical performance of an algorithm and to serve as a yardstick to design novel algorithms that perform well in practice. In this paper, we systematically survey the types of theoretical analysis techniques that have been applied to edit distance and evaluate the extent to which each one has achieved these two goals. These techniques include traditional worst-case analysis, worst-case analysis parametrized by edit distance or entropy or compressibility, average-case analysis, semi-random models, and advice-based models. We find that the track record is mixed. On one hand, two algorithms widely used in practice have been born out of theoretical analysis and their empirical performance is captured well by theoretical predictions. On the other hand, all the algorithms developed using theoretical analysis as a yardstick since then have not had any practical relevance. We conclude by discussing the remaining open problems and how they can be tackled.

The approximate uniform sampling of graph realizations with a given degree sequence is an everyday task in several social science, computer science, engineering etc. projects. One approach is using Markov chains. The best available current result about the well-studied switch Markov chain is that it is rapidly mixing on P-stable degree sequences (see DOI:10.1016/j.ejc.2021.103421). The switch Markov chain does not change any degree sequence. However, there are cases where degree intervals are specified rather than a single degree sequence. (A natural scenario where this problem arises is in hypothesis testing on social networks that are only partially observed.) Rechner, Strowick, and M\"uller-Hannemann introduced in 2018 the notion of degree interval Markov chain which uses three (separately well-studied) local operations (switch, hinge-flip and toggle), and employing on degree sequence realizations where any two sequences under scrutiny have very small coordinate-wise distance. Recently Amanatidis and Kleer published a beautiful paper (arXiv:2110.09068), showing that the degree interval Markov chain is rapidly mixing if the sequences are coming from a system of very thin intervals which are centered not far from a regular degree sequence. In this paper we extend substantially their result, showing that the degree interval Markov chain is rapidly mixing if the intervals are centred at P-stable degree sequences.

In this paper we introduce a new approach to discrete-time semi-Markov decision processes based on the sojourn time process. Different characterizations of discrete-time semi-Markov processes are exploited and decision processes are constructed by their means. With this new approach, the agent is allowed to consider different actions depending also on the sojourn time of the process in the current state. A numerical method based on $Q$-learning algorithms for finite horizon reinforcement learning and stochastic recursive relations is investigated. Finally, we consider two toy examples: one in which the reward depends on the sojourn-time, according to the gambler's fallacy; the other in which the environment is semi-Markov even if the reward function does not depend on the sojourn time. These are used to carry on some numerical evaluations on the previously presented $Q$-learning algorithm and on a different naive method based on deep reinforcement learning.

Common tasks encountered in epidemiology, including disease incidence estimation and causal inference, rely on predictive modeling. Constructing a predictive model can be thought of as learning a prediction function, i.e., a function that takes as input covariate data and outputs a predicted value. Many strategies for learning these functions from data are available, from parametric regressions to machine learning algorithms. It can be challenging to choose an approach, as it is impossible to know in advance which one is the most suitable for a particular dataset and prediction task at hand. The super learner (SL) is an algorithm that alleviates concerns over selecting the one "right" strategy while providing the freedom to consider many of them, such as those recommended by collaborators, used in related research, or specified by subject-matter experts. It is an entirely pre-specified and data-adaptive strategy for predictive modeling. To ensure the SL is well-specified for learning the prediction function, the analyst does need to make a few important choices. In this Education Corner article, we provide step-by-step guidelines for making these choices, walking the reader through each of them and providing intuition along the way. In doing so, we aim to empower the analyst to tailor the SL specification to their prediction task, thereby ensuring their SL performs as well as possible. A flowchart provides a concise, easy-to-follow summary of key suggestions and heuristics, based on our accumulated experience, and guided by theory.

Tokenization is an important text preprocessing step to prepare input tokens for deep language models. WordPiece and BPE are de facto methods employed by important models, such as BERT and GPT. However, the impact of tokenization can be different for morphologically rich languages, such as Turkic languages, where many words can be generated by adding prefixes and suffixes. We compare five tokenizers at different granularity levels, i.e. their outputs vary from smallest pieces of characters to the surface form of words, including a Morphological-level tokenizer. We train these tokenizers and pretrain medium-sized language models using RoBERTa pretraining procedure on the Turkish split of the OSCAR corpus. We then fine-tune our models on six downstream tasks. Our experiments, supported by statistical tests, reveal that Morphological-level tokenizer has challenging performance with de facto tokenizers. Furthermore, we find that increasing the vocabulary size improves the performance of Morphological and Word-level tokenizers more than that of de facto tokenizers. The ratio of the number of vocabulary parameters to the total number of model parameters can be empirically chosen as 20% for de facto tokenizers and 40% for other tokenizers to obtain a reasonable trade-off between model size and performance.

Reinforcement learning (RL) has shown promise as a tool for engineering safe, ethical, or legal behaviour in autonomous agents. Its use typically relies on assigning punishments to state-action pairs that constitute unsafe or unethical choices. Despite this assignment being a crucial step in this approach, however, there has been limited discussion on generalizing the process of selecting punishments and deciding where to apply them. In this paper, we adopt an approach that leverages an existing framework -- the normative supervisor of (Neufeld et al., 2021) -- during training. This normative supervisor is used to dynamically translate states and the applicable normative system into defeasible deontic logic theories, feed these theories to a theorem prover, and use the conclusions derived to decide whether or not to assign a punishment to the agent. We use multi-objective RL (MORL) to balance the ethical objective of avoiding violations with a non-ethical objective; we will demonstrate that our approach works for a multiplicity of MORL techniques, and show that it is effective regardless of the magnitude of the punishment we assign.

In this paper we get error bounds for fully discrete approximations of infinite horizon problems via the dynamic programming approach. It is well known that considering a time discretization with a positive step size $h$ an error bound of size $h$ can be proved for the difference between the value function (viscosity solution of the Hamilton-Jacobi-Bellman equation corresponding to the infinite horizon) and the value function of the discrete time problem. However, including also a spatial discretization based on elements of size $k$ an error bound of size $O(k/h)$ can be found in the literature for the error between the value functions of the continuous problem and the fully discrete problem. In this paper we revise the error bound of the fully discrete method and prove, under similar assumptions to those of the time discrete case, that the error of the fully discrete case is in fact $O(h+k)$ which gives first order in time and space for the method. This error bound matches the numerical experiments of many papers in the literature in which the behaviour $1/h$ from the bound $O(k/h)$ have not been observed.

Many forms of dependence manifest themselves over time, with behavior of variables in dynamical systems as a paradigmatic example. This paper studies temporal dependence in dynamical systems from a logical perspective, by extending a minimal modal base logic of static functional dependencies. We define a logic for dynamical systems with single time steps, provide a complete axiomatic proof calculus, and show the decidability of the satisfiability problem for a substantial fragment. The system comes in two guises: modal and first-order, that naturally complement each other. Next, we consider a timed semantics for our logic, as an intermediate between state spaces and temporal universes for the unfoldings of a dynamical system. We prove completeness and decidability by combining techniques from dynamic-epistemic logic and modal logic of functional dependencies with complex terms for objects. Also, we extend these results to the timed logic with functional symbols and term identity. Finally, we conclude with a brief outlook on how the system proposed here connects with richer temporal logics of system behavior, and with dynamic topological logic.

Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use the variational approach to conformation dynamics to discover the slowest dynamical modes of the simulations. This allows the different metastable states of the system to be located and organized hierarchically. The physical descriptors that characterize metastable states are discovered by means of a machine learning method. We show in the cases of two proteins, Chignolin and Bovine Pancreatic Trypsin Inhibitor, how such analysis can be effortlessly performed in a matter of seconds. Another strength of our approach is that it can be applied to the analysis of both unbiased and biased simulations.

We recall some of the history of the information-theoretic approach to deriving core results in probability theory and indicate parts of the recent resurgence of interest in this area with current progress along several interesting directions. Then we give a new information-theoretic proof of a finite version of de Finetti's classical representation theorem for finite-valued random variables. We derive an upper bound on the relative entropy between the distribution of the first $k$ in a sequence of $n$ exchangeable random variables, and an appropriate mixture over product distributions. The mixing measure is characterised as the law of the empirical measure of the original sequence, and de Finetti's result is recovered as a corollary. The proof is nicely motivated by the Gibbs conditioning principle in connection with statistical mechanics, and it follows along an appealing sequence of steps. The technical estimates required for these steps are obtained via the use of a collection of combinatorial tools known within information theory as `the method of types.'

Given its status as a classic problem and its importance to both theoreticians and practitioners, edit distance provides an excellent lens through which to understand how the theoretical analysis of algorithms impacts practical implementations. From an applied perspective, the goals of theoretical analysis are to predict the empirical performance of an algorithm and to serve as a yardstick to design novel algorithms that perform well in practice. In this paper, we systematically survey the types of theoretical analysis techniques that have been applied to edit distance and evaluate the extent to which each one has achieved these two goals. These techniques include traditional worst-case analysis, worst-case analysis parametrized by edit distance or entropy or compressibility, average-case analysis, semi-random models, and advice-based models. We find that the track record is mixed. On one hand, two algorithms widely used in practice have been born out of theoretical analysis and their empirical performance is captured well by theoretical predictions. On the other hand, all the algorithms developed using theoretical analysis as a yardstick since then have not had any practical relevance. We conclude by discussing the remaining open problems and how they can be tackled.

The approximate uniform sampling of graph realizations with a given degree sequence is an everyday task in several social science, computer science, engineering etc. projects. One approach is using Markov chains. The best available current result about the well-studied switch Markov chain is that it is rapidly mixing on P-stable degree sequences (see DOI:10.1016/j.ejc.2021.103421). The switch Markov chain does not change any degree sequence. However, there are cases where degree intervals are specified rather than a single degree sequence. (A natural scenario where this problem arises is in hypothesis testing on social networks that are only partially observed.) Rechner, Strowick, and M\"uller-Hannemann introduced in 2018 the notion of degree interval Markov chain which uses three (separately well-studied) local operations (switch, hinge-flip and toggle), and employing on degree sequence realizations where any two sequences under scrutiny have very small coordinate-wise distance. Recently Amanatidis and Kleer published a beautiful paper (arXiv:2110.09068), showing that the degree interval Markov chain is rapidly mixing if the sequences are coming from a system of very thin intervals which are centered not far from a regular degree sequence. In this paper we extend substantially their result, showing that the degree interval Markov chain is rapidly mixing if the intervals are centred at P-stable degree sequences.

In this paper we introduce a new approach to discrete-time semi-Markov decision processes based on the sojourn time process. Different characterizations of discrete-time semi-Markov processes are exploited and decision processes are constructed by their means. With this new approach, the agent is allowed to consider different actions depending also on the sojourn time of the process in the current state. A numerical method based on $Q$-learning algorithms for finite horizon reinforcement learning and stochastic recursive relations is investigated. Finally, we consider two toy examples: one in which the reward depends on the sojourn-time, according to the gambler's fallacy; the other in which the environment is semi-Markov even if the reward function does not depend on the sojourn time. These are used to carry on some numerical evaluations on the previously presented $Q$-learning algorithm and on a different naive method based on deep reinforcement learning.

Common tasks encountered in epidemiology, including disease incidence estimation and causal inference, rely on predictive modeling. Constructing a predictive model can be thought of as learning a prediction function, i.e., a function that takes as input covariate data and outputs a predicted value. Many strategies for learning these functions from data are available, from parametric regressions to machine learning algorithms. It can be challenging to choose an approach, as it is impossible to know in advance which one is the most suitable for a particular dataset and prediction task at hand. The super learner (SL) is an algorithm that alleviates concerns over selecting the one "right" strategy while providing the freedom to consider many of them, such as those recommended by collaborators, used in related research, or specified by subject-matter experts. It is an entirely pre-specified and data-adaptive strategy for predictive modeling. To ensure the SL is well-specified for learning the prediction function, the analyst does need to make a few important choices. In this Education Corner article, we provide step-by-step guidelines for making these choices, walking the reader through each of them and providing intuition along the way. In doing so, we aim to empower the analyst to tailor the SL specification to their prediction task, thereby ensuring their SL performs as well as possible. A flowchart provides a concise, easy-to-follow summary of key suggestions and heuristics, based on our accumulated experience, and guided by theory.

Tokenization is an important text preprocessing step to prepare input tokens for deep language models. WordPiece and BPE are de facto methods employed by important models, such as BERT and GPT. However, the impact of tokenization can be different for morphologically rich languages, such as Turkic languages, where many words can be generated by adding prefixes and suffixes. We compare five tokenizers at different granularity levels, i.e. their outputs vary from smallest pieces of characters to the surface form of words, including a Morphological-level tokenizer. We train these tokenizers and pretrain medium-sized language models using RoBERTa pretraining procedure on the Turkish split of the OSCAR corpus. We then fine-tune our models on six downstream tasks. Our experiments, supported by statistical tests, reveal that Morphological-level tokenizer has challenging performance with de facto tokenizers. Furthermore, we find that increasing the vocabulary size improves the performance of Morphological and Word-level tokenizers more than that of de facto tokenizers. The ratio of the number of vocabulary parameters to the total number of model parameters can be empirically chosen as 20% for de facto tokenizers and 40% for other tokenizers to obtain a reasonable trade-off between model size and performance.

Reinforcement learning (RL) has shown promise as a tool for engineering safe, ethical, or legal behaviour in autonomous agents. Its use typically relies on assigning punishments to state-action pairs that constitute unsafe or unethical choices. Despite this assignment being a crucial step in this approach, however, there has been limited discussion on generalizing the process of selecting punishments and deciding where to apply them. In this paper, we adopt an approach that leverages an existing framework -- the normative supervisor of (Neufeld et al., 2021) -- during training. This normative supervisor is used to dynamically translate states and the applicable normative system into defeasible deontic logic theories, feed these theories to a theorem prover, and use the conclusions derived to decide whether or not to assign a punishment to the agent. We use multi-objective RL (MORL) to balance the ethical objective of avoiding violations with a non-ethical objective; we will demonstrate that our approach works for a multiplicity of MORL techniques, and show that it is effective regardless of the magnitude of the punishment we assign.

In this paper we get error bounds for fully discrete approximations of infinite horizon problems via the dynamic programming approach. It is well known that considering a time discretization with a positive step size $h$ an error bound of size $h$ can be proved for the difference between the value function (viscosity solution of the Hamilton-Jacobi-Bellman equation corresponding to the infinite horizon) and the value function of the discrete time problem. However, including also a spatial discretization based on elements of size $k$ an error bound of size $O(k/h)$ can be found in the literature for the error between the value functions of the continuous problem and the fully discrete problem. In this paper we revise the error bound of the fully discrete method and prove, under similar assumptions to those of the time discrete case, that the error of the fully discrete case is in fact $O(h+k)$ which gives first order in time and space for the method. This error bound matches the numerical experiments of many papers in the literature in which the behaviour $1/h$ from the bound $O(k/h)$ have not been observed.

Many forms of dependence manifest themselves over time, with behavior of variables in dynamical systems as a paradigmatic example. This paper studies temporal dependence in dynamical systems from a logical perspective, by extending a minimal modal base logic of static functional dependencies. We define a logic for dynamical systems with single time steps, provide a complete axiomatic proof calculus, and show the decidability of the satisfiability problem for a substantial fragment. The system comes in two guises: modal and first-order, that naturally complement each other. Next, we consider a timed semantics for our logic, as an intermediate between state spaces and temporal universes for the unfoldings of a dynamical system. We prove completeness and decidability by combining techniques from dynamic-epistemic logic and modal logic of functional dependencies with complex terms for objects. Also, we extend these results to the timed logic with functional symbols and term identity. Finally, we conclude with a brief outlook on how the system proposed here connects with richer temporal logics of system behavior, and with dynamic topological logic.

Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use the variational approach to conformation dynamics to discover the slowest dynamical modes of the simulations. This allows the different metastable states of the system to be located and organized hierarchically. The physical descriptors that characterize metastable states are discovered by means of a machine learning method. We show in the cases of two proteins, Chignolin and Bovine Pancreatic Trypsin Inhibitor, how such analysis can be effortlessly performed in a matter of seconds. Another strength of our approach is that it can be applied to the analysis of both unbiased and biased simulations.

We recall some of the history of the information-theoretic approach to deriving core results in probability theory and indicate parts of the recent resurgence of interest in this area with current progress along several interesting directions. Then we give a new information-theoretic proof of a finite version of de Finetti's classical representation theorem for finite-valued random variables. We derive an upper bound on the relative entropy between the distribution of the first $k$ in a sequence of $n$ exchangeable random variables, and an appropriate mixture over product distributions. The mixing measure is characterised as the law of the empirical measure of the original sequence, and de Finetti's result is recovered as a corollary. The proof is nicely motivated by the Gibbs conditioning principle in connection with statistical mechanics, and it follows along an appealing sequence of steps. The technical estimates required for these steps are obtained via the use of a collection of combinatorial tools known within information theory as `the method of types.'