Massachusetts Institute of Technology

A Mathematical Theory of Communication

The recent development of various methods of modulation such as PCM and PPM which exchange bandwidth for signal-to-noise ratio has intensified the interest in a general theory of communication. A basis for such a theory is contained in the important papers of Nyquist1and Hartley2on this subject. In the present paper we will extend the theory to include a number of new factors, in particular the effect of noise in the channel, and the savings possible due to the statistical structure of the original message and due to the nature of the final destination of the information.

ImageNet Large Scale Visual Recognition Challenge

A Computational Approach to Edge Detection

This paper describes a computational approach to edge detection. The success of the approach depends on the definition of a comprehensive set of goals for the computation of edge points. These goals must be precise enough to delimit the desired behavior of the detector while making minimal assumptions about the form of the solution. We define detection and localization criteria for a class of edges, and present mathematical forms for these criteria as functionals on the operator impulse response. A third criterion is then added to ensure that the detector has only one response to a single edge. We use the criteria in numerical optimization to derive detectors for several common image features, including step edges. On specializing the analysis to step edges, we find that there is a natural uncertainty principle between detection and localization performance, which are the two main goals. With this principle we derive a single operator shape which is optimal at any scale. The optimal detector has a simple approximate implementation in which edges are marked at maxima in gradient magnitude of a Gaussian-smoothed image. We extend this simple detector using operators of several widths to cope with different signal-to-noise ratios in the image. We present a general method, called feature synthesis, for the fine-to-coarse integration of information from operators at different scales. Finally we show that step edge detector performance improves considerably as the operator point spread function is extended along the edge.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Multiplex Genome Engineering Using CRISPR/Cas Systems

Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

<i>The Mathematical Theory of Communication</i>

A Mathematical Theory of Communication

In this final installment of the paper we consider the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now. To a considerable extent the continuous case can be obtained through a limiting process from the discrete case by dividing the continuum of messages and signals into a large but finite number of small regions and calculating the various parameters involved on a discrete basis. As the size of the regions is decreased these parameters in general approach as limits the proper values for the continuous case. There are, however, a few new effects that appear and also a general change of emphasis in the direction of specialization of the general results to particular cases.

Physics-informed machine learning

A Model of Leptons

Received 17 October 1967DOI:https://doi.org/10.1103/PhysRevLett.19.1264©1967 American Physical Society

Adaptive background mixture models for real-time tracking

A common method for real-time segmentation of moving regions in image sequences involves "background subtraction", or thresholding the error between an estimate of the image without moving objects and the current image. The numerous approaches to this problem differ in the type of background model used and the procedure used to update the model. This paper discusses modeling each pixel as a mixture of Gaussians and using an on-line approximation to update the model. The Gaussian, distributions of the adaptive mixture model are then evaluated to determine which are most likely to result from a background process. Each pixel is classified based on whether the Gaussian distribution which represents it most effectively is considered part of the background model. This results in a stable, real-time outdoor tracker which reliably deals with lighting changes, repetitive motions from clutter, and long-term scene changes. This system has been run almost continuously for 16 months, 24 hours a day, through rain and snow.

Probabilistic graphical models : principles and techniques

Most tasks require a person or an automated system to reason -- to reach conclusions based on available information. The framework of probabilistic graphical models, presented in this book, provides a general approach for this task. The approach is model-based, allowing interpretable models to be constructed and then manipulated by reasoning algorithms. These models can also be learned automatically from data, allowing the approach to be used in cases where manually constructing a model is difficult or even impossible. Because uncertainty is an inescapable aspect of most real-world applications, the book focuses on probabilistic models, which make the uncertainty explicit and provide models that are more faithful to reality. Probabilistic Graphical Models discusses a variety of models, spanning Bayesian networks, undirected Markov networks, discrete and continuous models, and extensions to deal with dynamical systems and relational data. For each class of models, the text describes the three fundamental cornerstones: representation, inference, and learning, presenting both basic concepts and advanced techniques. Finally, the book considers the use of the proposed framework for causal reasoning and decision making under uncertainty. The main text in each chapter provides the detailed technical development of the key ideas. Most chapters also include boxes with additional material: skill boxes, which describe techniques; case study boxes, which discuss empirical cases related to the approach described in the text, including applications in computer vision, robotics, natural language understanding, and computational biology; and concept boxes, which present significant concepts drawn from the material in the chapter. Instructors (and readers) can group chapters in various combinations, from core topics to more technically advanced material, to suit their particular needs.

Optimum consumption and portfolio rules in a continuous-time model

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

The Entity Relationship Model — Toward a Unified View of Data

The entity-relationship model—toward a unified view of data

A data model, called the entity-relationship model, is proposed. This model incorporates some of the important semantic information about the real world. A special diagrammatic technique is introduced as a tool for database design. An example of database design and description using the model and the diagrammatic technique is given. Some implications for data integrity, information retrieval, and data manipulation are discussed. The entity-relationship model can be used as a basis for unification of different views of data: the network model, the relational model, and the entity set model. Semantic ambiguities in these models are analyzed. Possible ways to derive their views of data from the entity-relationship model are presented.

Doping a Mott insulator: Physics of high-temperature superconductivity

This article reviews the physics of high-temperature superconductors from the point of view of the doping of a Mott insulator. The basic electronic structure of cuprates is reviewed, emphasizing the physics of strong correlation and establishing the model of a doped Mott insulator as a starting point. A variety of experiments are discussed, focusing on the region of the phase diagram close to the Mott insulator (the underdoped region) where the behavior is most anomalous. The normal state in this region exhibits pseudogap phenomenon. In contrast, the quasiparticles in the superconducting state are well defined and behave according to theory. This review introduces Anderson's idea of the resonating valence bond and argues that it gives a qualitative account of the data. The importance of phase fluctuations is discussed, leading to a theory of the transition temperature, which is driven by phase fluctuations and the thermal excitation of quasiparticles. However, an argument is made that phase fluctuations can only explain pseudogap phenomenology over a limited temperature range, and some additional physics is needed to explain the onset of singlet formation at very high temperatures. A description of the numerical method of the projected wave function is presented, which turns out to be a very useful technique for implementing the strong correlation constraint and leads to a number of predictions which are in agreement with experiments. The remainder of the paper deals with an analytic treatment of the $t\text{\ensuremath{-}}J$ model, with the goal of putting the resonating valence bond idea on a more formal footing. The slave boson is introduced to enforce the constraint againt double occupation and it is shown that the implementation of this local constraint leads naturally to gauge theories. This review follows the historical order by first examining the U(1) formulation of the gauge theory. Some inadequacies of this formulation for underdoping are discussed, leading to the SU(2) formulation. Here follows a rather thorough discussion of the role of gauge theory in describing the spin-liquid phase of the undoped Mott insulator. The difference between the high-energy gauge group in the formulation of the problem versus the low-energy gauge group, which is an emergent phenomenon, is emphasized. Several possible routes to deconfinement based on different emergent gauge groups are discussed, which leads to the physics of fractionalization and spin-charge separation. Next the extension of the SU(2) formulation to nonzero doping is described with a focus on a part of the mean-field phase diagram called the staggered flux liquid phase. It will be shown that inclusion of the gauge fluctuation provides a reasonable description of the pseudogap phase. It is emphasized that $d$-wave superconductivity can be considered as evolving from a stable U(1) spin liquid. These ideas are applied to the high-${T}_{c}$ cuprates, and their implications for the vortex structure and the phase diagram are discussed. A possible test of the topological structure of the pseudogap phase is described.

The role of artificial intelligence in achieving the Sustainable Development Goals

The emergence of artificial intelligence (AI) and its progressively wider impact on many sectors requires an assessment of its effect on the achievement of the Sustainable Development Goals. Using a consensus-based expert elicitation process, we find that AI can enable the accomplishment of 134 targets across all the goals, but it may also inhibit 59 targets. However, current research foci overlook important aspects. The fast development of AI needs to be supported by the necessary regulatory insight and oversight for AI-based technologies to enable sustainable development. Failure to do so could result in gaps in transparency, safety, and ethical standards.

Theoretical Nuclear Physics

The Child's Learning of English Morphology

In this study we set out to discover what is learned by children exposed to English morphology. To test for knowledge of morphological rules, we use nonsense materials. We know that if the subject can supply the correct plural ending, for instance, to a noun we have made up, he has internalized a working system of the plural allomorphs in English, and is able to generalize to new cases and select the right form. If a child knows that the plural of witch is witches, he may simply have memorized the plural form. If, however, he tells us that the plural of * gutch is * gutches, we have evidence that he actually knows, albeit unconsciously, one of those rules which the descriptive linguist, too, would set forth in his grammar. And if children do have knowledge of morphological rules, how does this knowledge evolve? Is there a progression from simple, regular rules to the more irregular and qualified rules that are adequate fully to describe English? In very general terms, we undertake to discover the psychological status of a certain kind of linguistic description. It is evident that the acquisition of language is more than the storing up of rehearsed utterances, since we are all able to say what we have not practiced and what we have never before heard. In bringing descriptive linguistics to the study of language acquisition, we hope to gain knowledge of the systems and patterns used by the speaker. In order to test for children's knowledge of this sort, it was necessary to begin with an examination of their actual vocabulary. Accordingly, the 1000 most frequent words in the first-grader's vocabulary were selected from Rinsland's listing. This listing

<i>Methods of Experimental Physics</i>

Foundations for engineering biology

Event Generators for High-Energy Physics Experiments

We provide an overview of the status of Monte-Carlo event generators for high-energy particle physics. Guided by the experimental needs and requirements, we highlight areas of active development, and opportunities for future improvements. Particular emphasis is given to physics models and algorithms that are employed across a variety of experiments. These common themes in event generator development lead to a more comprehensive understanding of physics at the highest energies and intensities, and allow models to be tested against a wealth of data that have been accumulated over the past decades. A cohesive approach to event generator development will allow these models to be further improved and systematic uncertainties to be reduced, directly contributing to future experimental success. Event generators are part of a much larger ecosystem of computational tools. They typically involve a number of unknown model parameters that must be tuned to experimental data, while maintaining the integrity of the underlying physics models. Making both these data, and the analyses with which they have been obtained accessible to future users is an essential aspect of open science and data preservation. It ensures the consistency of physics models across a variety of experiments.

Out-of-plane measurements of the fifth response function of the exclusive electronuclear response

The first measurements of ${f}_{\mathrm{LT}}^{\ensuremath{'}},$ known as the fifth response function, have been made for the ${}^{2}\mathrm{H}(\stackrel{\ensuremath{\rightarrow}}{e}{,e}^{\ensuremath{'}}p)$ and ${}^{12}\mathrm{C}(\stackrel{\ensuremath{\rightarrow}}{e}{,e}^{\ensuremath{'}}p)$ reactions. This response is directly related to the imaginary part of the interference between the transverse and longitudinal nuclear electromagnetic currents. Its observation requires longitudinally polarized electron beams and out-of-plane detection, the latter made possible by the newly developed out-of-plane spectrometer system. The initial measurements were made by using a 560-MeV polarized electron beam and quasielastic kinematics at ${Q}^{2}=3.3 {\mathrm{fm}}^{\ensuremath{-}2}.$ The development of the methodology for out-of-plane physics, and the analysis of the data from the initial experiments are described in detail. The measured fifth response and the related asymmetry in the coincidence cross section are in agreement, albeit with large statistical errors, with the theoretical predictions. Future extensions of the out-of-plane program are also discussed.

Proton transparency and neutrino physics: New methods and modeling

Extracting accurate results from neutrino oscillation and cross section experiments requires accurate simulation of the neutrino-nucleus interaction. The rescattering of outgoing hadrons (final state interactions) by the rest of the nucleus is an important component of these interactions. We present a new measurement of proton transparency (defined as the fraction of outgoing protons that emerge without significant rescattering) using electron-nucleus scattering data recorded by the CLAS detector at Jefferson Laboratory on helium, carbon, and iron targets. This analysis uses a new data-driven method to extract the transparency. It defines transparency as the ratio of electron-scattering events with a detected proton to quasi-elastic electron-scattering events where a proton should have been knocked out. Our results are consistent with previous measurements that determined the transparency from the ratio of measured events to theoretically predicted events. We find that the GENIE event generator, which is widely used by oscillation experiments to simulate neutrino-nucleus interactions, needs to better describe both the nuclear ground state and proton rescattering in order to reproduce our measured transparency ratios, especially at lower proton momenta.