Segway is a widely-used method for performing automated genome annotation. Researchers usually use Segway to discover recurring patterns across multiple epigenomic datasets. Then they use Segway to annotate the genome with labels for these patterns, often called chromatin states. For example, one might learn labels for promoters, enhancers, or quiescent genomic regions from histone modification and open chromatin data.
Segway is implemented using the Graphical Models Toolkit, a flexible system for hidden Markov model and dynamic Bayesian network inference. While the prevailing use of Segway remains unsupervised annotation from epigenome data, it can also perform training, posterior probability estimation, and Viterbi decoding for a wide range of probabilistic models with a recurrent structure on a genomic axis. It can accept a wide variety of models that relate hidden and observed random variables at each genomic position with each other and neighboring positions and perform necessary inference without much additional programming.
We have developed a more configurable interface to Segway to allow its use for more diverse classes of problems, models, and algorithms. We will describe several of the extensions over a simple hidden Markov model, such as semi-Markov state durations, a transcriptome model with a reversed copy of the model for stranded data, a graph-based regularization method for incorporating long-range chromatin interaction data, a semi-supervised training approach, locus-specific prior knowledge, and modeling observations with arbitrary mixtures of Gaussians. We will use some of these examples to describe how you might develop your own models.
This document discusses common concurrency problems in Java and how to address them. It covers issues that can arise from shared mutable data being accessed without proper synchronization between threads, as well as problems related to visibility and atomicity of operations. Specific problems covered include mutable statics, double-checked locking, volatile arrays, and non-atomic operations like incrementing a long. The document provides best practices for locking, wait/notify, thread coordination, and avoiding deadlocks, spin locks, and lock contention.
This document discusses object-oriented programming concepts like classes, objects, encapsulation, and constructors. It provides an example of implementing a Time class with different constructors. The Time class encapsulates hour, minute and second variables and provides methods to set the time, and output it in universal and standard time formats. The document shows how to instantiate Time objects using various constructors, and how overloaded constructors allow initializing objects in different ways.
The Ring programming language version 1.5.4 book - Part 26 of 185Mahmoud Samir Fayed
This document discusses various file and system functions in Ring including:
- Rewind(), Fgetpos(), Fsetpos(), Clearerr(), Feof(), Ferror(), Perror(), Fgetc(), Fgets(), Fputc(), Fputs(), Ungetc(), Fread(), Fwrite(), and Fexists() functions for file handling
- System(), SystemCmd(), SysGet(), IsMSDOS(), IsWindows(), IsWindows64(), IsUnix(), IsMacOSX(), IsLinux(), IsFreeBSD(), IsAndroid(), and Windowsnl() functions for system/OS information and commands
- Examples of getting command line arguments, active source file name, and previous source file name
The Ring programming language version 1.5.2 book - Part 25 of 181Mahmoud Samir Fayed
This document summarizes Ring documentation for system functions. It describes functions to execute system commands like System() and SystemCmd(), check the operating system with functions like IsWindows() and IsLinux(), and get environment variables and file/folder paths with SysGet(), ExeFileName(), and CurrentDir(). Examples are provided to demonstrate usage of many of these functions.
This document defines a class called Clase that creates a graphical user interface for summing binary numbers. It contains methods to convert between binary and decimal representations. The Clase constructor defines the GUI layout and components, including labels, text fields, radio buttons, and buttons. An inner OyenteBoton class handles button clicks by parsing the text fields as binary, adding the numbers, converting the sum back to binary, and displaying the result.
The document discusses Java SE 7 features including Project Coin, NIO.2, invokedynamic, and Fork/Join framework. It provides examples of using try-with-resources to automatically close resources without finally blocks, and using the Fork/Join framework to easily parallelize tasks by splitting work, forking subtasks, and joining results.
The document discusses new features in Java SE 7 including Project Coin, NIO.2, invokedynamic, and try-with-resources. It also covers concurrency topics such as fork/join, executors, and synchronization patterns. Examples are provided for using fork/join tasks to sum arrays in parallel and the try-with-resources statement to ensure stream resources are closed automatically.
The Ring programming language version 1.9 book - Part 33 of 210Mahmoud Samir Fayed
This document section describes various system functions in Ring including:
- System() to execute system commands
- SysGet() to get environment variables
- Functions like IsWindows(), IsLinux() etc. to check the operating system
- Windowsnl() to get the newline string for Windows
- Getting command line arguments from sysargv
- Functions like filename() and prevfilename() to get the active source file name
This document discusses common concurrency problems in Java and how to address them. It covers issues that can arise from shared mutable data being accessed without proper synchronization between threads, as well as problems related to visibility and atomicity of operations. Specific problems covered include mutable statics, double-checked locking, volatile arrays, and non-atomic operations like incrementing a long. The document provides best practices for locking, wait/notify, thread coordination, and avoiding deadlocks, spin locks, and lock contention.
This document discusses object-oriented programming concepts like classes, objects, encapsulation, and constructors. It provides an example of implementing a Time class with different constructors. The Time class encapsulates hour, minute and second variables and provides methods to set the time, and output it in universal and standard time formats. The document shows how to instantiate Time objects using various constructors, and how overloaded constructors allow initializing objects in different ways.
The Ring programming language version 1.5.4 book - Part 26 of 185Mahmoud Samir Fayed
This document discusses various file and system functions in Ring including:
- Rewind(), Fgetpos(), Fsetpos(), Clearerr(), Feof(), Ferror(), Perror(), Fgetc(), Fgets(), Fputc(), Fputs(), Ungetc(), Fread(), Fwrite(), and Fexists() functions for file handling
- System(), SystemCmd(), SysGet(), IsMSDOS(), IsWindows(), IsWindows64(), IsUnix(), IsMacOSX(), IsLinux(), IsFreeBSD(), IsAndroid(), and Windowsnl() functions for system/OS information and commands
- Examples of getting command line arguments, active source file name, and previous source file name
The Ring programming language version 1.5.2 book - Part 25 of 181Mahmoud Samir Fayed
This document summarizes Ring documentation for system functions. It describes functions to execute system commands like System() and SystemCmd(), check the operating system with functions like IsWindows() and IsLinux(), and get environment variables and file/folder paths with SysGet(), ExeFileName(), and CurrentDir(). Examples are provided to demonstrate usage of many of these functions.
This document defines a class called Clase that creates a graphical user interface for summing binary numbers. It contains methods to convert between binary and decimal representations. The Clase constructor defines the GUI layout and components, including labels, text fields, radio buttons, and buttons. An inner OyenteBoton class handles button clicks by parsing the text fields as binary, adding the numbers, converting the sum back to binary, and displaying the result.
The document discusses Java SE 7 features including Project Coin, NIO.2, invokedynamic, and Fork/Join framework. It provides examples of using try-with-resources to automatically close resources without finally blocks, and using the Fork/Join framework to easily parallelize tasks by splitting work, forking subtasks, and joining results.
The document discusses new features in Java SE 7 including Project Coin, NIO.2, invokedynamic, and try-with-resources. It also covers concurrency topics such as fork/join, executors, and synchronization patterns. Examples are provided for using fork/join tasks to sum arrays in parallel and the try-with-resources statement to ensure stream resources are closed automatically.
The Ring programming language version 1.9 book - Part 33 of 210Mahmoud Samir Fayed
This document section describes various system functions in Ring including:
- System() to execute system commands
- SysGet() to get environment variables
- Functions like IsWindows(), IsLinux() etc. to check the operating system
- Windowsnl() to get the newline string for Windows
- Getting command line arguments from sysargv
- Functions like filename() and prevfilename() to get the active source file name
The document introduces two approaches to chemical prediction: quantum simulation based on density functional theory and machine learning based on data. It then discusses using graph-structured neural networks for chemical prediction on datasets like QM9. It presents Neural Fingerprint (NFP) and Gated Graph Neural Network (GGNN) models for predicting molecular properties from graph-structured data. Chainer Chemistry is introduced as a library for chemical and biological machine learning that implements these graph convolutional networks.
A walk through the intersection between machine learning and mechanistic mode...JuanPabloCarbajal3
Talk at EURECOM, France.
It overviews regression in several of its forms: regularized, constrained, and mixed. It builds the bridge between machine learning and dynamical models.
This document provides information about the Julia programming language. It discusses Julia's popularity, use cases in various fields like robotics and finance, benchmarks, and key features. It also demonstrates Julia code examples and highlights various Julia packages and tools for scientific computing, machine learning, and more.
This document summarizes the MATLAB Reservoir Simulation Toolbox (MRST), which provides an environment for reservoir modelling and simulation using MATLAB. MRST features fully unstructured grids, rapid prototyping capabilities through automatic differentiation and object-oriented design, and industry-standard simulation methods. It has a large international user base in both academia and industry and consists of over 50 modules and thousands of lines of code.
This document provides information about the Julia programming language. It discusses Julia's performance, use cases in different industries, available packages and tools, and ongoing development work. Key highlights include Julia's speed, its use in fields like robotics, quantitative finance, and science, and recent improvements to its machine learning and quantum computing capabilities.
[20240415_LabSeminar_Huy]Deciphering Spatio-Temporal Graph Forecasting: A Cau...thanhdowork
The document summarizes a paper that proposes a new framework called Causal Spatio-Temporal neural network (CaST) to tackle challenges in spatio-temporal graph forecasting. CaST uses a structural causal model and backdoor/frontdoor adjustments to enhance generalization for temporal out-of-distribution data and capture dynamic spatial causation. The framework was tested on traffic and air quality datasets and showed improved performance over baselines as well as providing interpretable analysis of environments and causation.
Protein functional site prediction using the shotest path graphnew1 2M Beneragama
This document summarizes a presentation on predicting protein functional sites using a shortest-path graph kernel method. The presentation introduces the problem of predicting functional sites on proteins, describes a graph-based approach to represent protein structures, and presents results applying a shortest-path graph kernel and nearest neighbor prediction methods to datasets of catalytic sites and phosphorylation sites. The approach achieved up to 77.1% accuracy on the catalytic site dataset. Future work could include adding more parameters to the graph representations and node labels, improving the method as a web service, and optimizing algorithms for large datasets.
⭐⭐⭐⭐⭐ Device Free Indoor Localization in the 28 GHz band based on machine lea...Victor Asanza
This document discusses device-free indoor localization using machine learning techniques at 28 GHz. The methodology uses ray tracing to generate fingerprint data and selects features from received power values. A random forest algorithm is used for classification and regression training on global and combined classifiers. Results show that combining independent classifiers from one or two transmitters reduces positioning error by at least 16-19% compared to global classification, and by at least 36-37% when combining two transmitters with classification-regression. The size and number of partition classes impacts error, and additional small improvements are achieved through classification-regression combination.
We approach the screening problem - i.e. detecting which inputs of a computer model significantly impact the output - from a formal Bayesian model selection point of view. That is, we place a Gaussian process prior on the computer model and consider the $2^p$ models that result from assuming that each of the subsets of the $p$ inputs affect the response. The goal is to obtain the posterior probabilities of each of these models. In this talk, we focus on the specification of objective priors on the model-specific parameters and on convenient ways to compute the associated marginal likelihoods. These two problems that normally are seen as unrelated, have challenging connections since the priors proposed in the literature are specifically designed to have posterior modes in the boundary of the parameter space, hence precluding the application of approximate integration techniques based on e.g. Laplace approximations. We explore several ways of circumventing this difficulty, comparing different methodologies with synthetic examples taken from the literature.
Authors: Gonzalo Garcia-Donato (Universidad de Castilla-La Mancha) and Rui Paulo (Universidade de Lisboa)
TEST GENERATION FOR ANALOG AND MIXED-SIGNAL CIRCUITS USING HYBRID SYSTEM MODELSVLSICS Design
In this paper we propose an approach for testing time-domain properties of analog and mixed-signal circuits. The approach is based on an adaptation of a recently developed test generation technique for hybrid systems and a new concept of coverage for such systems. The approach is illustrated by its application to some benchmark circuits.
Test Generation for Analog and Mixed-Signal Circuits Using Hybrid System Mode...VLSICS Design
In this paper we propose an approach for testing time-domain properties of analog and mixed-signal circuits. The approach is based on an adaptation of a recently developed test generation technique for hybrid systems and a new concept of coverage for such systems. The approach is illustrated by its application to some benchmark circuits.
Characterization of Subsurface Heterogeneity: Integration of Soft and Hard In...Amro Elfeki
Park, E., Elfeki, A. M. M., Dekking, F.M. (2003). Characterization of subsurface heterogeneity: Integration of soft and hard information using multi-dimensional Coupled Markov chain approach. Underground Injection Science and Technology Symposium, Lawrence Berkeley National Lab., October 22-25, 2003. p.49. Eds. Tsang, Chin.-Fu and Apps, John A.
http://www.lbl.gov/Conferences/UIST/index.html#topics
TMPA-2015: Implementing the MetaVCG Approach in the C-light SystemIosif Itkin
Alexei Promsky, Dmitry Kondtratyev, A.P. Ershov Institute of Informatics Systems, Novosibirsk
12 - 14 November 2015
Tools and Methods of Program Analysis in St. Petersburg
Convolutional networks and graph networks through kernelstuxette
This presentation discusses how convolutional kernel networks (CKNs) can be used to model sequential and graph-structured data through kernels defined over sequences and graphs. CKNs define feature maps from substructures like n-mers in sequences and paths in graphs into high-dimensional spaces, which are then approximated to obtain low-dimensional representations that can be used for prediction tasks like classification. This approach is analogous to convolutional neural networks and can be extended to multiple layers. The presentation provides examples showing CKNs achieve good performance on problems involving protein sequences and social networks.
Artificial software diversity: automatic synthesis of program sosiesFoCAS Initiative
The document discusses artificial software diversity through the automatic synthesis of program variants called "sosies". A sosie is a variant of a program that conforms to the same specification but may have different code. The document explores how to automatically generate sosies through code transformations while maintaining functional equivalence. It evaluates different transformation techniques and presents preliminary results on generating sosies for test programs. Potential applications of sosies include improving software robustness, resilience, self-repair, and creating a "moving target" to increase uncertainty for attackers.
This document describes an improved direct multiple shooting approach combined with collocation and parallel computing to handle path constraints in dynamic nonlinear optimization problems. It combines direct multiple shooting with collocation discretization to transform the dynamic optimization problem into a nonlinear programming problem. The approach discretizes the time horizon into finite elements and applies collocation at the nodes. It then uses parallel computing to simulate each time interval independently. Case studies on controlling a Van der Pol oscillator and continuous stirred tank reactor are presented to demonstrate the method.
OPTIMAL GLOBAL THRESHOLD ESTIMATION USING STATISTICAL CHANGE-POINT DETECTIONsipij
Aim of this paper is reformulation of global image thresholding problem as a well-founded statistical
method known as change-point detection (CPD) problem. Our proposed CPD thresholding algorithm does
not assume any prior statistical distribution of background and object grey levels. Further, this method is
less influenced by an outlier due to our judicious derivation of a robust criterion function depending on
Kullback-Leibler (KL) divergence measure. Experimental result shows efficacy of proposed method
compared to other popular methods available for global image thresholding. In this paper we also propose
a performance criterion for comparison of thresholding algorithms. This performance criteria does not
depend on any ground truth image. We have used this performance criterion to compare the results of
proposed thresholding algorithm with most cited global thresholding algorithms in the literature.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
The document introduces two approaches to chemical prediction: quantum simulation based on density functional theory and machine learning based on data. It then discusses using graph-structured neural networks for chemical prediction on datasets like QM9. It presents Neural Fingerprint (NFP) and Gated Graph Neural Network (GGNN) models for predicting molecular properties from graph-structured data. Chainer Chemistry is introduced as a library for chemical and biological machine learning that implements these graph convolutional networks.
A walk through the intersection between machine learning and mechanistic mode...JuanPabloCarbajal3
Talk at EURECOM, France.
It overviews regression in several of its forms: regularized, constrained, and mixed. It builds the bridge between machine learning and dynamical models.
This document provides information about the Julia programming language. It discusses Julia's popularity, use cases in various fields like robotics and finance, benchmarks, and key features. It also demonstrates Julia code examples and highlights various Julia packages and tools for scientific computing, machine learning, and more.
This document summarizes the MATLAB Reservoir Simulation Toolbox (MRST), which provides an environment for reservoir modelling and simulation using MATLAB. MRST features fully unstructured grids, rapid prototyping capabilities through automatic differentiation and object-oriented design, and industry-standard simulation methods. It has a large international user base in both academia and industry and consists of over 50 modules and thousands of lines of code.
This document provides information about the Julia programming language. It discusses Julia's performance, use cases in different industries, available packages and tools, and ongoing development work. Key highlights include Julia's speed, its use in fields like robotics, quantitative finance, and science, and recent improvements to its machine learning and quantum computing capabilities.
[20240415_LabSeminar_Huy]Deciphering Spatio-Temporal Graph Forecasting: A Cau...thanhdowork
The document summarizes a paper that proposes a new framework called Causal Spatio-Temporal neural network (CaST) to tackle challenges in spatio-temporal graph forecasting. CaST uses a structural causal model and backdoor/frontdoor adjustments to enhance generalization for temporal out-of-distribution data and capture dynamic spatial causation. The framework was tested on traffic and air quality datasets and showed improved performance over baselines as well as providing interpretable analysis of environments and causation.
Protein functional site prediction using the shotest path graphnew1 2M Beneragama
This document summarizes a presentation on predicting protein functional sites using a shortest-path graph kernel method. The presentation introduces the problem of predicting functional sites on proteins, describes a graph-based approach to represent protein structures, and presents results applying a shortest-path graph kernel and nearest neighbor prediction methods to datasets of catalytic sites and phosphorylation sites. The approach achieved up to 77.1% accuracy on the catalytic site dataset. Future work could include adding more parameters to the graph representations and node labels, improving the method as a web service, and optimizing algorithms for large datasets.
⭐⭐⭐⭐⭐ Device Free Indoor Localization in the 28 GHz band based on machine lea...Victor Asanza
This document discusses device-free indoor localization using machine learning techniques at 28 GHz. The methodology uses ray tracing to generate fingerprint data and selects features from received power values. A random forest algorithm is used for classification and regression training on global and combined classifiers. Results show that combining independent classifiers from one or two transmitters reduces positioning error by at least 16-19% compared to global classification, and by at least 36-37% when combining two transmitters with classification-regression. The size and number of partition classes impacts error, and additional small improvements are achieved through classification-regression combination.
We approach the screening problem - i.e. detecting which inputs of a computer model significantly impact the output - from a formal Bayesian model selection point of view. That is, we place a Gaussian process prior on the computer model and consider the $2^p$ models that result from assuming that each of the subsets of the $p$ inputs affect the response. The goal is to obtain the posterior probabilities of each of these models. In this talk, we focus on the specification of objective priors on the model-specific parameters and on convenient ways to compute the associated marginal likelihoods. These two problems that normally are seen as unrelated, have challenging connections since the priors proposed in the literature are specifically designed to have posterior modes in the boundary of the parameter space, hence precluding the application of approximate integration techniques based on e.g. Laplace approximations. We explore several ways of circumventing this difficulty, comparing different methodologies with synthetic examples taken from the literature.
Authors: Gonzalo Garcia-Donato (Universidad de Castilla-La Mancha) and Rui Paulo (Universidade de Lisboa)
TEST GENERATION FOR ANALOG AND MIXED-SIGNAL CIRCUITS USING HYBRID SYSTEM MODELSVLSICS Design
In this paper we propose an approach for testing time-domain properties of analog and mixed-signal circuits. The approach is based on an adaptation of a recently developed test generation technique for hybrid systems and a new concept of coverage for such systems. The approach is illustrated by its application to some benchmark circuits.
Test Generation for Analog and Mixed-Signal Circuits Using Hybrid System Mode...VLSICS Design
In this paper we propose an approach for testing time-domain properties of analog and mixed-signal circuits. The approach is based on an adaptation of a recently developed test generation technique for hybrid systems and a new concept of coverage for such systems. The approach is illustrated by its application to some benchmark circuits.
Characterization of Subsurface Heterogeneity: Integration of Soft and Hard In...Amro Elfeki
Park, E., Elfeki, A. M. M., Dekking, F.M. (2003). Characterization of subsurface heterogeneity: Integration of soft and hard information using multi-dimensional Coupled Markov chain approach. Underground Injection Science and Technology Symposium, Lawrence Berkeley National Lab., October 22-25, 2003. p.49. Eds. Tsang, Chin.-Fu and Apps, John A.
http://www.lbl.gov/Conferences/UIST/index.html#topics
TMPA-2015: Implementing the MetaVCG Approach in the C-light SystemIosif Itkin
Alexei Promsky, Dmitry Kondtratyev, A.P. Ershov Institute of Informatics Systems, Novosibirsk
12 - 14 November 2015
Tools and Methods of Program Analysis in St. Petersburg
Convolutional networks and graph networks through kernelstuxette
This presentation discusses how convolutional kernel networks (CKNs) can be used to model sequential and graph-structured data through kernels defined over sequences and graphs. CKNs define feature maps from substructures like n-mers in sequences and paths in graphs into high-dimensional spaces, which are then approximated to obtain low-dimensional representations that can be used for prediction tasks like classification. This approach is analogous to convolutional neural networks and can be extended to multiple layers. The presentation provides examples showing CKNs achieve good performance on problems involving protein sequences and social networks.
Artificial software diversity: automatic synthesis of program sosiesFoCAS Initiative
The document discusses artificial software diversity through the automatic synthesis of program variants called "sosies". A sosie is a variant of a program that conforms to the same specification but may have different code. The document explores how to automatically generate sosies through code transformations while maintaining functional equivalence. It evaluates different transformation techniques and presents preliminary results on generating sosies for test programs. Potential applications of sosies include improving software robustness, resilience, self-repair, and creating a "moving target" to increase uncertainty for attackers.
This document describes an improved direct multiple shooting approach combined with collocation and parallel computing to handle path constraints in dynamic nonlinear optimization problems. It combines direct multiple shooting with collocation discretization to transform the dynamic optimization problem into a nonlinear programming problem. The approach discretizes the time horizon into finite elements and applies collocation at the nodes. It then uses parallel computing to simulate each time interval independently. Case studies on controlling a Van der Pol oscillator and continuous stirred tank reactor are presented to demonstrate the method.
OPTIMAL GLOBAL THRESHOLD ESTIMATION USING STATISTICAL CHANGE-POINT DETECTIONsipij
Aim of this paper is reformulation of global image thresholding problem as a well-founded statistical
method known as change-point detection (CPD) problem. Our proposed CPD thresholding algorithm does
not assume any prior statistical distribution of background and object grey levels. Further, this method is
less influenced by an outlier due to our judicious derivation of a robust criterion function depending on
Kullback-Leibler (KL) divergence measure. Experimental result shows efficacy of proposed method
compared to other popular methods available for global image thresholding. In this paper we also propose
a performance criterion for comparison of thresholding algorithms. This performance criteria does not
depend on any ground truth image. We have used this performance criterion to compare the results of
proposed thresholding algorithm with most cited global thresholding algorithms in the literature.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
ESR spectroscopy in liquid food and beverages.pptx
Segway and the Graphical Models Toolkit: a framework for probabilistic genomic inference
1. Michael M. Hoffman
Princess Margaret Cancer Centre
Vector Institute
Department of Medical Biophysics
Department of Computer Science
University of Toronto
https://hoffmanlab.org/
Segway and the Graphical Models Toolkit:
A framework for probabilistic genomic inference
@michaelhoffman
#probgen18
2. Geographical maps have…
Figures from 1) National Geographic Society (2011) GIS.
street data
+ buildings data
+ vegetation data
= integrated map
Rachel Chan
30. What does Segway do, really?
1. Creates GMTKL structure and parameter files for semi-
automated genome annotation
2. Converts genomic data to a GMTK binary observation
format
3. Runs GMTK to perform EM training, Viterbi decoding,
posterior inference
4. Manages job execution via cluster (SGE, LSF, PBS,
Slurm), or local multiprocessing
5. Converts GMTK output to genomics formats (BED,
wiggle)
47. Acknowledgments
The Hoffman Lab
Jeff Bilmes
William Noble
Max Libbrecht
Funding:
Princess Margaret Cancer Foundation
Canadian Institutes of Health Research
Canadian Cancer Society
Natural Sciences and Engineering Research
Council
Ontario Institute for Cancer Research
Ontario Ministry of Research, Innovation and
Science
Medicine by Design
McLaughlin Centre
Samantha Wilson
Coby Viner
Mickaël Mendez
Danielle Denisko
Chang Cao
Lee Zamparo
Eric Roberts
Mehran Karimzadeh
Francis Nguyen
Rachel Chan
Matthew McNeil
Natalia Mukhina
48. Postdoctoral, MSc, PhD positions
available in my research lab at the
Princess Margaret Cancer Centre
Dept of Medical Biophysics
Dept of Computer Science
University of Toronto
Please approach me for details.
Michael Hoffman
https://hoffmanlab.org/
michael.hoffman@utoronto.ca
@michaelhoffman
Editor's Notes
- need laser pointer
- turn Workrave off
turn phone off
turn iPad off
Happy to answer questions in middle of talk except…
For example, geographical maps have street data…buildings data…vegetation data…all resulting in an integrated map
Semi-automated genomic annotation begins with pattern discovery from multiple genomic data sets and results in:
A simple annotation with a single label for each part of the genome using these patterns
We can use this annotation to visualise a huge number of datatracks, eg viewing the resulting patterns found and the annotation instead of looking at each datatrack individually
We can interpret the context and potential impact of the results, for example the meaning of the patterns and annotation we found.
Some questions that semi-automated annotation can answer include:
Pattern discovery: What signals from multiple experiments do we see over and over again?
Annotation: What does a particular piece of the genome do, in a nutshell?
Visualization: How can we make complex data comprehensible visually?
Interpretation: What is the context and potential impact of the results we are finding?
To perform genomic segmentation, Segway first ‘observes’ multiple datasets of genomic data.
Then, it splits the datasets up into non-overlapping segments.
To each segment, Segway assigns a label from a finite set
Segway then maximizes the similarity between segments of the same label by pushing around the boundaries of the segments. These are our ‘learned patterns’
For example, here we have a 0-label with a low-high-low pattern
1-label with a high-low-high pattern
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
DBNs can be thought of as a generalization of HMMs. This particular DBN is just another representation of an HMM. The DBN diagram itself does not contain the state transition information in an HMM diagram, but it is contained in the transition conditional probability table.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
A hidden Markov multimodel: “no longer a HMM, not yet a DBN”
dashed line = switching relationship
The default Segway model for three observations.
light blue fill = semiobserved random variable (observed random variable for the data switched by a discrete observed random variable for the nonmissingness of the data)
light blue fill = semiobserved random variable (observed random variable for the data switched by a discrete observed random variable for the nonmissingness of the data)
Discuss mixture model
light blue fill = semiobserved random variable (observed random variable for the data switched by a discrete observed random variable for the nonmissingness of the data)
light blue fill = semiobserved random variable (observed random variable for the data switched by a discrete observed random variable for the nonmissingness of the data)
And finally, I'd like to thank you for your very kind attention.