סמינר מחלקתי Jim Gregory

09 במרץ 2015, 15:00 
וולפסון 206  
0
סמינר מחלקתי Jim Gregory

EE Seminar: Dr. Gillat Kol

~~(The talk will be given in English)

Speaker: Dr. Gillat Kol
Institute for Advanced Study (IAS), Princeton
Wednesday, January 14th, 2015
15:00 - 16:00
Room 011, Kitot Bldg., Faculty of Engineering

Interactive Channel Capacity

Abstract
In a profoundly influential 1948 paper, Claude Shannon defined the entropy function H, and showed that the capacity of the eps-BSC, the binary symmetric channel with crossover probability eps, is 1-H(eps). This means that one can reliably communicate n bits by sending roughly n / (1-H(eps)) bits over this channel.
The extensive study of interactive communication protocols in the last decades gives rise to the related question of finding the capacity of the eps-BSC when it is used interactively. We define interactive channel capacity as the minimal ratio between the communication required to compute a function (over a noiseless channel), and the communication required to compute the same function over the eps-BSC. We show that the interactive channel capacity is roughly 1 - c * sqrt(H(eps)), for some constant c. Our result gives the first separation between interactive and non-interactive channel capacity.
Joint work with Ran Raz.

 

14 בינואר 2015, 15:00 
חדר 011, בניין כיתות-חשמל  

סמינר מחלקתי

08 בינואר 2015, 12:00 
חדר 206 בניין וולפסון  
סמינר מחלקתי

 

Aspects of Submodular Maximization Subject to a Matroid Constraint

 

Dr. Moran Feldman- EPFL University

 

Abstract:

Submodular functions form a large natural class of set functions with applications in many fields including social networks, machine learning and game theory. Optimization of submodular functions subject to various constraints attracted much attention in recent years, both from theoretical and practical points of view. This talk considers the problem of maximizing a submodular function subject to a matroid constraint, which is a central problem demonstrating many of the modern approaches and techniques used in the field of submodular maximization. Many aspects of this problem have been studied, including its polynomial time approximability, fast (almost linear time) algorithms and online models. This talk surveys some of these aspects and explores a few of the main results obtained recently.

 

 

 

סמינר מחלקתי

31 בדצמבר 2014, 14:00 
חדר 206 בניין וולפסון  
סמינר מחלקתי

Solving routing problems using math heuristics and decomposition methods

Iris Forma-  Ph.D. student

Abstract:

Studies in the field of transportation are expanding due to the growing need of reducing costs and emission of pollution. The development of new modes of transportation in cities and the development of new ways of distribution in the supply chain present new challenging routing problems in the field of operations research. In this talk we present solution methods for two emerging routing problems: a production and distribution problem in supply chains and a repositioning problem in bike sharing systems.

Supply chain management (SCM) involves making decisions on production scheduling, inventory levels of raw materials and finished products, transportation and related aspects, with the objective of minimizing the total cost associated with these activities. While in the past, policies of different functions of the supply chain were managed separately, more recent management practice and studies recognize the advantages of coordinated decision making. We formulate the problem as a Mixed Integer Linear Program (MILP) which integrates decisions of production, inventory, and distribution of products and pick-up of raw materials. We propose and analyze three decomposition methods for solving this problem.

Bike-sharing systems allow people to rent a bicycle at one of many automatic rental stations scattered in the city, use them for a short journey and return them at any station in the city. A crucial factor for the success of a bike sharing system is its ability to meet the fluctuating demand for bicycles at each station. Thus, operators of bike sharing systems are responsible to regularly remove bicycles from some stations and transfer them to other stations, using a dedicated fleet of light trucks. We refer to this activity as repositioning bicycles and formulate it as a MILP for the case of the Static repositioning, i.e., during the night when demand is negligible. Then, we propose a three step math heuristic for solving larger networks than those that can be solved by the MILP formulation.    

This work was performed under the supervision of Prof. Michal Tzur and Dr. Tal Raviv.

 

ההרצאה תתקיים ביום חמישי 1.1.15, בשעה 12:00 בחדר 206, בנין וולפסון הנדסה, הפקולטה להנדסה, אוניברסיטת תל-אביב.

סמינר

הנדסה ביו רפואית

04 בינואר 2015, 14:15 
חדר 315 , הבניין הרב תחומי  

Daphne Weihs

Faculty of Biomedical Engineering, Technion-IIT

 

Traction force microscopy: what cell-gel mechanical interactions can tell us

 

Traction force microscopy (TFM) is a method that has been utilized in the last decade to evaluate the forces applied by cells to underlying gels. Cells utilize traction forces to adhere, move, and apply force to their environment, as part of their normal function. Variation in forces between different cell types, following treatment, or following onset of disease and can reveal dynamic structural changes within the cell that may relate to changes in cell function. The mechanical interaction of cells with their environment depends on the cell type, its current activity, and the dimensionality and stiffness of the gel. Using 2-dimensional (2D), elastic polyacrylamide gels, with fluorescent particles embedded under their surface, or 3D collagen gels with dispersed particles, we are able to quantitatively evaluate forces applied by cells. In the current talk, I will explain the TFM method and approach in 2D and in 3D gel systems, providing detailed examples from three different cell types. I will provide examples on (1) invasive cancer cells (in 2D and 3D), showing differences between cancer and benign cells (2) changes in cell-gel interactions when undifferentiated stem cells grow into a 3D embryoid body; and (3) differences between pre-adipose cells and differentiated adipocytes. The experiments highlight quantitative similarities and differences relating to cell function and activity.

 

ההרצאה תתקיים ביום ראשון ה 04.01.15 בשעה 14:15

בחדר 315 ,הבניין הרב תחומי ,אוניברסיטת תל אביב

 

סמינר

הנדסה ביו רפואית 

30 בדצמבר 2014, 14:15 
חדר 315 , הבניין הרב תחומי  

Daphne Weihs

Faculty of Biomedical Engineering, Technion-IIT

 

Traction force microscopy: what cell-gel mechanical interactions can tell us

 

Traction force microscopy (TFM) is a method that has been utilized in the last decade to evaluate the forces applied by cells to underlying gels. Cells utilize traction forces to adhere, move, and apply force to their environment, as part of their normal function. Variation in forces between different cell types, following treatment, or following onset of disease and can reveal dynamic structural changes within the cell that may relate to changes in cell function. The mechanical interaction of cells with their environment depends on the cell type, its current activity, and the dimensionality and stiffness of the gel. Using 2-dimensional (2D), elastic polyacrylamide gels, with fluorescent particles embedded under their surface, or 3D collagen gels with dispersed particles, we are able to quantitatively evaluate forces applied by cells. In the current talk, I will explain the TFM method and approach in 2D and in 3D gel systems, providing detailed examples from three different cell types. I will provide examples on (1) invasive cancer cells (in 2D and 3D), showing differences between cancer and benign cells (2) changes in cell-gel interactions when undifferentiated stem cells grow into a 3D embryoid body; and (3) differences between pre-adipose cells and differentiated adipocytes. The experiments highlight quantitative similarities and differences relating to cell function and activity.

 

ההרצאה תתקיים ביום ראשון ה 04.01.15 בשעה 14:15

בחדר 315 ,הבניין הרב תחומי ,אוניברסיטת תל אביב

סמינר

הנדסה ביו רפואית

04 בינואר 2015, 14:15 
חדר 315 , הבניין הרב תחומי  

 

 

 

אלכסנדרה דנה

תלמידת המחלקה להנדסה ביו רפואית לתואר שלישי תרצה בנושא:

Understanding and modeling mRNA translation based on ribosome profiling data

Gene expression is the process in which information encoded in the DNA is used to synthesize new proteins. Naturally, understanding, modeling and engineering this fundamental process has important contribution to every biomedical discipline, including human health and biotechnology. Gene expression has two major steps: transcription of the DNA to mRNA molecules and the translation of the mRNA molecules to proteins by molecular machines called ribosomes.

During mRNA translation ribosomes attach to the messenger RNA (mRNA) and then scan it in a sequential manner; each such scanning produces a new protein. Recently, a new experimental method - ribosome profiling was suggested for large scale study of ribosomal movement on the transcript. This method is based on next-generation sequencing and enables simultaneous estimation of the relative time ribosomes spend on the messenger RNAs of all translated transcripts in a genome, at a resolution of single nucleotides.

This work presents various new aspects of translation that were studied by analyzing ribosome profiles of thousands of genes in various organisms and their relation to translation efficiency.  Among others, I decipher the way biophysical properties of the mRNA molecules affect translation; I develop novel computational simulation of this experiment; and I suggest novel filters for analyzing these data. The reported results should improve the understanding of the translation process and also contribute towards developing new methods for gene expression engineering.

The talk is mainly based on four papers published in the recent years:  Dana and Tuller, PLoS Comput Biol. 2012; Dana and Tuller, Nucleic Acids Res. 2014; Dana and Tuller, BMC Genomics. 2014; Dana and Tuller, G3. 2014.

העבודה נעשתה בהנחיית  דר' תמיר טולר, המחלקה להנדסה ביו-רפואית, אוניברסיטת תל-אביב

 

ההרצאה תתקיים ביום ראשון 04.01.15, בשעה 14:15,

בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב

סמינר המחלקה להנדסה ביו רפואית

Traction force microscopy: what cell-gel mechanical interactions can tell us

04 בינואר 2014, 14:15 
חדר 315 , הבניין הרב תחומי  

 

Daphne Weihs

Faculty of Biomedical Engineering, Technion-IIT

 

Traction force microscopy: what cell-gel mechanical interactions can tell us

 

Traction force microscopy (TFM) is a method that has been utilized in the last decade to evaluate the forces applied by cells to underlying gels. Cells utilize traction forces to adhere, move, and apply force to their environment, as part of their normal function. Variation in forces between different cell types, following treatment, or following onset of disease and can reveal dynamic structural changes within the cell that may relate to changes in cell function. The mechanical interaction of cells with their environment depends on the cell type, its current activity, and the dimensionality and stiffness of the gel. Using 2-dimensional (2D), elastic polyacrylamide gels, with fluorescent particles embedded under their surface, or 3D collagen gels with dispersed particles, we are able to quantitatively evaluate forces applied by cells. In the current talk, I will explain the TFM method and approach in 2D and in 3D gel systems, providing detailed examples from three different cell types. I will provide examples on (1) invasive cancer cells (in 2D and 3D), showing differences between cancer and benign cells (2) changes in cell-gel interactions when undifferentiated stem cells grow into a 3D embryoid body; and (3) differences between pre-adipose cells and differentiated adipocytes. The experiments highlight quantitative similarities and differences relating to cell function and activity.

 

ההרצאה תתקיים ביום ראשון ה 04.01.15 בשעה 14:15

בחדר 315 ,הבניין הרב תחומי ,אוניברסיטת תל אביב

 

הנדסה ביו רפואית - סמינר 04.01.15

 

Understanding and modeling mRNA translation based on ribosome profiling data

04 בינואר 2014, 14:15 
חדר 315 , הבניין הרב תחומי  

תלמידת המחלקה להנדסה ביו רפואית לתואר שלישי תרצה בנושא:

Understanding and modeling mRNA translation based on ribosome profiling data

Gene expression is the process in which information encoded in the DNA is used to synthesize new proteins. Naturally, understanding, modeling and engineering this fundamental process has important contribution to every biomedical discipline, including human health and biotechnology. Gene expression has two major steps: transcription of the DNA to mRNA molecules and the translation of the mRNA molecules to proteins by molecular machines called ribosomes.

During mRNA translation ribosomes attach to the messenger RNA (mRNA) and then scan it in a sequential manner; each such scanning produces a new protein. Recently, a new experimental method - ribosome profiling was suggested for large scale study of ribosomal movement on the transcript. This method is based on next-generation sequencing and enables simultaneous estimation of the relative time ribosomes spend on the messenger RNAs of all translated transcripts in a genome, at a resolution of single nucleotides.

This work presents various new aspects of translation that were studied by analyzing ribosome profiles of thousands of genes in various organisms and their relation to translation efficiency.  Among others, I decipher the way biophysical properties of the mRNA molecules affect translation; I develop novel computational simulation of this experiment; and I suggest novel filters for analyzing these data. The reported results should improve the understanding of the translation process and also contribute towards developing new methods for gene expression engineering.

The talk is mainly based on four papers published in the recent years:  Dana and Tuller, PLoS Comput Biol. 2012; Dana and Tuller, Nucleic Acids Res. 2014; Dana and Tuller, BMC Genomics. 2014; Dana and Tuller, G3. 2014.

העבודה נעשתה בהנחיית  דר' תמיר טולר, המחלקה להנדסה ביו-רפואית, אוניברסיטת תל-אביב

 

ההרצאה תתקיים ביום ראשון 04.01.15, בשעה 14:15,

בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב

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