Inferring the immune systems dynamics from high throughput antibody sequencing data

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

דר' גור יערי

אוניברסיטת בר אילן

 

Inferring the immune systems dynamics from high throughput antibody sequencing data

The ability of our immune system to recognize threats is critical to survival. It operates through clonal expansion and selection of lymphocytes (B and T cells), that produce an immense, diverse repertoire of receptors. Analyzing the collection of receptors expressed by naïve and memory B cells offers insights into the infection history of individuals. It can teach us about fundamental immune processes, and reveal disregulation. The recent development of high-throughput sequencing brings exciting possibilities, allowing for large-scale characterization of antibody repertoires. However, the statistical methods and models to plan these high-throughput experiments and analyze their results are lacking. Hereby, I will present several new computational tools that were designed to address crucial steps in lymphocyte receptor repertoire analysis: process raw data, infer an individual genotype from mRNA sequences, quantify affinity dependent selection and build a targeting model for the observed mutation spectrum. Examples of the applicability of these tools will be demonstrated through the analysis of next generation antibody sequencing dataset

​ built from samples of individuals with multiple sclerosis​

. I will share my view of the major obstacles that still need to be confronted before we can utilize lymphocyte receptor repertoire analysis for diagnosis and prognosis.

 

סמינר מחלקתי Guy Shiber and Mor Elias

18 במרץ 2015, 15:00 
וולפסון 206  
0
סמינר מחלקתי   Guy Shiber and Mor Elias

 

 

 

School of Mechanical Engineering Seminar
Wednesday, March 18, 2015 at 15:00
Wolfson Building of Mechanical Engineering, Room 206

 

Offspring Creation Mechanisms for Multi-objective Evolutionary Algorithms

 

Mor Elias

 

MSc student of Dr. Amiram Moshaiov

 

Offspring Creation Mechanisms for Multi-objective Evolutionary Algorithms

 

Mor Elias

 

MSc student of Dr. Amiram Moshaiov

 

Evolutionary algorithms are designed to solve optimization problems using an iterative process. These algorithms are inspired by the biological evolution process. One of the main mechanisms used in evolutionary algorithms is the solution ('offspring') creation method. This study explores the influence of several different offspring creation methods on evolutionary multi-objective optimization. An innovative method of variable-based offspring creation is suggested and studied. It involves independent adaptation of the solution's parameters. The suggested approach is implemented in an algorithm which is termed Variable-based -PAES. Another mutation-based algorithm, -MO-CMA-ES (multi objective covariance matrix adaptation evolutionary strategy), is also proposed based on the well-known CMA-ES algorithm. The CMA-ES method takes under consideration the mutual influence of the solution's variables. These mutation-based algorithms are compared with each other and with a state-of-the-art algorithm, known as -MOEA, which uses an offspring creation method based on recombination.

A statistical comparison is performed on a variety of problems, using repeated runs. The comparison refers to the exploration and exploitation capabilities of the algorithms. First, the comparison is carried out on several test functions of two and three objectives. Next, it is performed on several academic path planning problems. The comparison results reveal several characteristics of the algorithms. It is shown that using a combination of multiple runs the ES-based algorithms are better than -MOEA.

School of Mechanical Engineering Seminar
Wednesday, March 18, 2015 at 15:00
Wolfson Building of Mechanical Engineering, Room 206

 

 

Mechanical Properties of Poly(Methyl Methacrylate)                                    

Enhanced by Functionalized Carbon nanotubes

 

Guy Shiber

M.Sc. Student of Prof. Leslie Banks-Silis

 

Carbon nanotubes (CNTs) were discovered approximately 25 years ago and they are amongst the strongest materials known to man.  This material is a carbon allotrope like graphite, diamond and fullerene.  Apart from their excellent mechanical properties, they have unique electrical, thermal and optical properties, as well.  Upon discovery of this unique material, investigators were led to believe that a huge breakthrough would be made in many fields including composite materials; but soon after their discovery, challenges arose.  The two main challenges in using CNTs as a reinforcement phase in a composite are homogenous dispersion and distribution of the CNTs in the matrix, as well as improving the interfacial bond between them.  Functionalization of CNTs has proved an effective method for overcoming these challenges.  Since this material was discovered, numerous studies have been dedicated to finding effective functionalization methods. 

The goal of this study, is to determine the mechanical properties of a composite material using experimental and micro-mechanical methods.  The composite consists of a poly(methyl methacrylate), or PMMA, matrix enhanced by different weight fractions (wt%) of nanotubes functionalized by two methods.  Carboxilated CNTs were further functionalized by the grafting from (GF) or the grafting to (GT) methods.  The effect of these functionalization methods on the CNTs is evaluated through measurement of the effective mechanical properties of the composite; as well as, through a comparison to a previous investigation, in which non-functionalized (NF) CNTs were employed.  A micro-mechanical model (HFGMC) was used to evaluate the effective mechanical properties of the material.

Uniaxial tensile tests were conducted according to the ASTM D 638-10 standard (2013) with six batches of dog-bone specimens.  Specimens were produced by means of a melt-mixing process, followed by injection molding.  These batches were manufactured from neat PMMA, PMMA with 0.8 and 1.5 wt% of GF CNTs, and PMMA with 1.5, 3.0 and 6.0 wt% of GT CNTs.  Displacements were recorded using the digital image correlation method (DIC).  A comprehensive study regarding the DIC parameters and computational error of this approach was conducted.  A MATLAB code was employed for two purposes, to calculate the strain measurements from the displacement field, and to combine these measurements with the applied load reading.  Four mechanical properties were determined, elastic modulus, E, Poisson’s ratio, n, tensile strength, suts, and strain to failure, ef.

Both functionalization methods showed improved results for the elastic modulus of the high weight fraction batches, compared to the NF CNTs.  The highest rate of change in the elastic modulus was reported for the GF 1.5 and GT 3.0 wt% batches, while the latter is a more robust process.  This property decreased or was unaffected, for the low CNT content batches.  The tensile strength showed a similar trend for the GT batches and a monotonic increase for the GF batches.  In general, the strain to failure decreased with increasing CNT content.  A lower CNT content was needed to induce the same change in the mechanical properties, when functionalized nanotubes were used.  Good agreement is reported with the micro-mechanical model, as well.

כנס קריירה

15 בינואר 2015, 16:15 
אולם רוזנבלט הפקולטה להנדסה  
כנס קריירה

שילובים דואגים לקריירה שלכם לבכירים ולצעירים כאחד ולשם כך יהיו:

  • הרצאות תוכן בנושא קריירה
  •  הצעות עבודה מחברות בתעשייה : אינטל, אפל, ברודקום, טבע, תעשייה אווירית  CPS וחברת השמה 
  •  בוגרים מייעצים לאורך הכנס - כי תמיד טוב לשמוע עצה מבעל ניסיון

 

  • הכנס מיועד לבוגרים של שילובים בשלבים השונים של הקריירה המקצועית ולסטודנטים שיוצאים לקריירה חדשה. 
  • החברות שמשתתפות בכנס מביאות איתן הצעות עבודה על פי הצרכים שלהן ובהתאם לניסיון המקצועי שנדרש עבורן. מומלץ להגיע עם קורות חיים.
  • הכנס ללא תשלום אך יש להרשם על מנת להבטיח את מקומך!

סמינר מחלקתי Kul Karcz

16 במרץ 2015, 15:00 
וולפסון 206  
0
סמינר מחלקתי Kul Karcz

סמינר מחלקתי Gali Hendin

27 באפריל 2015, 15:00 
וולפסון 206  
0
סמינר מחלקתי Gali Hendin

 

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.

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