Tag Archives: seminars

Mbbfac REVISED for CLARITY: SAVE THE DATES: 2018-2019 Search candidate visit dates confirmed

Lilian Kabeche, 10/22-10/24 (Monday seminar, Wednesday chalk talk; shared visit w/YCBI)
Morgan DeSantis, 11/5-11/6 (Monday seminar, Tuesday chalk talk) Seychelle Vos, 11/7-11/8 (Wednesday seminar, Thursday chalk talk) Anders Hansen, 11/26-11/28 (Monday seminar, Wednesday chalk talk; shared visit w/YCBI)
Franziska Bleichert, 12/3-12/4 (Monday seminar, Tuesday chalk talk)

Biostatistics Seminar: 10/23/18 – 12:00 Noon – 47 College St, 106B

Please join the Biostatistics Seminar scheduled for Tuesday, October 23, 2018 at 12:00 Noon at 47 College St., Room 106B.

Yale calendar Link: “YSPH Biostatistics Seminar: “Testing for Balance in Social Networks”

Thank you,

Speaker: Derek Feng, PhD

Institution: Yale University

Time & Place: 12:00 Noon in Room 106B, 47 College St.

11:45 AM Lunch outside Rm. 106B

Title: “Testing for Balance in Social Networks”


Friendship and antipathy exist in concert with one another in real social networks. Despite the role they play in social interactions, antagonistic ties are poorly understood and infrequently measured. One important theory of negative ties that has received relatively little empirical evaluation is balance theory, the codification of the adage `the enemy of my enemy is my friend’ and similar sayings. Unbalanced triangles are those with an odd number of negative ties, and the theory posits that such triangles are rare. To test for balance, previous works have utilized a permutation test on the edge signs. The flaw in this method, however, is that it assumes that negative and positive edges are interchangeable. In reality, they could not be more different. Here, we propose a novel test of balance that accounts for this discrepancy and show that our test is more accurate at detecting balance. Along the way, we prove asymptotic normality of the test statistic under our null model, which is of independent interest. Our case study is a novel dataset of signed networks we collected from 32 isolated, rural villages in Honduras. Contrary to previous results, we find that there is only marginal evidence for balance in social tie formation in this setting.
BIS Seminar Notice Oct 23_2018.pdf

ST Retreat – “Cancer In Translation” October 16, 2018

Dear YCC Members and Community,

Attached are the flyer and the agenda for the “Cancer In Translation” A Signal Transduction Retreat scheduled for Tuesday, October 16, 2018 in the Conference Center at West Campus. The keynote speaker will be David Solit, MD from the Memorial Sloan Kettering Cancer Center.

Please register by end of day Friday, October 12, 2018. For those who have not yet registered, please click the link below:


Feel free to post in your area and forward to anyone who may be interested. Please contact Susan Silva (susan.silva@yale.edu) with any questions.
ST Retreat Agenda – Final.pdf
Cancer In Translation E-Flyer FINAL.pdf

Biostatistics Seminar: Transcription factor target identification via knock-down experiments

Please join the Biostatistics Seminar October 22, 2018 at 12:00 Noon at 60 College Street, Rm. 216. Please also refer to the flyer attached.

Thank you.

Speaker: Leying Guan

Institution: Stanford University

Time & Place: 12:00 Noon in Room 216, 60 College Street

Title: “Transcription factor target identification via knock-down experiments”


The perturbation of a transcription factor should affect the expression levels of its direct targets. However, not all genes showing changes in expression are direct targets. To increase the chance of detecting direct targets, we propose two new methods. The first one is a modified two-group model using data from a single knock-down experiment. The null group corresponds to genes that are not direct targets, but can have small non-zero effects. The second method constructs a depth constrained network using data from multiple knock-down experiments. I will give details of both methods and present some simulated as well as real data examples.

Math-applied Next week: Applied Math Program: Seminar & Refreshments Wednesday, Oct 10, 2018



Speaker: David van Dijk, Yale

Date: Wednesday, October 10, 2018

Time: 3:45p.m. Refreshments (AKW, 1st Floor Break Area)
4:00p.m. Seminar (LOM 214)

Title: Understanding neural networks inside and out: designing constraints to enhance interpretability

Deep neural networks can learn meaningful representations of data. However, these representations are hard to interpret. In this talk I will present three ongoing projects in which I use specially designed constraints on latent representations of neural nets in order to make them more interpretable. First, I will present SAUCIE (Sparse Autoencoder for Clustering Imputation and Embedding) which is a framework for performing several data analysis tasks on a unified data representation. In SAUCIE we constrain the latent dimensions to be amenable to clustering, batch correction, imputation, and
visualization. Next, I will present a novel class of regularizations termed Graph Spectral Regularizations that impose graph structure on the otherwise unstructured activations of latent layers. By
considering the activations as signals on this graph we can use graph signal processing, and specifically graph filtering, to constrain the activations. I will show that, among other uses, this allows us to extract topological structure, such as clusters and progressions from data. Further, I will show that when the imposed graph is a 2D grid, with a smoothing penalty, the latent encodings become image-like. Such imposed grid structure also allows for addition of convolutional layers, even when the input data is naturally unstructured. Finally, in the third project, I propose a neural network framework, termed DyMoN (Dynamics Modeling network), that is capable of learning any stochastic dynamic process. I show that a DyMoN can learn harmonic and chaotic behavior, of single and double pendula respectively, and can give insight into the dynamics of biological systems.

YINS 9/17 Applied DS Seminar, Andrew Barron: Deep Learning

“Accuracy of High-Dimensional Deep Learning Networks”

Speaker: Andrew Barron
Professor of Statistics and Data Science at Yale University

Monday, September 17, 4:15-5:30pm

Location: Yale Institute for Network Science, 17 Hillhouse Ave, Room 328

Talk summary: It has been experimentally observed in recent years that multi-layer artificial neural networks have a surprising ability to generalize, even when trained with far more parameters than observations. Is there a theoretical basis for this? The best available bounds on their metric entropy and associated complexity measures are essentially linear in the number of parameters, which is inadequate to explain this phenomenon. Here we examine the statistical risk (mean squared predictive error) of multi-layer networks with L1 controls on their parameters and with ramp activation functions (also called lower-rectified linear units). In this setting, the risk is shown to be upper-bounded by [(L^3 log d)/n]^{1/2}, where d is the input dimension to each layer, L is the number of layers, and n is the sample size. In this way, the input dimension can be much larger than the sample size and the estimator can still be accurate, provided the target function has such L1 controls and that the sample size is at least moderately large compared to L^3 log d. The heart of the analysis is the development of a sampling strategy that demonstrates the accuracy of a sparse covering of deep ramp networks. Lower bounds show that the identified risk is minimax optimal, this being so already in the subclass of functions with L = 2. This is joint work with Jason Klusowski.

Statseminars Fwd: YINS 9/12 YINS Seminar, Constantinos Daskalakis: Adversarial Networks

“Improving Generative Adversarial Networks using Game Theory and Statistics”

Speaker: Constantinos Daskalakis
Professor of Computer Science and Electrical Engineering at MIT

Wednesday, September 12, 12:00-1:00pm

Location: Yale Institute for Network Science, 17 Hillhouse Ave, Room 328

Talk summary: Generative Adversarial Networks (aka GANs) are a recently proposed approach for learning samplers of high-dimensional distributions with intricate structure, such as distributions over natural images, given samples from these distributions. They are obtained by setting up a two-player zero-sum game between two neural networks, which learn statistics of a target distribution by adapting their strategies in the game using gradient descent. Despite their intriguing performance in practice, GANs pose great challenges to both optimization and statistics. Their training suffers from oscillations, and they are difficult to scale to high-dimensional settings. We study how game-theoretic and statistical techniques can be brought to bear on these important challenges. We use Game Theory towards improving GAN training, and Statistics towards scaling up the dimensionality of the generated distributions.

CMG_Data GSP_All Fwd: Announcement of the 2018 Conference of the Program in Quantitative Genomics: “B iobanks: Study Design and Data Analysis”

The GSP Analysis Centers co-organized the 2018 Harvard Program in Quantitative Genomics Conference on Biobanks: Study Design and Data Analysis. See https://www.hsph.harvard.edu/2018-pqg-conference/. Below is the conference announcement. The GSP investigators are welcome to attend it if interested.

Biobanks: Study Design and Data Analysis

November 1-2, 2018
Harvard Medical School Conference Center | Boston, MA

The impetus for the 2018 Conference of the Program in Quantitative Genomics of Harvard T.H. Chan School of Public Health comes from the proliferation of large scale biobanks worldwide. Biobanks are composed of massive genetic and genomic data, epidemiological data, Electronic Medical Records, wearable devices and imaging data. Examples of large biobanks include UK Biobank, China Kadoorie Biobank, eMERGE, Finland Biobank, Million Veteran Program, and MyCode Project of the Geisinger Health System, among others. The use of biobanks is becoming an essential and potentially revolutionary approach to biomedical research, with the capacity to improve the prevention, diagnosis, and treatment of a wide range of illnesses, and to advance personalized health. To take full advantage of the enormous opportunities presented in biobanks, there is an urgent need for discussing important quantitative issues, leveraging interdisciplinary expertise, and designing studies with increased scale and power. This conference aims at discussing several key quantitative challenges in biobank studies, including designing biobanks to meet a wide array of needs, developing strategies for improving phenotyping accuracy, harmonizing data across biobanks, and developing analytic methods for biobank data.

The conference will be centered on the following three topics:

SESSION 1: Types of Biobanks
SESSION 2: Biobank Data Analysis
SESSION 3: Phenotyping and Harmonization Across Biobanks

Keynote Speakers:
Tianxi Cai Harvard T.H. Chan School of Public Health
Gil McVean Oxford University
Catherine Sudlow UK Biobank, University of Edinburgh

Distinguished Speakers:
Zhengming Chen China Kadoorie Biobank, Oxford University
Kelly Cho Brigham and Women’s Hospital, Harvard Medical School Joshua Denny Vanderbilt University
David Ledbettter Geisinger Health System
Seunggeun Shawn Lee University of Michigan
Shawn Murphy Massachusetts General Hospital, Harvard Medical School Benjamin Neale Massachusetts General Hospital, Harvard Medical School Samuli Ripatti University of Helsinki, Institute for Molecular Medicine Finland (FIMM)
Manuel Rivas Stanford University

The conference program includes time for scientific presentations and a poster session and reception for submitted abstracts. Please visit the conference website for more details.

Registration + travel awards will be provided to support junior researchers who submit abstracts.
*Three abstracts will be selected to be presented as 10-minute platform talks


Submit Abstract

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