United States

We present a new non-negative matrix factorization model for $(0,1)$

UAI 2021

Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data

beta distribution

nonnegative matrix factorization

dna methylation

**Epigenetic Inheritance across species**

We are happy to invite you to register for the GECKO Conference – inspired by the Gametic Epigenetics Consortium Against Obesity (hence, GECKO). Professor Romain Barrès Head of the GECKO Consortium, and his research group will be hosting the conference, which will take place virtually between **May 25-28, 2021**. **Sessions will be live daily from 8.00-10.30 and 17.00-19.30 CET.**

The theme of the conference is intentionally broad. We will have sessions dedicated to the technical aspects of studying epigenetic inheritance, how we can use a comparative approach to understand inheritance mechanisms, the evolutionary explanations for epigenetic inheritance and a session focused on how our research could influence reproductive biology. 

We already have a fantastic line-up of speakers, including Noora Kotaja (University of Turku), Qi Chen (University of California), Michael Wilson (University of Toronto), Isabelle Mansuy (University and ETH Zurich), Oliver Rando (University of Massachusetts), Anita Öst (Linköping University) and Tobias Uller (Lund University).

The conference format will include panel discussions, short talks selected from submitted abstracts, poster sessions and a set of short and sharp talks to accompany these.

The deadline for submitting an abstract to be considered for a talk or poster is **May 4th .** 
Those selected to present will be informed in the following week, with **final posters due May 17th .**
![](https://assets.underline.io/uploads/markdown_image/1/image/ea7614ef58a8f691e8295529020987ea.png)
[![](https://assets.underline.io/uploads/markdown_image/1/image/6b2bc323e45f696b7cd29d1650a5e2cc.jpg)](https://zmxuhia1.paperform.co/)

![](https://assets.underline.io/uploads/markdown_image/1/image/ea7614ef58a8f691e8295529020987ea.png)

[![](https://assets.underline.io/uploads/markdown_image/1/image/ac0bcdd33edcb55782729d3b03c29bdc.png)](https://drive.google.com/file/d/1AzPiQQYPvStIzAApkEk4AqejZs6HHhEc/view?usp=sharing)

### ** Program at a Glance **
![](https://assets.underline.io/uploads/markdown_image/1/image/17617a252626cfe73fc1a894e7d68ab1.png)
![](https://assets.underline.io/uploads/markdown_image/1/image/ea7614ef58a8f691e8295529020987ea.png)


# About GECKO

The Gametic Epigenetics Consortium Against Obesity (GECKO) is a research consortium funded by a Novo Nordisk Foundation Challenge grant from 2019 to 2025. The main goal of the consortium is to understand the effect of diet on the epigenetic signatures that are passed through sperm to offspring, and the effect these signatures have on the developing offspring and future generations. 

The GECKO is comprised of three leading research groups headed by Professor Romain Barrès at the University of Copenhagen, Professor Stephen Simpson at the University of Sydney and Professor Marcelo Nobrega at the University of Chicago.



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Find out more information and register to the event **for free** by making an account in Underline.

GECKO Conference 2021

technical paper

The Conference on Uncertainty in Artificial Intelligence (UAI) is one of the premier international conferences on research related to knowledge representation, learning, and reasoning in the presence of uncertainty. It is supported by the [Association for Uncertainty in Artificial Intelligence (AUAI).](https://www.auai.org/)

The 37th Conference on Uncertainty in Artificial Intelligence (UAI 2021) is held fully online. We have an exciting program consisting of keynote talks by [Susan Murphy](https://www.auai.org/uai2021/program?block=A), [Eric Horvitz](https://www.auai.org/uai2021/program?block=B), [Lenka Zdeborová](https://www.auai.org/uai2021/program?block=C), [Judea Pearl](https://www.auai.org/uai2021/program?block=D) and [Ankur Moitra](https://www.auai.org/uai2021/program?block=E), a town hall meeting, peer-reviewed papers, and three workshops. The main conference is single-track and each paper is show-cased with a live component (either a live discussion and Q&A, or a live lightning talk). All papers are also featured in video presentations and in poster sessions in gather.town. The three parallel workshops on Friday allow for smaller meetings on current topics.

The walkthrough video below shows how you can navigate this site and use the different possibilities for interaction: UAIsland2021 on gather.town for posters and social interactions, the mementor platform for virtual mentoring sessions, and the chat and Q&A systems for discussions about talks and posters.

Have a great UAI 2021! 
<br>
<br>Cassio de Campos and Marloes Maathuis
<br>UAI 2021 Program Chairs
<br>uai2021programchairs@gmail.com

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A ticket is required to access this conference. Please use the provided link to register for the event.

https://auai.org/uai2021/registration

The Conference on Uncertainty in Artificial Intelligence (UAI) is one of the premier international conferences on research related to knowledge representation, learning, and reasoning in the presence of uncertainty. It is supported by the [Association for Uncertainty in Artificial Intelligence (AUAI).](https://www.auai.org/)

This paper describes a new probabilistic generative model for noisy, sparse, and heterogeneous relational data called the hierarchical infinite relational model (HIRM). Given a set of relations defined over a collection of domains, the model first infers multiple non-overlapping clusters of relations using a top-level Chinese restaurant process. Within each cluster of relations, a Dirichlet process mixture is then used to partition the domain entities and model the probability distribution of relation values. The HIRM generalizes the standard infinite relational model and can be used for a variety of data analysis tasks including dependence detection, clustering, and density estimation. We present new algorithms for fully Bayesian posterior inference via Gibbs sampling. We illustrate the efficacy of the method on a density estimation benchmark of twenty object-attribute datasets with up to 18 million cells and use it to discover relational structure in real-world datasets from politics and genomics.

Hierarchical Infinite Relational Model

In this paper, we present a non-parametric structured latent variable model for image generation, called NP-DRAW, which sequentially draws on a latent canvas in a part-by-part fashion and then decodes the image from the canvas.

A Non-Parametric Structured Latent Variable Model for Image Generation

Protein sequence alignment is a fundamental problem in computational structure biology and popular for protein 3D structural prediction and protein homology detection. Most of the developed programs for detecting protein sequence alignments are based upon the likelihood information of amino acids and are sensitive to alignment noises. We present a robust method PALM for modeling pairwise protein structure alignments, using the area distance to reduce the biological measurement noise. PALM generatively learn the alignment of two protein sequences with probabilistic area distance objective, which can denoise the measurement errors and offsets from different biologists. During learning, we show that the optimization is computationally efficient by estimating the gradients via dynamically sampling alignments. Empirically, we show that PALM can generate sequence alignments with higher precision and recall, as well as smaller area distance than the competing methods especially for long protein sequences and remote homologies. This study implies for learning over large-scale protein sequence alignment problems, one could potentially give PALM a try.

Probabilistic Area Loss Minimization for Protein Sequence Alignment

A butterfly network consists of logarithmically many layers, each with a linear number of non-zero weights (pre-specified). The fast Johnson-Lindenstrauss transform (FJLT) can be represented as a butterfly network followed by a projection onto a random subset of the coordinates. Moreover, a random matrix based on FJLT with high probability approximates the action of any matrix on a vector. Motivated by these facts, we propose to replace a dense linear layer in any neural network by an architecture based on the butterfly network. The proposed architecture significantly improves upon the quadratic number of weights required in a standard dense layer to nearly linear with little compromise in expressibility of the resulting operator. In a collection of wide variety of experiments, including supervised prediction on both the NLP and vision data, we show that this not only produces results that match and at times outperform existing well-known architectures, but it also offers faster training and prediction in deployment. To understand the optimization problems posed by neural networks with a butterfly network, we also study the optimization landscape of the encoder-decoder network, where the encoder is replaced by a butterfly network followed by a dense linear layer in smaller dimension. Theoretical result presented in the paper explains why the training speed and outcome are not compromised by our proposed approach.

Sparse Linear Networks with a Fixed Butterfly Structure: Theory and Practice

Deep kernel learning and related techniques promise to combine the representational power of neural networks with the reliable uncertainty estimates of Gaussian processes. One crucial aspect of these models is an expectation that, because they are treated as Gaussian process models optimized using the marginal likelihood, they are protected from overfitting. However, we identify pathological behavior, including overfitting, on a simple toy example. We explore this pathology, explaining its origins and considering how it applies to real datasets. Through careful experimentation on UCI datasets, CIFAR-10, and the UTKFace dataset, we find that the overfitting from overparameterized deep kernel learning, in which the model is ``somewhat Bayesian'', can in certain scenarios be worse than that from not being Bayesian at all. However, we find that a fully Bayesian treatment of deep kernel learning can rectify this overfitting and obtain the desired performance improvements over standard neural networks and Gaussian processes.

The Promises and Pitfalls of Deep Kernel Learning

Structural causal models postulate noisy functional relations among a set of interacting variables. The causal structure underlying each such model is naturally represented by a directed graph whose edges indicate for each variable which other variables it causally depends upon. Under a number of different model assumptions, it has been shown that this causal graph and, thus also, causal effects are identifiable from mere observational data. For these models, practical algorithms have been devised to learn the graph. Moreover, when the graph is known, standard techniques may be used to give estimates and confidence intervals for causal effects. We argue, however, that a two-step method that first learns a graph and then treats the graph as known yields confidence intervals that are overly optimistic and can drastically fail to account for the uncertain causal structure. To address this issue we lay out a framework based on test inversion that allows us to give confidence regions for total causal effects that capture both sources of uncertainty: causal structure and numerical size of nonzero effects. Our ideas are developed in the context of bivariate linear causal models with homoscedastic errors, but as we exemplify they are generalizable to larger systems as well as other settings such as, in particular, linear non-Gaussian models.

Confidence in Causal Discovery with Linear Causal Models

Updating observations of a signal due to the delays in the measurement process is a common problem in signal processing, with prominent examples in a wide range of fields.

Gaussian Process Nowcasting: Application to COVID-19 Mortality Reporting

We present a novel model for capturing the behavior of an agent exhibiting sunk-cost bias in a stochastic environment. Agents exhibiting sunk-cost bias take into account the effort they have already spent on an endeavor when they evaluate whether to continue or abandon it. We model planning tasks in which an agent with this type of bias tries to reach a designated goal. Our model structures this problem as a type of Markov decision process: loosely speaking, the agent traverses a directed acyclic graph with probabilistic transitions, paying costs for its actions as it tries to reach a target node containing a specified reward. The agent's sunk cost bias is modeled by a cost that it incurs for abandoning the traversal: if the agent decides to stop traversing the graph, it incurs a cost of $\lambda \cdot C_{sunk}$, where ${\lambda \geq 0}$ is a parameter that captures the extent of the bias and $C_{sunk}$ is the sum of costs already invested.

Stochastic Model for Sunk Cost Bias

Auxiliary particle filters (APFs) are a class of sequential Monte Carlo (SMC) methods for Bayesian inference in state-space models. In their original derivation, APFs operate in an extended state space using an auxiliary variable to improve inference. In this work, we propose optimized auxiliary particle filters, a framework where the traditional APF auxiliary variables are interpreted as weights in a importance sampling mixture proposal. Under this interpretation, we devise a mechanism for proposing the mixture weights that is inspired by recent advances in multiple and adaptive importance sampling. In particular, we propose to select the mixture weights by formulating a convex optimization problem, with the aim of approximating the filtering posterior at each timestep. Further, we propose a weighting scheme that generalizes previous results on the APF (Pitt et al. 2012), proving unbiasedness and consistency of our estimators. Our framework demonstrates significantly improved estimates on a range of metrics compared to state-of-the-art particle filters at similar computational complexity in challenging and widely used dynamical models.

Optimized Auxiliary Particle Filters

Conventional methods in causal effect inferencetypically rely on specifying a valid set of control variables. When this set is unknown or misspecified, inferences will be erroneous. We propose a method for inferring average causal effects when all potential confounders are observed, but thecontrol variables are unknown. When the data-generating process belongs to the class of acyclical linear structural causal models, we prove that themethod yields asymptotically valid confidence intervals. Our results build upon a smooth characterization of linear directed acyclic graphs. We verify the capability of the method to produce valid confidence intervals for average causal effects using synthetic data, even when the appropriate specification of control variables is unknown.

Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data

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DNA methylation editing at gametic hotspots of epigenetic variation

Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data

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