United States

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.

UAI 2021

Probabilistic Area Loss Minimization for Protein Sequence Alignment

markov random field

area loss

protein sequence alignment

Naval Information Warfare Center Pacific is partnering with AFCEA San Diego chapter to host the workshop.

The NAML workshop is an opportunity for researchers from Navy research and development centers and our partner organizations to exchange technical ideas and to come together as a team.

The goals of NAML are:

* To spread awareness of current machine learning research relevant to Naval applications

* To connect machine learning researchers with experts in military requirements

* To build and strengthen collaborations within the defense research community

**Watch this video to hear about the AFCEA purpose.**

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NAML 2021

lightning talk

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/)

Necessity and sufficiency are the building blocks of all successful explanations. Yet despite their importance, these notions have been conceptually underdeveloped and inconsistently applied in explainable artificial intelligence (XAI), a fast-growing research area that is so far lacking in firm theoretical foundations. Building on work in logic, probability, and causality, we establish the central role of necessity and sufficiency in XAI, unifying seemingly disparate methods in a single formal framework. We provide a sound and complete algorithm for computing explanatory factors with respect to a given context, and demonstrate its flexibility and competitive performance against state of the art alternatives on various tasks.

Local Explanations via Necessity and Sufficiency: Unifying Theory and Practice

Bayesian optimization (BO) is a popular method for optimizing expensive-to-evaluate black-box functions. BO budgets are typically given in iterations, which implicitly assumes each evaluation has the same cost. In fact, in many BO applications, evaluation costs vary significantly in different regions of the search space. In hyperparameter optimization, the time spent on neural network training increases with layer size; in clinical trials, the monetary cost of drug compounds vary; and in optimal control, control actions have differing complexities. Cost-constrained BO measures convergence with alternative cost metrics such as time, money, or energy, for which the sample efficiency of standard BO methods is ill-suited. For cost-constrained BO, cost efficiency is far more important than sample efficiency. In this paper, we formulate cost-constrained BO as a constrained Markov decision process (CMDP), and develop an efficient rollout approximation to the optimal CMDP policy that takes both the cost and future iterations into account. We validate our method on a collection of hyperparameter optimization problems as well as a sensor set selection application.

Nonmyopic Approach to Cost-Constrained Bayesian Optimization

The sample efficiency of Bayesian optimization(BO) is often boosted by Gaussian Process(GP) surrogate models. However, on mixed variable spaces, surrogate models other than GPs are prevalent, mainly due to the lack of kernels which can model complex dependencies across different types of variables. In this paper, we propose the frequency modulated(FM) kernel flexibly modeling dependencies among different types of variables, so that BO can enjoy the further improved sample efficiency. The FM kernel uses distances on continuous variables to modulate the graph Fourier spectrum derived from discrete variables. However, the frequency modulation does not always define a kernel with the similarity measure behavior which returns higher values for pairs of more similar points. Therefore, we specify and prove conditions for FM kernels to be positive definite and to exhibit the similarity measure behavior. In experiments, we demonstrate the improved sample efficiency of GP BO using FM kernels(BO-FM). On synthetic problems and hyperparameter optimization problems, BO-FM outperforms competitors consistently. Also, the importance of the frequency modulation principle is empirically demonstrated on the same problems. On joint optimization of neural architectures and SGD hyperparameters, BO-FM outperforms competitors including Regularized evolution (RE) and BOHB. Remarkably, BO-FM performs better even than RE using three times evaluations.

Mixed Variable Bayesian Optimization with Frequency Modulated Kernels

Subseasonal climate forecasting is the task of predicting climate variables, such as temperature and precipitation, in a two-week to two-month time horizon. The primary predictors for such prediction problem are spatio-temporal satellite and ground measurements of a variety of climate variables in the atmosphere, ocean, and land, which however have rather limited predictive signal at the subseasonal time horizon. We propose a carefully constructed spatial hierarchical Bayesian regression model that makes use of the inherent spatial structure of the subseasonal climate prediction task. We use our Bayesian model to then derive decision-theoretically optimal point estimates with respect to various performance measures of interest to climate science. As we show, our approach handily improves on various off-the-shelf ML baselines. Since our method is based on a Bayesian framework, we are also able to quantify the uncertainty in our predictions, which is particularly crucial for difficult tasks such as the subseasonal prediction, where we expect any model to have considerable uncertainty at different test locations under different scenarios.

Subseasonal Climate Prediction in the Western US using Bayesian Spatial Models

Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (MCMC) or Combinatorial Sequential Monte Carlo (CSMC). However, when MCMC is used for evolutionary parameter learning, convergence requires long runs with inefficient exploration of the state space. We introduce Variational Combinatorial Sequential Monte Carlo (VCSMC), a powerful framework that establishes variational sequential search to learn distributions over intricate combinatorial structures. We then develop nested CSMC, an efficient proposal distribution for CSMC and prove that nested CSMC is an exact approximation to the (intractable) locally optimal proposal. We use nested CSMC to define a second objective, VNCSMC which yields tighter lower bounds than VCSMC. We show that VCSMC and VNCSMC are computationally efficient and explore higher probability spaces than existing methods on a range of tasks.

Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inference

Interventional causal models describe several joint distributions over some variables used to describe a system, one for each intervention setting. They provide a formal recipe for how to move between the different joint distributions and make predictions about the variables upon intervening on the system. Yet, it is difficult to formalise how we may change the underlying variables used to describe the system, say moving from fine-grained to coarse-grained variables. Here, we argue that compositionality is a desideratum for such model transformations and the associated errors: When abstracting a reference model M iteratively, first obtaining M' and then further simplifying that to obtain M'', we expect the composite transformation from M to M'' to exist and its error to be bounded by the errors incurred by each individual transformation step. Category theory, the study of mathematical objects via compositional transformations between them, offers a natural language to develop our framework for model transformations and abstractions. We introduce a category of finite interventional causal models and, leveraging theory of enriched categories, prove the desired compositionality properties for our framework.

Compositional Abstraction Error and a Category of Causal Models

Most existing black-box optimization methods assume that all variables in the system being optimized have equal cost and can change freely at each iteration. However, in many real-world systems, inputs are passed through a sequence of different operations or modules, making variables in earlier stages of processing more costly to update. Such structure induces a dynamic cost from switching variables in the early parts of a data processing pipeline. In this work, we propose a new algorithm for switch-cost-aware optimization called Lazy Modular Bayesian Optimization (LaMBO). This method efficiently identifies the global optimum while minimizing cost through a passive change of variables in early modules.

Bayesian optimization for modular black-box systems with switching costs

Directed acyclic graphs (DAGs) with hidden variables are often used to characterize causal relations between variables in a system. When some variables are unobserved, DAGs imply a notoriously complicated set of constraints on the distribution of observed variables. In this work, we present entropic inequality constraints that are implied by e-separation relations in hidden variable DAGs with discrete observed variables. The constraints can intuitively be understood to follow from the fact that the capacity of variables along a causal pathway to convey information is restricted by their entropy; e.g. at the extreme case, a variable with entropy 0 can convey no information. We show how these constraints can be used to learn about the true causal model from an observed data distribution. In addition, we propose a measure of causal influence called the minimal mediary entropy, and demonstrate that it can augment traditional measures such as the average causal effect.

Entropic Inequality Constraints from e-separation Relations in Directed Acyclic Graphs with Hidden Variables

We develop operators for construction of proposals in probabilistic programs, which we refer to as inference combinators. Inference combinators define a grammar over importance samplers that compose primitive operations such as application of a transition kernel and importance resampling. Proposals in these samplers can be parameterized using neural networks, which in turn can be trained by optimizing variational objectives. The result is a framework for user-programmable variational methods that are correct by construction, and can be tailored to specific models. We demonstrate the flexibility of this framework in applications to advanced variational methods based on Gibbs sampling and annealing.

Learning Proposals for Probabilistic Programs with Inference Combinators

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.

Probabilistic Area Loss Minimization for Protein Sequence Alignment

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