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 Learning Graphical Models


Reviews: Dichotomize and Generalize: PAC-Bayesian Binary Activated Deep Neural Networks

Neural Information Processing Systems

One contribution is a new approach for training neural networks with binary activations. The second contribution is PAC-Bayesian generalization bounds for binary activated neural networks that, when used as the training objective, come very close to test accuracy (i.e. The gap between the training and test performance is also much smaller. I think this is very promising for training more robust networks. The method actually recovers variational Bayesian learning when the coefficient C is fixed, but in contrast to it, this coefficient is learned in a principled way.


A New Approach for Knowledge Generation Using Active Inference

arXiv.org Artificial Intelligence

There are various models proposed on how knowledge is generated in the human brain including the semantic networks model. Although this model has been widely studied and even computational models are presented, but, due to various limits and inefficiencies in the generation of different types of knowledge, its application is limited to semantic knowledge because of has been formed according to semantic memory and declarative knowledge and has many limits in explaining various procedural and conditional knowledge. Given the importance of providing an appropriate model for knowledge generation, especially in the areas of improving human cognitive functions or building intelligent machines, improving existing models in knowledge generation or providing more comprehensive models is of great importance. In the current study, based on the free energy principle of the brain, is the researchers proposed a model for generating three types of declarative, procedural, and conditional knowledge. While explaining different types of knowledge, this model is capable to compute and generate concepts from stimuli based on probabilistic mathematics and the action-perception process (active inference). The proposed model is unsupervised learning that can update itself using a combination of different stimuli as a generative model can generate new concepts of unsupervised received stimuli. In this model, the active inference process is used in the generation of procedural and conditional knowledge and the perception process is used to generate declarative knowledge.


Computational Protein Science in the Era of Large Language Models (LLMs)

arXiv.org Artificial Intelligence

Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In the last few decades, Artificial Intelligence (AI) has made significant impacts in computational protein science, leading to notable successes in specific protein modeling tasks. However, those previous AI models still meet limitations, such as the difficulty in comprehending the semantics of protein sequences, and the inability to generalize across a wide range of protein modeling tasks. Recently, LLMs have emerged as a milestone in AI due to their unprecedented language processing & generalization capability. They can promote comprehensive progress in fields rather than solving individual tasks. As a result, researchers have actively introduced LLM techniques in computational protein science, developing protein Language Models (pLMs) that skillfully grasp the foundational knowledge of proteins and can be effectively generalized to solve a diversity of sequence-structure-function reasoning problems. While witnessing prosperous developments, it's necessary to present a systematic overview of computational protein science empowered by LLM techniques. First, we summarize existing pLMs into categories based on their mastered protein knowledge, i.e., underlying sequence patterns, explicit structural and functional information, and external scientific languages. Second, we introduce the utilization and adaptation of pLMs, highlighting their remarkable achievements in promoting protein structure prediction, protein function prediction, and protein design studies. Then, we describe the practical application of pLMs in antibody design, enzyme design, and drug discovery. Finally, we specifically discuss the promising future directions in this fast-growing field.


Review for NeurIPS paper: Natural Policy Gradient Primal-Dual Method for Constrained Markov Decision Processes

Neural Information Processing Systems

Strengths: Comments about the paper: This paper presents convergence analysis of primal-dual natural policy gradient methods under the CMDP framework. Several recent works have shown convergence of policy gradients and optimality bounds (e.g Agarwal et al., Mei et al), but the paper extends similar analysis to (a) natural policy gradients (b) CMDP framework with constraints. Overall, it archives a sublinear rate of convergence in the CMDP framework, similar to other related works with convergence analysis. The analysis of the paper is done for the general MDP case with function approximation and restricted policy classes. It is a very well written paper that is easy to follow with significant theoretical derivation and proof details.


Review for NeurIPS paper: Natural Policy Gradient Primal-Dual Method for Constrained Markov Decision Processes

Neural Information Processing Systems

After reading the authors' rebuttal, the reviewers discussed their concerns about this paper. Ultimately, a consensus was not reached asreviewer #1 feels that the issues raised in her/his review were not properly addressed in the authors' feedback. The other reviewers also share some of the concerns raised by reviewer #1, but, given the rebuttals, they believe the authors can fix them in the final version and make the contribution of their paper clearer. I agree with them and so I suggest to accept the paper, but I recommend that the authors take into consideration the issues raised in the reviews and address them carefully in the final version of the paper.


Reviews: A Polynomial Time Algorithm for Log-Concave Maximum Likelihood via Locally Exponential Families

Neural Information Processing Systems

Post-rebuttal: The authors have promised to incorporate an exposition of the sampler in the revised paper, I believe that will make the paper a more self-contained read. I maintain my rating of strong accept (8). I think this paper makes very nice contributions to the fundamental question of estimating the MLE distribution given a bunch of observations. I think the key contributions can be broken up into two key parts: - A bunch of simple but elegant structural results for the MLE distribution in terms of'tent distributions' -- distributions such that its log-density is piecewise linear, and is supported over subdivisions of the convex hull of the datapoints. This allows them to write a convex program for optimizing over tent distributions.


Reviews: A Polynomial Time Algorithm for Log-Concave Maximum Likelihood via Locally Exponential Families

Neural Information Processing Systems

The submission provides a polynomial-time approximation algorithm for finding the maximum-likelihood log-concave density for a given set of data points in R d, for arbitrary d. The work is theoretical in nature, with proofs and no experiments. The problem is very interesting, since log-concave distributions include may of the commonly used parametric families (such as Gaussian), and the log-concave MLE has also other interesting properties. Previously the sample-complexity of learning a log-concave distribution has been studied, but a polynomial-time algorithm has been lacking. The present work provides such an algorithm.


Review for NeurIPS paper: Distributionally Robust Parametric Maximum Likelihood Estimation

Neural Information Processing Systems

Since everything is parametric, I'd expect explicit rates of convergence involvind all probalem complexity parameters (n, m, p, etc.) To make the rest of my points clear, let me recall the following notations are used in the paper: - n: the dimensionality of the covariate (i.e feature vector) X. Thus X is random vector in R n. BTW, in the context of ML or stats, I'd use another notation here, as n conventionally stands for "sample size".


Review for NeurIPS paper: Distributionally Robust Parametric Maximum Likelihood Estimation

Neural Information Processing Systems

This paper proposes a method for distributionally robust optimization under KL ambiguity sets for exponential families. Although KL ambiguity sets have their drawbacks, in particular not covering any changes in the inputs x, the present work produces a standard conic problem for a wide problem class via a novel analysis, provides good theoretical analysis, and yields good numerical results for a variety of small-scale classification problems. With the various clarifications that came up in the reviews, this paper makes a solid contribution to the DRO literature and will be quite welcome to the NeurIPS audience.


Reviews: A state-space model for inferring effective connectivity of latent neural dynamics from simultaneous EEG/fMRI

Neural Information Processing Systems

This paper develops a novel method to infer directional relationships between cortical areas of the brain based on simultaneously acquired EEG and fMRI data. Specifically, the fMRI activations are used to select ROIs related to the paradigm of interest. This information is used in a coupled state-space and forward propagation model to identify robust spatial sources and directional connectivity. The authors use a variational Bayesian framework to infer the latent posteriors and noise covariances. They demonstrate the power of joint EEG/fMRI analysis using two simulated experiments and a real-world dataset.