Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic features which would require pre-sampled tree topologies and may suffer from limited approximation capability. In this paper, we propose a deep autoregressive model for phylogenetic inference based on graph neural networks (GNNs), called ARTree. By decomposing a tree topology into a sequence of leaf node addition operations and modeling the involved conditional distributions based on learnable topological features via GNNs, ARTree can provide a rich family of distributions over the entire tree topology space that have simple sampling algorithms and density estimation procedures, without using heuristic features. We demonstrate the effectiveness and efficiency of our method on a benchmark of challenging real data tree topology density estimation and variational Bayesian phylogenetic inference problems.

Recently, there has been a surge in methodological development for the difference-in-differences (DiD) approach to evaluate causal effects. Standard methods in the literature rely on the parallel trends assumption to identify the average treatment effect on the treated. However, the parallel trends assumption may be violated in the presence of unmeasured confounding, and the average treatment effect on the treated may not be useful in learning a treatment assignment policy for the entire population. In this article, we propose a general instrumented DiD approach for learning the optimal treatment policy. Specifically, we establish identification results using a binary instrumental variable (IV) when the parallel trends assumption fails to hold. Additionally, we construct a Wald estimator, novel inverse probability weighting (IPW) estimators, and a class of semiparametric efficient and multiply robust estimators, with theoretical guarantees on consistency and asymptotic normality, even when relying on flexible machine learning algorithms for nuisance parameters estimation. Furthermore, we extend the instrumented DiD to the panel data setting. We evaluate our methods in extensive simulations and a real data application.

Graph neural networks (GNNs) for link prediction can loosely be divided into two broad categories. First, \emph{node-wise} architectures pre-compute individual embeddings for each node that are later combined by a simple decoder to make predictions. While extremely efficient at inference time (since node embeddings are only computed once and repeatedly reused), model expressiveness is limited such that isomorphic nodes contributing to candidate edges may not be distinguishable, compromising accuracy. In contrast, \emph{edge-wise} methods rely on the formation of edge-specific subgraph embeddings to enrich the representation of pair-wise relationships, disambiguating isomorphic nodes to improve accuracy, but with the cost of increased model complexity. To better navigate this trade-off, we propose a novel GNN architecture whereby the \emph{forward pass} explicitly depends on \emph{both} positive (as is typical) and negative (unique to our approach) edges to inform more flexible, yet still cheap node-wise embeddings. This is achieved by recasting the embeddings themselves as minimizers of a forward-pass-specific energy function (distinct from the actual training loss) that favors separation of positive and negative samples. As demonstrated by extensive empirical evaluations, the resulting architecture retains the inference speed of node-wise models, while producing competitive accuracy with edge-wise alternatives.

Long-term time series forecasting (LTSF) is important for various domains but is confronted by challenges in handling the complex temporal-contextual relationships. As multivariate input models underperforming some recent univariate counterparts, we posit that the issue lies in the inefficiency of existing multivariate LTSF Transformers to model series-wise relationships: the characteristic differences between series are often captured incorrectly. To address this, we introduce ARM: a multivariate temporal-contextual adaptive learning method, which is an enhanced architecture specifically designed for multivariate LTSF modelling. ARM employs Adaptive Univariate Effect Learning (AUEL), Random Dropping (RD) training strategy, and Multi-kernel Local Smoothing (MKLS), to better handle individual series temporal patterns and correctly learn inter-series dependencies. ARM demonstrates superior performance on multiple benchmarks without significantly increasing computational costs compared to vanilla Transformer, thereby advancing the state-of-the-art in LTSF. ARM is also generally applicable to other LTSF architecture beyond vanilla Transformer.

This paper explores the generalization characteristics of iterative learning algorithms with bounded updates for non-convex loss functions, employing information-theoretic techniques. Our key contribution is a novel bound for the generalization error of these algorithms with bounded updates. Our approach introduces two main novelties: 1) we reformulate the mutual information as the uncertainty of updates, providing a new perspective, and 2) instead of using the chaining rule of mutual information, we employ a variance decomposition technique to decompose information across iterations, allowing for a simpler surrogate process. We analyze our generalization bound under various settings and demonstrate improved bounds. To bridge the gap between theory and practice, we also examine the previously observed scaling behavior in large language models. Ultimately, our work takes a further step for developing practical generalization theories. The majority of machine learning techniques utilize the empirical risk minimization framework. Within this framework, the optimization objective is to minimize empirical risk, which is the average risk over a finite set of training samples.

Bayesian methods for solving inverse problems are a powerful alternative to classical methods since the Bayesian approach offers the ability to quantify the uncertainty in the solution. In recent years, data-driven techniques for solving inverse problems have also been remarkably successful, due to their superior representation ability. In this work, we incorporate data-based models into a class of Langevin-based sampling algorithms for Bayesian inference in imaging inverse problems. In particular, we introduce NF-ULA (Normalizing Flow-based Unadjusted Langevin algorithm), which involves learning a normalizing flow (NF) as the image prior. We use NF to learn the prior because a tractable closed-form expression for the log prior enables the differentiation of it using autograd libraries. Our algorithm only requires a normalizing flow-based generative network, which can be pre-trained independently of the considered inverse problem and the forward operator. We perform theoretical analysis by investigating the well-posedness and non-asymptotic convergence of the resulting NF-ULA algorithm. The efficacy of the proposed NF-ULA algorithm is demonstrated in various image restoration problems such as image deblurring, image inpainting, and limited-angle X-ray computed tomography (CT) reconstruction. NF-ULA is found to perform better than competing methods for severely ill-posed inverse problems.

The following work is a preprint collection of formal proofs regarding the convergence properties of the AdaBoost machine learning algorithm's classifier and margins. Various math and computer science papers have been written regarding conjectures and special cases of these convergence properties. Furthermore, the margins of AdaBoost feature prominently in the research surrounding the algorithm. At the zenith of this paper we present how AdaBoost's classifier and margins converge on a value that agrees with decades of research. After this, we show how various quantities associated with the combined classifier converge.

Topological Data Analysis (TDA) is a mathematical method using techniques from topology for the analysis of complex, multi-dimensional data that has been widely and successfully applied in several fields such as medicine, material science, biology, and others. This survey summarizes the state of the art of TDA in yet another application area: industrial manufacturing and production in the context of Industry 4.0. We perform a rigorous and reproducible literature search of applications of TDA on the setting of industrial production and manufacturing. The resulting works are clustered and analyzed based on their application area within the manufacturing process and their input data type. We highlight the key benefits of TDA and their tools in this area and describe its challenges, as well as future potential. Finally, we discuss which TDA methods are underutilized in (the specific area of) industry and the identified types of application, with the goal of prompting more research in this profitable area of application.

Patterns of microcircuitry suggest that the brain has an array of repeated canonical computational units. Yet neural representations are distributed, so the relevant computations may only be related indirectly to single-neuron transformations. It thus remains an open challenge how to define canonical distributed computations. We integrate normative and algorithmic theories of neural computation into a mathematical framework for inferring canonical distributed computations from large-scale neural activity patterns. At the normative level, we hypothesize that the brain creates a structured internal model of its environment, positing latent causes that explain its sensory inputs, and uses those sensory inputs to infer the latent causes. At the algorithmic level, we propose that this inference process is a nonlinear message-passing algorithm on a graph-structured model of the world. Given a time series of neural activity during a perceptual inference task, our framework finds (i) the neural representation of relevant latent variables, (ii) interactions between these variables that define the brain's internal model of the world, and (iii) message-functions specifying the inference algorithm. These targeted computational properties are then statistically distinguishable due to the symmetries inherent in any canonical computation, up to a global transformation. As a demonstration, we simulate recordings for a model brain that implicitly implements an approximate inference algorithm on a probabilistic graphical model. Given its external inputs and noisy neural activity, we recover the latent variables, their neural representation and dynamics, and canonical message-functions. We highlight features of experimental design needed to successfully extract canonical computations from neural data. Overall, this framework provides a new tool for discovering interpretable structure in neural recordings.

In this paper, we focus on a general yet important learning problem, pairwise similarity learning (PSL). PSL subsumes a wide range of important applications, such as open-set face recognition, speaker verification, image retrieval and person re-identification. The goal of PSL is to learn a pairwise similarity function assigning a higher similarity score to positive pairs (i.e., a pair of samples with the same label) than to negative pairs (i.e., a pair of samples with different label). We start by identifying a key desideratum for PSL, and then discuss how existing methods can achieve this desideratum. We then propose a surprisingly simple proxy-free method, called SimPLE, which requires neither feature/proxy normalization nor angular margin and yet is able to generalize well in open-set recognition. We apply the proposed method to three challenging PSL tasks: open-set face recognition, image retrieval and speaker verification. Comprehensive experimental results on large-scale benchmarks show that our method performs significantly better than current state-of-the-art methods.