Cheng Zhang

Cheng Zhang, Frederick A. Matsen

Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper, we present an alternative approach: a variational framework for Bayesian phylogenetic analysis. We propose combining subsplit Bayesian networks, an expressive graphical model for tree topology distributions, and a structured amortization of the branch lengths over tree topologies for a suitable variational family of distributions. We train the variational approximation via stochastic gradient ascent and adopt gradient estimators for continuous and discrete variational parameters separately to deal with the composite latent space of phylogenetic models. We show that our variational approach provides competitive performance to MCMC, while requiring much fewer (though more costly) iterations due to a more efficient exploration mechanism enabled by variational inference. Experiments on a benchmark of challenging real data Bayesian phylogenetic inference problems demonstrate the effectiveness and efficiency of our methods.

Tianyu Xie, Cheng Zhang · pku

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.

Shihan Feng, Cheng Zhang, Michael Xi et al.

Modern neural networks rarely have a single way to be right. For many tasks, multiple models can achieve identical performance while relying on different features or reasoning patterns, a property known as the Rashomon Effect. However, uncovering this diversity in deep architectures is challenging as their continuous parameter spaces contain countless near-optimal solutions that are numerically distinct but often behaviorally similar. We introduce Rashomon Concept Bottleneck Models, a framework that learns multiple neural networks which are all accurate yet reason through distinct human-understandable concepts. By combining lightweight adapter modules with a diversity-regularized training objective, our method constructs a diverse set of deep concept-based models efficiently without retraining from scratch. The resulting networks provide fundamentally different reasoning processes for the same predictions, revealing how concept reliance and decision making vary across equally performing solutions. Our framework enables systematic exploration of data-driven reasoning diversity in deep models, offering a new mechanism for auditing, comparison, and alignment across equally accurate solutions.

Ali Momeni, Babak Rahmani, Benjamin Scellier et al.

Physical neural networks (PNNs) are a class of neural-like networks that leverage the properties of physical systems to perform computation. While PNNs are so far a niche research area with small-scale laboratory demonstrations, they are arguably one of the most underappreciated important opportunities in modern AI. Could we train AI models 1000x larger than current ones? Could we do this and also have them perform inference locally and privately on edge devices, such as smartphones or sensors? Research over the past few years has shown that the answer to all these questions is likely "yes, with enough research": PNNs could one day radically change what is possible and practical for AI systems. To do this will however require rethinking both how AI models work, and how they are trained - primarily by considering the problems through the constraints of the underlying hardware physics. To train PNNs at large scale, many methods including backpropagation-based and backpropagation-free approaches are now being explored. These methods have various trade-offs, and so far no method has been shown to scale to the same scale and performance as the backpropagation algorithm widely used in deep learning today. However, this is rapidly changing, and a diverse ecosystem of training techniques provides clues for how PNNs may one day be utilized to create both more efficient realizations of current-scale AI models, and to enable unprecedented-scale models.