Cheng Zhang

Desi R. Ivanova, Joel Jennings, Tom Rainforth et al. · microsoft-research

We formalize the problem of contextual optimization through the lens of Bayesian experimental design and propose CO-BED -- a general, model-agnostic framework for designing contextual experiments using information-theoretic principles. After formulating a suitable information-based objective, we employ black-box variational methods to simultaneously estimate it and optimize the designs in a single stochastic gradient scheme. In addition, to accommodate discrete actions within our framework, we propose leveraging continuous relaxation schemes, which can naturally be integrated into our variational objective. As a result, CO-BED provides a general and automated solution to a wide range of contextual optimization problems. We illustrate its effectiveness in a number of experiments, where CO-BED demonstrates competitive performance even when compared to bespoke, model-specific alternatives.

Ruibo Tu, Chao Ma, Cheng Zhang

ChatGPT has demonstrated exceptional proficiency in natural language conversation, e.g., it can answer a wide range of questions while no previous large language models can. Thus, we would like to push its limit and explore its ability to answer causal discovery questions by using a medical benchmark (Tu et al. 2019) in causal discovery.

Xin Hua, Zhijiang Du, Hongjian Yu et al.

Cochlear implantation is currently the most effective treatment for patients with severe deafness, but mastering cochlear implantation is extremely challenging because the temporal bone has extremely complex and small three-dimensional anatomical structures, and it is important to avoid damaging the corresponding structures when performing surgery. The spatial location of the relevant anatomical tissues within the target area needs to be determined using CT prior to the procedure. Considering that the target structures are too small and complex, the time required for manual segmentation is too long, and it is extremely challenging to segment the temporal bone and its nearby anatomical structures quickly and accurately. To overcome this difficulty, we propose a deep learning-based algorithm, a 3D network model for automatic segmentation of multi-structural targets in temporal bone CT that can automatically segment the cochlea, facial nerve, auditory tubercle, vestibule and semicircular canal. The algorithm combines CNN and Transformer for feature extraction and takes advantage of spatial attention and channel attention mechanisms to further improve the segmentation effect, the experimental results comparing with the results of various existing segmentation algorithms show that the dice similarity scores, Jaccard coefficients of all targets anatomical structures are significantly higher while HD95 and ASSD scores are lower, effectively proving that our method outperforms other advanced methods.

Cheng Zhang

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort and domain expertise. In this paper, we propose a novel structural representation method for phylogenetic inference based on learnable topological features. By combining the raw node features that minimize the Dirichlet energy with modern graph representation learning techniques, our learnable topological features can provide efficient structural information of phylogenetic trees that automatically adapts to different downstream tasks without requiring domain expertise. We demonstrate the effectiveness and efficiency of our method on a simulated data tree probability estimation task and a benchmark of challenging real data variational Bayesian phylogenetic inference problems.

Michael Karcher, Cheng Zhang, Frederick A Matsen

Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire taxon set? Although the equivalent problem for in the non-Bayesian case has attracted substantial research, the Bayesian case has not attracted the attention it deserves. In this paper we develop a variational Bayes approach to this problem and demonstrate its effectiveness.