Modern multivariate regression problems involve several related outcomes whose regression effects are not only nonlinear, heterogeneous, and outcome-specific, but also where the residual dependence among outcomes is scientifically meaningful. Existing multivariate Bayesian tree-based methods typically address only part of this problem: some impose substantial sharing of tree architecture across outcomes, which is overly restrictive when responses depend on distinct predictors or effect modifiers, while others accommodate residual dependence but retain simpler mean structures. This paper develops multiVCBART, a multivariate varying-coefficient Bayesian additive regression tree framework that jointly models flexible outcome-specific coefficient surfaces and a sparse residual precision matrix. Each entry of the coefficient matrix $B(x)$ is represented by an independent BART ensemble, allowing predictor effects to vary nonlinearly with modifiers $x$ across outcomes, while a Graphical Horseshoe prior on the precision matrix $Ω$ captures parsimonious residual conditional dependence. To permit efficient computation, we introduce a sampler that reduces the multivariate Gaussian likelihood to a sequence of scalar pseudo-response updates, decoupling the tree backfitting from the Graphical Horseshoe step. Theoretically, we establish the first posterior contraction rates for a multivariate BART model with jointly estimated residual dependence, proving near-minimax adaptation to underlying smoothness and structural sparsity. Empirically, multiVCBART outperforms existing multivariate tree models and Bayesian SUR competitors on sparse, high-dimensional datasets. Finally, in a re-analysis of the Genomics of Drug Sensitivity in Cancer dataset, our method identifies distinct biomarker signals and recovers a coherent residual pharmacologic network.

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems.

With the popularity of automatic code generation tools, such as Copilot, the study of the potential hazards of these tools is gaining importance. In this work, we explore the social bias problem in pre-trained code generation models. We propose a new paradigm to construct code prompts and successfully uncover social biases in code generation models. To quantify the severity of social biases in generated code, we develop a dataset along with three metrics to evaluate the overall social bias and fine-grained unfairness across different demographics. Experimental results on three pre-trained code generation models (Codex, InCoder, and CodeGen) with varying sizes, reveal severe social biases. Moreover, we conduct analysis to provide useful insights for further choice of code generation models with low social bias1.

A.1 TPPE Method We present the pseudo code for TPPE in this paper, using the Insertion mode as an example. According to Alg. 1, we reduce the query time complexity from In our study, we assume the worst-case scenario of applying punctuation-level attacks. Softmax layer is adopted to predict the label of the input text. Paraphrase (TPPEP) to achieve a single-shot attack. We describe the TPPEP method as being decomposed into two parts: training and searching.

When inserting a new trial, the oldest trial will be removed. We use a population size of 25 and tournament size of 5.

We conduct a preliminary study on finding a proper prompt construction strategy. Further research can utilize our analysis to construct more powerful code prompts. Table 1: Code prompt study results of CBS. N" means there are one human-relevant function Table 2: Automatic and human evaluation results of social biases in the generated code on GPT -4. We also conduct experiments on GPT -4.

We propose a new paradigm to construct code prompts and successfully uncover social biases in code generation models.