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  1. Cussens, James ; Zhang, Kun (Ed.)
    Nonlinear monotone transformations are used extensively in normalizing flows to construct invertible triangular mappings from simple distributions to complex ones. In existing literature, monotonicity is usually enforced by restricting function classes or model parameters and the inverse transformation is often approximated by root-finding algorithms as a closed-form inverse is unavailable. In this paper, we introduce a new integral-based approach termed: Atomic Unrestricted Time Machine (AUTM), equipped with unrestricted integrands and easy-to-compute explicit inverse. AUTM offers a versatile and efficient way to the design of normalizing flows with explicit inverse and unrestricted function classes or parameters. Theoretically, we present a constructive proof that AUTM is universal: all monotonic normalizing flows can be viewed as limits of AUTM flows. We provide a concrete example to show how to approximate any given monotonic normalizing flow using AUTM flows with guaranteed convergence. The result implies that AUTM can be used to transform an existing flow into a new one equipped with explicit inverse and unrestricted parameters. The performance of the new approach is evaluated on high dimensional density estimation, variational inference and image generation. Experiments demonstrate superior speed and memory efficiency of AUTM. 
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  2. Cussens, James ; Zhang, Kun (Ed.)
    Metric elicitation is a recent framework for eliciting classification performance metrics that best reflect implicit user preferences based on the task and context. However, available elicitation strategies have been limited to linear (or quasi-linear) functions of predictive rates, which can be practically restrictive for many applications including fairness. This paper develops a strategy for eliciting more flexible multiclass metrics defined by quadratic functions of rates, designed to reflect human preferences better. We show its application in eliciting quadratic violation-based group-fair metrics. Our strategy requires only relative preference feedback, is robust to noise, and achieves near-optimal query complexity. We further extend this strategy to eliciting polynomial metrics – thus broadening the use cases for metric elicitation. 
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  3. Cussens, James ; Zhang, Kun (Ed.)
    A major limiting factor in graphical model inference is the complexity of computing the partition function. Exact message-passing algorithms such as Bucket Elimination (BE) require exponential memory to compute the partition function; therefore, approximations are necessary. In this paper, we build upon a recently introduced methodology called Deep Bucket Elimination (DBE) that uses classical Neural Networks to approximate messages generated by BE for large buckets. The main feature of our new scheme, renamed NeuroBE, is that it customizes the architecture of the neural networks, their learning process and in particular, adapts the loss function to the internal form or distribution of messages. Our experiments demonstrate significant improvements in accuracy and time compared with the earlier DBE scheme. 
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  4. Cussens, James ; Zhang, Kun (Ed.)
    We investigate the problem of combinatorial multi-armed bandits with stochastic submodular (in expectation) rewards and full-bandit feedback, where no extra information other than the reward of selected action at each time step $t$ is observed. We propose a simple algorithm, Explore-Then-Commit Greedy (ETCG) and prove that it achieves a $(1-1/e)$-regret upper bound of $\mathcal{O}(n^\frac{1}{3}k^\frac{4}{3}T^\frac{2}{3}\log(T)^\frac{1}{2})$ for a horizon $T$, number of base elements $n$, and cardinality constraint $k$. We also show in experiments with synthetic and real-world data that the ETCG empirically outperforms other full-bandit methods. 
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  5. Cussens, James ; Zhang, Kun (Ed.)
    The importance of designing proteins, such as high affinity antibodies, has become ever more apparent. Computational Protein Design can cast such design problems as optimization tasks with the objective of maximizing K*, an approximation of binding affinity. Here we lay out a graphical model framework for K* optimization that enables use of compact AND/OR search algorithms. We designed an AND/OR branch-and-bound algorithm, AOBB-K*, for optimizing K* that is guided by a new K* heuristic and can incorporate specialized performance improvements with theoretical guarantees. As AOBB-K* is inspired by algorithms from the well studied task of Marginal MAP, this work provides a foundation for harnessing advancements in state-of-the-art mixed inference schemes and adapting them to protein design. 
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