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We study the problem of training diffusion models to sample from a distribution with a given unnormalized density or energy function. We benchmark several diffusion-structured inference methods, including simulation-based variational approaches and off-policy methods (continuous generative flow networks). Our results shed light on the relative advantages of existing algorithms while bringing into question some claims from past work. We also propose a novel exploration strategy for off-policy methods, based on local search in the target space with the use of a replay buffer, and show that it improves the quality of samples on a variety of target distributions. Our code for the sampling methods and benchmarks studied is made public at //github.com/GFNOrg/gfn-diffusion as a base for future work on diffusion models for amortized inference.

Objective Function Mismatch (OFM) occurs when the optimization of one objective has a negative impact on the optimization of another objective. In this work we study OFM in deep clustering, and find that the popular autoencoder-based approach to deep clustering can lead to both reduced clustering performance, and a significant amount of OFM between the reconstruction and clustering objectives. To reduce the mismatch, while maintaining the structure-preserving property of an auxiliary objective, we propose a set of new auxiliary objectives for deep clustering, referred to as the Unsupervised Companion Objectives (UCOs). The UCOs rely on a kernel function to formulate a clustering objective on intermediate representations in the network. Generally, intermediate representations can include other dimensions, for instance spatial or temporal, in addition to the feature dimension. We therefore argue that the na\"ive approach of vectorizing and applying a vector kernel is suboptimal for such representations, as it ignores the information contained in the other dimensions. To address this drawback, we equip the UCOs with structure-exploiting tensor kernels, designed for tensors of arbitrary rank. The UCOs can thus be adapted to a broad class of network architectures. We also propose a novel, regression-based measure of OFM, allowing us to accurately quantify the amount of OFM observed during training. Our experiments show that the OFM between the UCOs and the main clustering objective is lower, compared to a similar autoencoder-based model. Further, we illustrate that the UCOs improve the clustering performance of the model, in contrast to the autoencoder-based approach. The code for our experiments is available at //github.com/danieltrosten/tk-uco.

Open sets are central to mathematics, especially analysis and topology, in ways few notions are. In most, if not all, computational approaches to mathematics, open sets are only studied indirectly via their 'codes' or 'representations'. In this paper, we study how hard it is to compute, given an arbitrary open set of reals, the most common representation, i.e. a countable set of open intervals. We work in Kleene's higher-order computability theory, which was historically based on the S1-S9 schemes and which now has an intuitive lambda calculus formulation due to the authors. We establish many computational equivalences between on one hand the 'structure' functional that converts open sets to the aforementioned representation, and on the other hand functionals arising from mainstream mathematics, like basic properties of semi-continuous functions, the Urysohn lemma, and the Tietze extension theorem. We also compare these functionals to known operations on regulated and bounded variation functions, and the Lebesgue measure restricted to closed sets. We obtain a number of natural computational equivalences for the latter involving theorems from mainstream mathematics.

Using a fully Bayesian approach, Gaussian Process regression is extended to include marginalisation over the kernel choice and kernel hyperparameters. In addition, Bayesian model comparison via the evidence enables direct kernel comparison. The calculation of the joint posterior was implemented with a transdimensional sampler which simultaneously samples over the discrete kernel choice and their hyperparameters by embedding these in a higher-dimensional space, from which samples are taken using nested sampling. Kernel recovery and mean function inference were explored on synthetic data from exoplanet transit light curve simulations. Subsequently, the method was extended to marginalisation over mean functions and noise models and applied to the inference of the present-day Hubble parameter, $H_0$, from real measurements of the Hubble parameter as a function of redshift, derived from the cosmologically model-independent cosmic chronometer and $\Lambda$CDM-dependent baryon acoustic oscillation observations. The inferred $H_0$ values from the cosmic chronometers, baryon acoustic oscillations and combined datasets are $H_0= 66 \pm 6\, \mathrm{km}\,\mathrm{s}^{-1}\,\mathrm{Mpc}^{-1}$, $H_0= 67 \pm 10\, \mathrm{km}\,\mathrm{s}^{-1}\,\mathrm{Mpc}^{-1}$ and $H_0= 69 \pm 6\, \mathrm{km}\,\mathrm{s}^{-1}\,\mathrm{Mpc}^{-1}$, respectively. The kernel posterior of the cosmic chronometers dataset prefers a non-stationary linear kernel. Finally, the datasets are shown to be not in tension with $\ln R=12.17\pm 0.02$.

In 2012 Chen and Singer introduced the notion of discrete residues for rational functions as a complete obstruction to rational summability. More explicitly, for a given rational function f(x), there exists a rational function g(x) such that f(x) = g(x+1) - g(x) if and only if every discrete residue of f(x) is zero. Discrete residues have many important further applications beyond summability: to creative telescoping problems, thence to the determination of (differential-)algebraic relations among hypergeometric sequences, and subsequently to the computation of (differential) Galois groups of difference equations. However, the discrete residues of a rational function are defined in terms of its complete partial fraction decomposition, which makes their direct computation impractical due to the high complexity of completely factoring arbitrary denominator polynomials into linear factors. We develop a factorization-free algorithm to compute discrete residues of rational functions, relying only on gcd computations and linear algebra.

The evaluation of text-generative vision-language models is a challenging yet crucial endeavor. By addressing the limitations of existing Visual Question Answering (VQA) benchmarks and proposing innovative evaluation methodologies, our research seeks to advance our understanding of these models' capabilities. We propose a novel VQA benchmark based on well-known visual classification datasets which allows a granular evaluation of text-generative vision-language models and their comparison with discriminative vision-language models. To improve the assessment of coarse answers on fine-grained classification tasks, we suggest using the semantic hierarchy of the label space to ask automatically generated follow-up questions about the ground-truth category. Finally, we compare traditional NLP and LLM-based metrics for the problem of evaluating model predictions given ground-truth answers. We perform a human evaluation study upon which we base our decision on the final metric. We apply our benchmark to a suite of vision-language models and show a detailed comparison of their abilities on object, action, and attribute classification. Our contributions aim to lay the foundation for more precise and meaningful assessments, facilitating targeted progress in the exciting field of vision-language modeling.

Mendelian randomization (MR) is an instrumental variable (IV) approach to infer causal relationships between exposures and outcomes with genome-wide association studies (GWAS) summary data. However, the multivariable inverse-variance weighting (IVW) approach, which serves as the foundation for most MR approaches, cannot yield unbiased causal effect estimates in the presence of many weak IVs. To address this problem, we proposed the MR using Bias-corrected Estimating Equation (MRBEE) that can infer unbiased causal relationships with many weak IVs and account for horizontal pleiotropy simultaneously. While the practical significance of MRBEE was demonstrated in our parallel work (Lorincz-Comi (2023)), this paper established the statistical theories of multivariable IVW and MRBEE with many weak IVs. First, we showed that the bias of the multivariable IVW estimate is caused by the error-in-variable bias, whose scale and direction are inflated and influenced by weak instrument bias and sample overlaps of exposures and outcome GWAS cohorts, respectively. Second, we investigated the asymptotic properties of multivariable IVW and MRBEE, showing that MRBEE outperforms multivariable IVW regarding unbiasedness of causal effect estimation and asymptotic validity of causal inference. Finally, we applied MRBEE to examine myopia and revealed that education and outdoor activity are causal to myopia whereas indoor activity is not.

The stochastic simulation algorithm (SSA) and the corresponding Monte Carlo (MC) method are among the most common approaches for studying stochastic processes. They rely on knowledge of interevent probability density functions (PDFs) and on information about dependencies between all possible events. Analytical representations of a PDF are difficult to specify in advance, in many real life applications. Knowing the shapes of PDFs, and using experimental data, different optimization schemes can be applied in order to evaluate probability density functions and, therefore, the properties of the studied system. Such methods, however, are computationally demanding, and often not feasible. We show that, in the case where experimentally accessed properties are directly related to the frequencies of events involved, it may be possible to replace the heavy Monte Carlo core of optimization schemes with an analytical solution. Such a replacement not only provides a more accurate estimation of the properties of the process, but also reduces the simulation time by a factor of order of the sample size (at least $\approx 10^4$). The proposed analytical approach is valid for any choice of PDF. The accuracy, computational efficiency, and advantages of the method over MC procedures are demonstrated in the exactly solvable case and in the evaluation of branching fractions in controlled radical polymerization (CRP) of acrylic monomers. This polymerization can be modeled by a constrained stochastic process. Constrained systems are quite common, and this makes the method useful for various applications.

Policymaking for complex challenges such as pandemics necessitates the consideration of intricate implications across multiple domains and scales. Computational models can support policymaking, but a single model is often insufficient for such multidomain and scale challenges. Multi-models comprising several interacting computational models at different scales or relying on different modeling paradigms offer a potential solution. Such multi-models can be assembled from existing computational models (i.e., integrated modeling) or be designed conceptually as a whole before their computational implementation (i.e., integral modeling). Integral modeling is particularly valuable for novel policy problems, such as those faced in the early stages of a pandemic, where relevant models may be unavailable or lack standard documentation. Designing such multi-models through an integral approach is, however, a complex task requiring the collaboration of modelers and experts from various domains. In this collaborative effort, modelers must precisely define the domain knowledge needed from experts and establish a systematic procedure for translating such knowledge into a multi-model. Yet, these requirements and systematic procedures are currently lacking for multi-models that are both multiscale and multi-paradigm. We address this challenge by introducing a procedure for developing multi-models with an integral approach based on clearly defined domain knowledge requirements derived from literature. We illustrate this procedure using the case of school closure policies in the Netherlands during the COVID-19 pandemic, revealing their potential implications in the short and long term and across the healthcare and educational domains. The requirements and procedure provided in this article advance the application of integral multi-modeling for policy support in multiscale and multidomain contexts.

In recent years, object detection has experienced impressive progress. Despite these improvements, there is still a significant gap in the performance between the detection of small and large objects. We analyze the current state-of-the-art model, Mask-RCNN, on a challenging dataset, MS COCO. We show that the overlap between small ground-truth objects and the predicted anchors is much lower than the expected IoU threshold. We conjecture this is due to two factors; (1) only a few images are containing small objects, and (2) small objects do not appear enough even within each image containing them. We thus propose to oversample those images with small objects and augment each of those images by copy-pasting small objects many times. It allows us to trade off the quality of the detector on large objects with that on small objects. We evaluate different pasting augmentation strategies, and ultimately, we achieve 9.7\% relative improvement on the instance segmentation and 7.1\% on the object detection of small objects, compared to the current state of the art method on MS COCO.