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Causal investigations in observational studies pose a great challenge in research where randomized trials or intervention-based studies are not feasible. We develop an information geometric causal discovery and inference framework of "predictive asymmetry". For $(X, Y)$, predictive asymmetry enables assessment of whether $X$ is more likely to cause $Y$ or vice-versa. The asymmetry between cause and effect becomes particularly simple if $X$ and $Y$ are deterministically related. We propose a new metric called the Directed Mutual Information ($DMI$) and establish its key statistical properties. $DMI$ is not only able to detect complex non-linear association patterns in bivariate data, but also is able to detect and infer causal relations. Our proposed methodology relies on scalable non-parametric density estimation using Fourier transform. The resulting estimation method is manyfold faster than the classical bandwidth-based density estimation. We investigate key asymptotic properties of the $DMI$ methodology and a data-splitting technique is utilized to facilitate causal inference using the $DMI$. Through simulation studies and an application, we illustrate the performance of $DMI$.

We combine Kronecker products, and quantitative information flow, to give a novel formal analysis for the fine-grained verification of utility in complex privacy pipelines. The combination explains a surprising anomaly in the behaviour of utility of privacy-preserving pipelines -- that sometimes a reduction in privacy results also in a decrease in utility. We use the standard measure of utility for Bayesian analysis, introduced by Ghosh at al., to produce tractable and rigorous proofs of the fine-grained statistical behaviour leading to the anomaly. More generally, we offer the prospect of formal-analysis tools for utility that complement extant formal analyses of privacy. We demonstrate our results on a number of common privacy-preserving designs.

This paper introduces an assumption-lean method that constructs valid and efficient lower predictive bounds (LPBs) for survival times with censored data. We build on recent work by Cand\`es et al. (2021), whose approach first subsets the data to discard any data points with early censoring times, and then uses a reweighting technique (namely, weighted conformal inference (Tibshirani et al., 2019)) to correct for the distribution shift introduced by this subsetting procedure. For our new method, instead of constraining to a fixed threshold for the censoring time when subsetting the data, we allow for a covariate-dependent and data-adaptive subsetting step, which is better able to capture the heterogeneity of the censoring mechanism. As a result, our method can lead to LPBs that are less conservative and give more accurate information. We show that in the Type I right-censoring setting, if either of the censoring mechanism or the conditional quantile of survival time is well estimated, our proposed procedure achieves nearly exact marginal coverage, where in the latter case we additionally have approximate conditional coverage. We evaluate the validity and efficiency of our proposed algorithm in numerical experiments, illustrating its advantage when compared with other competing methods. Finally, our method is applied to a real dataset to generate LPBs for users' active times on a mobile app.

We study optimal data pooling for shared learning in two common maintenance operations: condition-based maintenance and spare parts management. We consider a set of systems subject to Poisson input -- the degradation or demand process -- that are coupled through an a-priori unknown rate. Decision problems involving these systems are high-dimensional Markov decision processes (MDPs) and hence notoriously difficult to solve. We present a decomposition result that reduces such an MDP to two-dimensional MDPs, enabling structural analyses and computations. Leveraging this decomposition, we (i) demonstrate that pooling data can lead to significant cost reductions compared to not pooling, and (ii) show that the optimal policy for the condition-based maintenance problem is a control limit policy, while for the spare parts management problem, it is an order-up-to level policy, both dependent on the pooled data.

The semantic segmentation of pelvic organs via MRI has important clinical significance. Recently, deep learning-enabled semantic segmentation has facilitated the three-dimensional geometric reconstruction of pelvic floor organs, providing clinicians with accurate and intuitive diagnostic results. However, the task of labeling pelvic floor MRI segmentation, typically performed by clinicians, is labor-intensive and costly, leading to a scarcity of labels. Insufficient segmentation labels limit the precise segmentation and reconstruction of pelvic floor organs. To address these issues, we propose a semi-supervised framework for pelvic organ segmentation. The implementation of this framework comprises two stages. In the first stage, it performs self-supervised pre-training using image restoration tasks. Subsequently, fine-tuning of the self-supervised model is performed, using labeled data to train the segmentation model. In the second stage, the self-supervised segmentation model is used to generate pseudo labels for unlabeled data. Ultimately, both labeled and unlabeled data are utilized in semi-supervised training. Upon evaluation, our method significantly enhances the performance in the semantic segmentation and geometric reconstruction of pelvic organs, Dice coefficient can increase by 2.65% averagely. Especially for organs that are difficult to segment, such as the uterus, the accuracy of semantic segmentation can be improved by up to 3.70%.

Motivation: Curation of literature in life sciences is a growing challenge. The continued increase in the rate of publication, coupled with the relatively fixed number of curators worldwide presents a major challenge to developers of biomedical knowledgebases. Very few knowledgebases have resources to scale to the whole relevant literature and all have to prioritise their efforts. Results: In this work, we take a first step to alleviating the lack of curator time in RNA science by generating summaries of literature for non-coding RNAs using large language models (LLMs). We demonstrate that high-quality, factually accurate summaries with accurate references can be automatically generated from the literature using a commercial LLM and a chain of prompts and checks. Manual assessment was carried out for a subset of summaries, with the majority being rated extremely high quality. We also applied the most commonly used automated evaluation approaches, finding that they do not correlate with human assessment. Finally, we apply our tool to a selection of over 4,600 ncRNAs and make the generated summaries available via the RNAcentral resource. We conclude that automated literature summarization is feasible with the current generation of LLMs, provided careful prompting and automated checking are applied. Availability: Code used to produce these summaries can be found here: //github.com/RNAcentral/litscan-summarization and the dataset of contexts and summaries can be found here: //huggingface.co/datasets/RNAcentral/litsumm-v1. Summaries are also displayed on the RNA report pages in RNAcentral (//rnacentral.org/)

Quantum computing has recently emerged as a transformative technology. Yet, its promised advantages rely on efficiently translating quantum operations into viable physical realizations. In this work, we use generative machine learning models, specifically denoising diffusion models (DMs), to facilitate this transformation. Leveraging text-conditioning, we steer the model to produce desired quantum operations within gate-based quantum circuits. Notably, DMs allow to sidestep during training the exponential overhead inherent in the classical simulation of quantum dynamics -- a consistent bottleneck in preceding ML techniques. We demonstrate the model's capabilities across two tasks: entanglement generation and unitary compilation. The model excels at generating new circuits and supports typical DM extensions such as masking and editing to, for instance, align the circuit generation to the constraints of the targeted quantum device. Given their flexibility and generalization abilities, we envision DMs as pivotal in quantum circuit synthesis, enhancing both practical applications but also insights into theoretical quantum computation.

Augmented Reality (AR) has emerged as a significant advancement in surgical procedures, offering a solution to the challenges posed by traditional neuronavigation methods. These conventional techniques often necessitate surgeons to split their focus between the surgical site and a separate monitor that displays guiding images. Over the years, many systems have been developed to register and track the hologram at the targeted locations, each employed its own evaluation technique. On the other hand, hologram displacement measurement is not a straightforward task because of various factors such as occlusion, Vengence-Accomodation Conflict, and unstable holograms in space. In this study, we explore and classify different techniques for assessing an AR-assisted neurosurgery system and propose a new technique to systematize the assessment procedure. Moreover, we conduct a deeper investigation to assess surgeon error in the pre- and intra-operative phases of the surgery based on the respective feedback given. We found that although the system can undergo registration and tracking errors, physical feedback can significantly reduce the error caused by hologram displacement. However, the lack of visual feedback on the hologram does not have a significant effect on the user 3D perception.

We study two classic variants of block-structured integer programming. Two-stage stochastic programs are integer programs of the form $\{A_i \mathbf{x} + D_i \mathbf{y}_i = \mathbf{b}_i\textrm{ for all }i=1,\ldots,n\}$, where $A_i$ and $D_i$ are bounded-size matrices. On the other hand, $n$-fold programs are integer programs of the form $\{{\sum_{i=1}^n C_i\mathbf{y}_i=\mathbf{a}} \textrm{ and } D_i\mathbf{y}_i=\mathbf{b}_i\textrm{ for all }i=1,\ldots,n\}$, where again $C_i$ and $D_i$ are bounded-size matrices. It is known that solving these kind of programs is fixed-parameter tractable when parameterized by the maximum dimension among the relevant matrices $A_i,C_i,D_i$ and the maximum absolute value of any entry appearing in the constraint matrix. We show that the parameterized tractability results for two-stage stochastic and $n$-fold programs persist even when one allows large entries in the global part of the program. More precisely, we prove that: - The feasibility problem for two-stage stochastic programs is fixed-parameter tractable when parameterized by the dimensions of matrices $A_i,D_i$ and by the maximum absolute value of the entries of matrices $D_i$. That is, we allow matrices $A_i$ to have arbitrarily large entries. - The linear optimization problem for $n$-fold integer programs that are uniform -- all matrices $C_i$ are equal -- is fixed-parameter tractable when parameterized by the dimensions of matrices $C_i$ and $D_i$ and by the maximum absolute value of the entries of matrices $D_i$. That is, we require that $C_i=C$ for all $i=1,\ldots,n$, but we allow $C$ to have arbitrarily large entries. In the second result, the uniformity assumption is necessary; otherwise the problem is $\mathsf{NP}$-hard already when the parameters take constant values. Both our algorithms are weakly polynomial: the running time is measured in the total bitsize of the input.

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.