Miracle-dz/UniFAR-FTUs huggingface dataset:
Coronavirus Pandemic Incidence and risk factors of sarcopenia in hospitalized survivors of COVID-19; a retrospective cohort study

Introduction: Among the persistent conditions affecting patients in the post-acute COVID-19 period, sarcopenia is increasingly emphasized. In this study, we aimed to determine the incidence of sarcopenia and to reveal the risk factors predicting it in hospitalized survivors of COVID-19. Methodology: This is a retrospective cohort study conducted between December 2021 and May 2022 in the post-COVID follow-up center of a tertiary hospital in Turkey. One hundred and sixty-eight patients who were hospitalized because of COVID-19 and discharged were included in the study. The SARC-F scale was applied to determine the risk of sarcopenia in the participants. Twelve patients with a SARC-F score ≥ 4 before COVID-19 were excluded from the study. The medical records of the remaining 156 participants were reviewed, and their demographic characteristics, COVID-19 disease data, hemogram, and CRP parameters were also noted. Results: Sarcopenia risk was detected in 17 (10.9%) patients whose median age was higher than the others. Increased risk for sarcopenia was higher in women, lack of education, use of assisted respirators at home, having a psychiatric illness, losing > 10% weight during the hospitalization, and being treated in the intensive care unit. Multiple regression analysis showed that female gender (OR: 8. 04 [1.51 - 42.76]), having a psychiatric illness (OR: 13.23 [2.12 - 82.51]), and losing > 10% weight during hospitalization (OR: 18.46 [2.57 - 132.72]) predicted the sarcopenia risk. Conclusions: Sarcopenia should be closely monitored in patients with cases of severe inflammatory effect, inadequate food intake, and diminished physical activity such as hospitalized survivors of COVID-19.
Uncertainty Driven Bottleneck Attention U-net for Organ at Risk Segmentation

Organ at risk (OAR) segmentation in computed tomography (CT) imagery is a difficult task for automated segmentation methods and can be crucial for downstream radiation treatment planning. U-net has become a de-facto standard for medical image segmentation and is frequently used as a common baseline in medical image segmentation tasks. In this paper, we propose a multiple decoder U-net architecture and use the segmentation disagreement between the decoders as attention to the bottleneck of the network for segmentation refinement. While feature correlation is considered as attention in most cases, in our case it is the uncertainty from the network used as attention. For accurate segmentation, we also proposed a CT intensity integrated regularization loss. Proposed regularisation helps model understand the intensity distribution of low contrast tissues. We tested our model on two publicly available OAR challenge datasets. We also conducted the ablation on each datasets with the proposed attention module and regularization loss. Experimental results demonstrate a clear accuracy improvement on both datasets.
Rigidity of nearly planar classes of graphs

We explore the rigidity of generic frameworks in 3-dimensions whose underlying graph is close to being planar. Specifically we consider apex graphs, edge-apex graphs and their variants and prove independence results in the generic 3-dimensional rigidity matroid adding to the short list of graph classes for which 3-dimensional rigidity is understood. We then analyse global rigidity for these graph classes and use our results to deduce bounds on the maximum likelihood threshold of graphs in these nearly planar classes.
Open Your Ears to Take a Look: A State-of-the-Art Report on the Integration of Sonification and Visualization

The research communities studying visualization and sonification for data display and analysis share exceptionally similar goals, essentially making data of any kind interpretable to humans. One community does so by using visual representations of data, the other community does so by employing auditory (non-speech) representations of data. While the two communities have a lot in common, they developed mostly in parallel over the course of the last few decades. With this STAR, we discuss a collection of work that bridges the borders of the two communities, hence a collection of work that aims to integrate the two techniques to one form of audiovisual display, which we argue to be"more than the sum of the two. "We introduce and motivate a classification system applicable to such audiovisual displays and categorize a corpus of 57 academic publications that appeared between 2011 and 2023 in categories such as reading level, dataset type, or evaluation system, to mention a few. The corpus also enables a meta-analysis of the field, including regularly occurring design patterns such as type of visualization and sonification techniques, or the use of visual and auditory channels, and the analysis of a co-author network of the field which shows individual teams without much interconnection. The body of work covered in this STAR also relates to three adjacent topics: audiovisual monitoring, accessibility, and audiovisual data art. These three topics are discussed individually in addition to the systematically conducted part of this research. The findings of this report may be used by researchers from both fields to understand the potentials and challenges of such integrated designs, while inspiring them for future collaboration with experts from the respective other field.
Weighted EF1 and PO Allocations with Few Types of Agents or Chores

We investigate the existence of fair and efficient allocations of indivisible chores to asymmetric agents who have unequal entitlements or weights. We consider the fairness notion of weighted envy-freeness up to one chore (wEF1) and the efficiency notion of Pareto-optimality (PO). The existence of EF1 and PO allocations of chores to symmetric agents is a major open problem in discrete fair division, and positive results are known only for certain structured instances. In this paper, we study this problem for a more general setting of asymmetric agents and show that an allocation that is wEF1 and PO exists and can be computed in polynomial time for instances with: - Three types of agents, where agents with the same type have identical preferences but can have different weights. - Two types of chores, where the chores can be partitioned into two sets, each containing copies of the same chore. For symmetric agents, our results establish that EF1 and PO allocations exist for three types of agents and also generalize known results for three agents, two types of agents, and two types of chores. Our algorithms use a weighted picking sequence algorithm as a subroutine; we expect this idea and our analysis to be of independent interest.
Training Neural Networks from Scratch with Parallel Low-Rank Adapters

The scalability of deep learning models is fundamentally limited by computing resources, memory, and communication. Although methods like low-rank adaptation (LoRA) have reduced the cost of model finetuning, its application in model pre-training remains largely unexplored. This paper explores extending LoRA to model pre-training, identifying the inherent constraints and limitations of standard LoRA in this context. We introduce LoRA-the-Explorer (LTE), a novel bi-level optimization algorithm designed to enable parallel training of multiple low-rank heads across computing nodes, thereby reducing the need for frequent synchronization. Our approach includes extensive experimentation on vision transformers using various vision datasets, demonstrating that LTE is competitive with standard pre-training.
Structure-Guided Adversarial Training of Diffusion Models

Diffusion models have demonstrated exceptional efficacy in various generative applications. While existing models focus on minimizing a weighted sum of denoising score matching losses for data distribution modeling, their training primarily emphasizes instance-level optimization, overlooking valuable structural information within each mini-batch, indicative of pair-wise relationships among samples. To address this limitation, we introduce Structure-guided Adversarial training of Diffusion Models (SADM). In this pioneering approach, we compel the model to learn manifold structures between samples in each training batch. To ensure the model captures authentic manifold structures in the data distribution, we advocate adversarial training of the diffusion generator against a novel structure discriminator in a minimax game, distinguishing real manifold structures from the generated ones. SADM substantially improves existing diffusion transformers (DiT) and outperforms existing methods in image generation and cross-domain fine-tuning tasks across 12 datasets, establishing a new state-of-the-art FID of 1.58 and 2.11 on ImageNet for class-conditional image generation at resolutions of 256x256 and 512x512, respectively.
Performance analysis of MUSIC-type imaging without diagonal elements of multi-static response matrix

Generally, to apply the MUltiple SIgnal Classification (MUSIC) algorithm for the rapid imaging of small inhomogeneities, the complete elements of the multi-static response (MSR) matrix must be collected. However, in real-world applications such as microwave imaging or bistatic measurement configuration, diagonal elements of the MSR matrix are unknown. Nevertheless, it is possible to obtain imaging results using a traditional approach but theoretical reason of the applicability has not been investigated yet. In this paper, we establish mathematical structures of the imaging function of MUSIC from an MSR matrix without diagonal elements in both transverse magnetic (TM) and transverse electric (TE) polarizations. The established structures demonstrate why the shape of the location of small inhomogeneities can be retrieved via MUSIC without the diagonal elements of the MSR matrix. In addition, they reveal the intrinsic properties of imaging and the fundamental limitations. Results of numerical simulations are also provided to support the identified structures.
Rose: Efficient and Extensible Autodiff on the Web

Automatic differentiation (AD) has become the backbone for a new wave of optimization-driven domains such as computer graphics and machine learning over the past decade. However, existing AD systems face limitations, either lacking support for in-browser development or failing to harness more recent, compilerbased approaches to achieve both expressiveness and size-preserving differentiation. This work introduces Rose, a portable, extensible AD library that runs on the web. Rose allows users to write opaque functions with custom derivatives and supports dynamic construction of AD functions. We integrated Rose into two differentiable simulations and a diagram authoring tool to demonstrate the utility of Rose's design. Finally, we show that Rose is 173x as fast as TensorFlow.js in compiling and running a benchmark suite of optimized diagrams.
DeepDRK: Deep Dependency Regularized Knockoff for Feature Selection

Model-X knockoff, among various feature selection methods, received much attention recently due to its guarantee on false discovery rate (FDR) control. Subsequent to its introduction in parametric design, knockoff is advanced to handle arbitrary data distributions using deep learning-based generative modeling. However, we observed that current implementations of the deep Model-X knockoff framework exhibit limitations. Notably, the"swap property"that knockoffs necessitate frequently encounter challenges on sample level, leading to a diminished selection power. To overcome, we develop"Deep Dependency Regularized Knockoff (DeepDRK)", a distribution-free deep learning method that strikes a balance between FDR and power. In DeepDRK, a generative model grounded in a transformer architecture is introduced to better achieve the"swap property". Novel efficient regularization techniques are also proposed to reach higher power. Our model outperforms other benchmarks in synthetic, semi-synthetic, and real-world data, especially when sample size is small and data distribution is complex.
Order $p$ quantum Wasserstein distances from couplings

Optimal transport provides a powerful mathematical framework with applications spanning numerous fields. A cornerstone within this domain is the $p$-Wasserstein distance, which serves to quantify the cost of transporting one probability measure to another. While recent attempts have sought to extend this measure to the realm of quantum states, existing definitions often present certain limitations, such as not being faithful. In this work, we present a new definition of quantum Wasserstein distances. This definition, leveraging the coupling method and a metric applicable to pure states, draws inspiration from a property characterising the classical Wasserstein distance - its determination based on its value on point masses. Subject to certain continuity properties, our definition exhibits numerous attributes expected of an optimal quantum rendition of the Wasserstein distance. Notably, our approach seamlessly integrates metrics familiar to quantum information theory, such as the trace distance. Moreover, it provides an organic extension for metrics, like Nielsen's complexity metric, allowing their application to mixed states with a natural operational interpretation. Furthermore, we analyze this metric's attributes in the context of random quantum states and unveil phase transitions concerning the complexity of subsystems of random states.
RAVEL: Evaluating Interpretability Methods on Disentangling Language Model Representations

Individual neurons participate in the representation of multiple high-level concepts. To what extent can different interpretability methods successfully disentangle these roles? To help address this question, we introduce RAVEL (Resolving Attribute-Value Entanglements in Language Models), a dataset that enables tightly controlled, quantitative comparisons between a variety of existing interpretability methods. We use the resulting conceptual framework to define the new method of Multi-task Distributed Alignment Search (MDAS), which allows us to find distributed representations satisfying multiple causal criteria. With Llama2-7B as the target language model, MDAS achieves state-of-the-art results on RAVEL, demonstrating the importance of going beyond neuron-level analyses to identify features distributed across activations. We release our benchmark at https://github.com/explanare/ravel.
Assessment of Precision and Accuracy of Brain White Matter Microstructure using Combined Diffusion MRI and Relaxometry

Joint modeling of diffusion and relaxation has seen growing interest due to its potential to provide complementary information about tissue microstructure. For brain white matter, we designed an optimal diffusion-relaxometry MRI protocol that samples multiple b-values, B-tensor shapes, and echo times (TE). This variable-TE protocol (27 min) has as subsets a fixed-TE protocol (15 min) and a 2-shell dMRI protocol (7 min), both characterizing diffusion only. We assessed the sensitivity, specificity and reproducibility of these protocols with synthetic experiments and in six healthy volunteers. Compared with the fixed-TE protocol, the variable-TE protocol enables estimation of free water fractions while also capturing compartmental T2 relaxation times. Jointly measuring diffusion and relaxation offers increased sensitivity and specificity to microstructure parameters in brain white matter with voxelwise coefficients of variation below 10%.
Bit Distribution Study and Implementation of Spatial Quality Map in the JPEG-AI Standardization

Currently, there is a high demand for neural network-based image compression codecs. These codecs employ non-linear transforms to create compact bit representations and facilitate faster coding speeds on devices compared to the hand-crafted transforms used in classical frameworks. The scientific and industrial communities are highly interested in these properties, leading to the standardization effort of JPEG-AI. The JPEG-AI verification model has been released and is currently under development for standardization. Utilizing neural networks, it can outperform the classic codec VVC intra by over 10% BD-rate operating at base operation point. Researchers attribute this success to the flexible bit distribution in the spatial domain, in contrast to VVC intra's anchor that is generated with a constant quality point. However, our study reveals that VVC intra displays a more adaptable bit distribution structure through the implementation of various block sizes. As a result of our observations, we have proposed a spatial bit allocation method to optimize the JPEG-AI verification model's bit distribution and enhance the visual quality. Furthermore, by applying the VVC bit distribution strategy, the objective performance of JPEG-AI verification mode can be further improved, resulting in a maximum gain of 0.45 dB in PSNR-Y.
An Empirical Study of the Generalization Ability of Lidar 3D Object Detectors to Unseen Domains

3D Object Detectors (3D-OD) are crucial for understanding the environment in many robotic tasks, especially autonomous driving. Including 3D information via Lidar sensors improves accuracy greatly. However, such detectors perform poorly on domains they were not trained on, i.e. different locations, sensors, weather, etc., limiting their reliability in safety-critical applications. There exist methods to adapt 3D-ODs to these domains; however, these methods treat 3D-ODs as a black box, neglecting underlying architectural decisions and source-domain training strategies. Instead, we dive deep into the details of 3D-ODs, focusing our efforts on fundamental factors that influence robustness prior to domain adaptation. We systematically investigate four design choices (and the interplay between them) often overlooked in 3D-OD robustness and domain adaptation: architecture, voxel encoding, data augmentations, and anchor strategies. We assess their impact on the robustness of nine state-of-the-art 3D-ODs across six benchmarks encompassing three types of domain gaps - sensor type, weather, and location. Our main findings are: (1) transformer backbones with local point features are more robust than 3D CNNs, (2) test-time anchor size adjustment is crucial for adaptation across geographical locations, significantly boosting scores without retraining, (3) source-domain augmentations allow the model to generalize to low-resolution sensors, and (4) surprisingly, robustness to bad weather is improved when training directly on more clean weather data than on training with bad weather data. We outline our main conclusions and findings to provide practical guidance on developing more robust 3D-ODs.
Constraining Asymmetric Dark Matter using Colliders and Direct Detection

We reappraise the viability of asymmetric dark matter (ADM) realized as a Dirac fermion coupling dominantly to the Standard Model fermions. Treating the interactions of such a DM particle with quarks/leptons in an effective-interactions framework, we derive updated constraints using mono-jet searches from the Large Hadron Collider (LHC) and mono-photon searches at the Large Electron-Positron (LEP) collider. We carefully model the detectors used in these experiments, which is found to have significant impact. The constraint of efficient annihilation of the symmetric part of the ADM, as well as other observational constraints are synthesized to produce a global picture. Consistent with previous work, we find that ADM with mass in the range $1-100$ GeV is strongly constrained, thus ruling out its best motivated mass range. However, we find that leptophilic ADM remains allowed for $\gtrsim 10$ GeV DM, including bounds from colliders, direct detection, and stellar heating. We forecast that the Future Circular Collider for electron-positron collisions (FCC-ee) will improve sensitivity to DM-lepton interactions by almost an order of magnitude.
DRSI-Net: Dual-Residual Spatial Interaction Network for Multi-Person Pose Estimation

Multi-person pose estimation (MPPE), which aims to locate keypoints for all persons in the frames, is an active research branch of computer vision. Variable human poses and complex scenes make MPPE dependent on both local details and global structures, and the absence of them may cause keypoint feature misalignment. In this case, high-order spatial interactions that can effectively link the local and global information of features are particularly important. However, most methods do not have spatial interactions, and a few methods have low-order spatial interactions but they are difficult to achieve a good balance between accuracy and complexity. To address the above problems, a Dual-Residual Spatial Interaction Network (DRSI-Net) for MPPE with high accuracy and low complexity is proposed in this paper. DRSI-Net recursively performs residual spatial information interactions on neighbor features, so that more useful spatial information can be retained and more similarities can be obtained between shallow and deep extracted features. The channel and spatial dual attention mechanism introduced in the multi-scale feature fusion also helps the network to adaptively focus on features relevant to target keypoints and further refine generated poses. At the same time, by optimizing interactive channel dimensions and dividing gradient flow, the spatial interaction module is designed to be lightweight, which reduces the complexity of the network. According to the experimental results on the COCO dataset, the proposed DRSI-Net outperforms other state-of-the-art methods in both accuracy and complexity.
On the connection between Noise-Contrastive Estimation and Contrastive Divergence

Noise-contrastive estimation (NCE) is a popular method for estimating unnormalised probabilistic models, such as energy-based models, which are effective for modelling complex data distributions. Unlike classical maximum likelihood (ML) estimation that relies on importance sampling (resulting in ML-IS) or MCMC (resulting in contrastive divergence, CD), NCE uses a proxy criterion to avoid the need for evaluating an often intractable normalisation constant. Despite apparent conceptual differences, we show that two NCE criteria, ranking NCE (RNCE) and conditional NCE (CNCE), can be viewed as ML estimation methods. Specifically, RNCE is equivalent to ML estimation combined with conditional importance sampling, and both RNCE and CNCE are special cases of CD. These findings bridge the gap between the two method classes and allow us to apply techniques from the ML-IS and CD literature to NCE, offering several advantageous extensions.