Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid

Post-acute sequelae of SARS-CoV-2 infection (PASC) or Long COVID is an emerging medical condition that has been observed in several patients with a positive diagnosis for COVID-19. Historical Electronic Health Records (EHR) like diagnosis codes, lab results and clinical notes have been analyzed using deep learning and have been used to predict future clinical events. In this paper, we propose an interpretable deep learning approach to analyze historical diagnosis code data from the National COVID Cohort Collective (N3C)1 to find the risk factors contributing to developing Long COVID. Using our deep learning approach, we are able to predict if a patient is suffering from Long COVID from a temporally ordered list of diagnosis codes up to 45 days post the first COVID positive test or diagnosis for each patient, with an accuracy of 70.48%. We are then able to examine the trained model using Gradient-weighted Class Activation Mapping (GradCAM) to give each input diagnoses a score. The highest scored diagnosis were deemed to be the most important for making the correct prediction for a patient. We also propose a way to summarize these top diagnoses for each patient in our cohort and look at their temporal trends to determine which codes contribute towards a positive Long COVID diagnosis.
Token Classification for Disambiguating Medical Abbreviations

Abbreviations are unavoidable yet critical parts of the medical text. Using abbreviations, especially in clinical patient notes, can save time and space, protect sensitive information, and help avoid repetitions. However, most abbreviations might have multiple senses, and the lack of a standardized mapping system makes disambiguating abbreviations a difficult and time-consuming task. The main objective of this study is to examine the feasibility of token classification methods for medical abbreviation disambiguation. Specifically, we explore the capability of token classification methods to deal with multiple unique abbreviations in a single text. We use two public datasets to compare and contrast the performance of several transformer models pre-trained on different scientific and medical corpora. Our proposed token classification approach outperforms the more commonly used text classification models for the abbreviation disambiguation task. In particular, the SciBERT model shows a strong performance for both token and text classification tasks over the two considered datasets. Furthermore, we find that abbreviation disambiguation performance for the text classification models becomes comparable to that of token classification only when postprocessing is applied to their predictions, which involves filtering possible labels for an abbreviation based on the training data.
On the Interplay Between Deadline-Constrained Traffic and the Number of Allowed Retransmissions in Random Access Networks

—In this paper, a network comprising wireless devices equipped with buffers transmitting deadline-constrained data packets over a slotted-ALOHA random-access channel is studied. Although communication protocols facilitating retransmissions increase reliability, packet transmission from the queue experi- ences delays and thus, packets with time constraints might be dropped before being successfully transmitted, while at the same time causing the queue size of the buffer to increase. Towards understanding the trade-off between reliability and delays that might lead to packet drops due to the deadline-constrained bursty trafﬁc with retransmissions, a scenario of a wireless network utilizing a slotted-ALOHA random-access channel is investigated. The main focus is to reveal and investigate further the trade-off between the number of retransmissions and the packet deadline as a function of the arrival rate. Hence, we are able to determine numerically the optimal probability of transmissions and number of retransmissions, given the packet arrival rate and the packet deadline. The analysis of the system was done by means of discrete-time Markov chains. Two scenarios are studied: i) the collision channel model (in which a receiver can decode only when a single packet is transmitted), and ii) the case for which receivers have multi-packet reception capabilities. A performance evaluation for a user with different transmit probability and number of retransmissions is conducted, demonstrating their impact on the average drop rate and throughput, while at the same time showing that there exists a set of values, under which improved performance can be acquired.
Neural Matching Fields: Implicit Representation of Matching Fields for Visual Correspondence

Existing pipelines of semantic correspondence commonly include extracting high-level semantic features for the invariance against intra-class variations and background clutters. This architecture, however, inevitably results in a low-resolution matching field that additionally requires an ad-hoc interpolation process as a post-processing for converting it into a high-resolution one, certainly limiting the overall performance of matching results. To overcome this, inspired by recent success of implicit neural representation, we present a novel method for semantic correspondence, called Neural Matching Field (NeMF). However, complicacy and high-dimensionality of a 4D matching field are the major hindrances, which we propose a cost embedding network to process a coarse cost volume to use as a guidance for establishing high-precision matching field through the following fully-connected network. Nevertheless, learning a high-dimensional matching field remains challenging mainly due to computational complexity, since a naive exhaustive inference would require querying from all pixels in the 4D space to infer pixel-wise correspondences. To overcome this, we propose adequate training and inference procedures, which in the training phase, we randomly sample matching candidates and in the inference phase, we iteratively performs PatchMatch-based inference and coordinate optimization at test time. With these combined, competitive results are attained on several standard benchmarks for semantic correspondence. Code and pre-trained weights are available at https://ku-cvlab.github. io/NeMF/.
What Can We Compute in a Single Round of the Congested Clique?

We show that any one-round algorithm that computes a minimum spanning tree (MST) in the unicast congested clique must use a link bandwidth of $\Omega(\log^3 n)$ bits in the worst case. Consequently, computing an MST under the standard assumption of $O(\log n)$-size messages requires at least $2$ rounds. This is the first round complexity lower bound in the unicast congested clique for a problem where the output size is small, i.e., $O(n\log n)$ bits. Our lower bound holds as long as every edge of the MST is output by an incident node. To the best of our knowledge, all prior lower bounds for the unicast congested clique either considered problems with large output sizes (e.g., triangle enumeration) or required every node to learn the entire output.
Roaring Storms in the Planetary-mass Companion VHS 1256-1257 b: Hubble Space Telescope Multiepoch Monitoring Reveals Vigorous Evolution in an Ultracool Atmosphere

The photometric and spectral variability of brown dwarfs probes heterogeneous temperature and cloud distributions and traces the atmospheric circulation patterns. We present a new 42 hr Hubble Space Telescope (HST) Wide Field Camera 3 G141 spectral time series of VHS 1256-1257 b, a late L-type planetary-mass companion that has been shown to have one of the highest variability amplitudes among substellar objects. The light curve is rapidly evolving and best fit by a combination of three sine waves with different periods and a linear trend. The amplitudes of the sine waves and the linear slope vary with the wavelength, and the corresponding spectral variability patterns match the predictions by models invoking either heterogeneous clouds or thermal profile anomalies. Combining these observations with previous HST monitoring data, we find that the peak-to-valley flux difference is 33% ± 2% with an even higher amplitude reaching 38% in the J band, the highest amplitude ever observed in a substellar object. The observed light curve can be explained by maps that are composed of zonal waves, spots, or a mixture of the two. Distinguishing the origin of rapid light curve evolution requires additional long-term monitoring. Our findings underscore the essential role of atmospheric dynamics in shaping brown-dwarf atmospheres and highlight VHS 1256-1257 b as one of the most favorable targets for studying the atmospheres, clouds, and atmospheric circulation of planets and brown dwarfs.
MOCAS: A Multimodal Dataset for Objective Cognitive Workload Assessment on Simultaneous Tasks

This paper presents MOCAS, a multimodal dataset dedicated for human cognitive workload (CWL) assessment. In contrast to existing datasets based on virtual game stimuli, the data in MOCAS was collected from realistic closed-circuit television (CCTV) monitoring tasks, increasing its applicability for real-world scenarios. To build MOCAS, two off-the-shelf wearable sensors and one webcam were utilized to collect physiological signals and behavioral features from 21 human subjects. After each task, participants reported their CWL by completing the NASA-Task Load Index (NASA-TLX) and Instantaneous Self-Assessment (ISA). Personal background (e.g., personality and prior experience) was surveyed using demographic and Big Five Factor personality questionnaires, and two domains of subjective emotion information (i.e., arousal and valence) were obtained from the Self-Assessment Manikin, which could serve as potential indicators for improving CWL recognition performance. Technical validation was conducted to demonstrate that target CWL levels were elicited during simultaneous CCTV monitoring tasks; its results support the high quality of the collected multimodal signals.
Pose Guided Multi-person Image Generation From Text

Transformers have recently been shown to generate high quality images from texts. However, existing methods struggle to create high fidelity full-body images, especially multiple people. A person’s pose has a high degree of freedom that is difficult to describe using words only; this creates errors in the generated image, such as incorrect body proportions and pose. We propose a pose-guided text-to-image model, using pose as an additional input constraint. Using the proposed Key-point Pose Encoding (KPE) to encode human pose into low dimensional representation, our model can generate novel multi-person images accurately representing the pose and text descriptions provided, with minimal errors. We demonstrate that KPE is invariant to changes in the target image domain and image resolution; we show results on the Deepfash-ion dataset and create a new multi-person Deepfashion dataset [1] to demonstrate the multi-capabilities of our approach.
Maximal qubit tomography

A new qubit tomography protocol is introduced, based on a continuous positive operator valued measure, which is supported by the set of pure states, and equivariant under the symmetry group SO(3,R) of the qubit state space. Thus the sample data for the tomography protocol is a discrete set of points on the Bloch sphere obtained by a series of independent measurements on identical replicas of the qubit. Although the maximum likelihood estimator uniquely exists, it cannot be explicitly calculated. Instead, we present another convenient, simple estimator, show that it is unbiased and calculate its variance. Furthermore, a detailed account is given about known properties of related discrete qubit state estimation protocols (like ``minimal qubit tomography''), and the results are compared, discussed.
Transferring Knowledge for Reinforcement Learning in Contact-Rich Manipulation

In manufacturing, assembly tasks have been a challenge for learning algorithms due to variant dynamics of different environments. Reinforcement learning (RL) is a promising framework to automatically learn these tasks, yet it is still not easy to apply a learned policy or skill, that is the ability of solving a task, to a similar environment even if the deployment conditions are only slightly different. In this paper, we address the challenge of transferring knowledge within a family of similar tasks by leveraging multiple skill priors. We propose to learn prior distribution over the specific skill required to accomplish each task and compose the family of skill priors to guide learning the policy for a new task by comparing the similarity between the target task and the prior ones. Our method learns a latent action space representing the skill embedding from demonstrated trajectories for each prior task. We have evaluated our method on a set of peg-in-hole insertion tasks and demonstrate better generalization to new tasks that have never been encountered during training.
Video Referring Expression Comprehension via Transformer with Content-aware Query

Video Referring Expression Comprehension (REC) aims to localize a target object in video frames referred by the natural language expression. Recently, the Transformerbased methods have greatly boosted the performance limit. However, we argue that the current query design is suboptima and suffers from two drawbacks: 1) the slow training convergence process; 2) the lack of fine-grained alignment. To alleviate this, we aim to couple the pure learnable queries with the content information. Specifically, we set up a fixed number of learnable bounding boxes across the frame and the aligned region features are employed to provide fruitful clues. Besides, we explicitly link certain phrases in the sentence to the semantically relevant visual areas. To this end, we introduce two new datasets (i.e., VID-Entity and VidSTG-Entity) by augmenting the VIDSentence and VidSTG datasets with the explicitly referred words in the whole sentence, respectively. Benefiting from this, we conduct the fine-grained cross-modal alignment at the region-phrase level, which ensures more detailed feature representations. Incorporating these two designs, our proposed model (dubbed as ContFormer) achieves the state-of-the-art performance on widely benchmarked datasets. For example on VID-Entity dataset, compared to the previous SOTA, ContFormer achieves 8.75% absolute improvement on Accu. @0.6.
Sequentially Swapping Tokens: Further on Graph Classes

We study the following variant of the 15 puzzle. Given a graph and two token placements on the vertices, we want to find a walk of the minimum length (if any exists) such that the sequence of token swappings along the walk obtains one of the given token placements from the other one. This problem was introduced as Sequential Token Swapping by Yamanaka et al. [JGAA 2019], who showed that the problem is intractable in general but polynomial-time solvable for trees, complete graphs, and cycles. In this paper, we present a polynomial-time algorithm for block-cactus graphs, which include all previously known cases. We also present general tools for showing the hardness of the problem on restricted graph classes such as chordal graphs and chordal bipartite graphs. We also show that the problem is hard on grids and king's graphs, which are the graphs corresponding to the 15 puzzle and its variant with relaxed moves.
IR-MCL: Implicit Representation-Based Online Global Localization

Determining the state of a mobile robot is an essential building block of robot navigation systems. In this letter, we address the problem of estimating the robot's pose in an indoor environment using 2D LiDAR data and investigate how modern environment models can improve gold standard Monte-Carlo localization (MCL) systems. We propose a neural occupancy field to implicitly represent the scene using a neural network. With the pretrained network, we can synthesize 2D LiDAR scans for an arbitrary robot pose through volume rendering. Based on the implicit representation, we can obtain the similarity between a synthesized and actual scan as an observation model and integrate it into an MCL system to perform accurate localization. We evaluate our approach on self-recorded datasets and three publicly available ones. We show that we can accurately and efficiently localize a robot using our approach surpassing the localization performance of state-of-the-art methods. The experiments suggest that the presented implicit representation is able to predict more accurate 2D LiDAR scans leading to an improved observation model for our particle filter-based localization.
Spot-on: A Checkpointing Framework for Fault-Tolerant Long-running Workloads on Cloud Spot Instances

Spot instances offer a cost-effective solution for applications running in the cloud computing environment. However, it is challenging to run long-running jobs on spot instances because they are subject to unpredictable evictions. Here, we present Spot-on, a generic software framework that supports fault-tolerant long-running workloads on spot instances through checkpoint and restart. Spot-on leverages existing checkpointing packages and is compatible with the major cloud vendors. Using a genomics application as a test case, we demonstrated that Spot-on supports both application-specific and transparent checkpointing methods. Compared to running applications using on-demand instances, it allows the completion of these workloads for a significant reduction in computing costs. Compared to running applications using application-specific checkpoint mechanisms, transparent checkpoint-protected applications reduce runtime by up to 40%, leading to further cost savings of up to 86%.
Text-driven Video Prediction

Current video generation models usually convert signals indicating appearance and motion received from inputs (e.g., image, text) or latent spaces (e.g., noise vectors) into consecutive frames, fulfilling a stochastic generation process for the uncertainty introduced by latent code sampling. However, this generation pattern lacks deterministic constraints for both appearance and motion, leading to uncontrollable and undesirable outcomes. To this end, we propose a new task called Text-driven Video Prediction (TVP). Taking the first frame and text caption as inputs, this task aims to synthesize the following frames. Specifically, appearance and motion components are provided by the image and caption separately. The key to addressing the TVP task depends on fully exploring the underlying motion information in text descriptions, thus facilitating plausible video generation. In fact, this task is intrinsically a cause-and-effect problem, as the text content directly influences the motion changes of frames. To investigate the capability of text in causal inference for progressive motion information, our TVP framework contains a Text Inference Module (TIM), producing step-wise embeddings to regulate motion inference for subsequent frames. In particular, a refinement mechanism incorporating global motion semantics guarantees coherent generation. Extensive experiments are conducted on Something-Something V2 and Single Moving MNIST datasets. Experimental results demonstrate that our model achieves better results over other baselines, verifying the effectiveness of the proposed framework.
Communication-Efficient and Drift-Robust Federated Learning via Elastic Net

Federated learning (FL) is a distributed method to train a global model over a set of local clients while keeping data localized. It reduces the risks of privacy and security but faces important challenges including expensive communication costs and client drift issues. To address these issues, we propose FedElasticNet, a communication-efﬁcient and drift-robust FL framework leveraging the elastic net. It repurposes two types of the elastic net regularizers (i.e., (cid:96) 1 and (cid:96) 2 penalties on the local model updates): (1) the (cid:96) 1 -norm regularizer sparsiﬁes the local updates to reduce the communication costs and (2) the (cid:96) 2 -norm regularizer resolves the client drift problem by limiting the impact of drifting local updates due to data heterogeneity. FedElasticNet is a general framework for FL; hence, without additional costs, it can be integrated into prior FL techniques, e.g., FedAvg, FedProx, SCAFFOLD, and FedDyn. We show that our framework effectively resolves the communication cost and client drift problems simultaneously.
Effect of lensing magnification on the apparent distribution of black hole mergers

The recent detection of gravitational waves indicates that stellar-mass black hole binaries are likely to be a key population of sources for forthcoming observations. With future upgrades, ground-based detectors could detect merging black hole binaries out to cosmological distances. Gravitational-wave bursts from high redshifts ($z\ensuremath{\gtrsim}1$) can be strongly magnified by gravitational lensing due to intervening galaxies along the line of sight. In the absence of electromagnetic counterparts, the mergers' intrinsic mass scale and redshift are degenerate with the unknown magnification factor $\ensuremath{\mu}$. Hence, strongly magnified low-mass mergers from high redshifts appear as higher-mass mergers from lower redshifts. We assess the impact of this degeneracy on the mass-redshift distribution of observable events for generic models of binary black hole formation from normal stellar evolution, Pop III star remnants, or a primordial black hole population. We find that strong magnification ($\ensuremath{\mu}\ensuremath{\gtrsim}3$) generally creates a heavy tail of apparently massive mergers in the event distribution from a given detector. For LIGO and its future upgrades, this tail may dominate the population of intrinsically massive, but unlensed mergers in binary black hole formation models involving normal stellar evolution or primordial black holes. Modeling the statistics of lensing magnification can help account for this magnification bias when testing astrophysical scenarios of black hole binary formation and evolution.
Designing a Robust Low-Level Agnostic Controller for a Quadrotor with Actor-Critic Reinforcement Learning

Purpose: Real-life applications using quadrotors introduce a number of disturbances and time-varying properties that pose a challenge to ﬂight controllers. We observed that, when a quadrotor is tasked with picking up and dropping a payload, traditional PID and RL-based controllers found in literature struggle to maintain ﬂight after the vehicle changes its dynamics due to interaction with this external object. Methods: In this work, we introduce domain randomization during the training phase of a low-level waypoint guidance controller based on Soft Actor-Critic. The resulting controller is evaluated on the proposed payload pick up and drop task with added disturbances that emulate real-life operation of the vehicle. Results & Conclusion: We show that, by introducing a certain degree of uncertainty in quadrotor dynamics during training, we can obtain a controller that is capable to perform the proposed task using a larger variation of quadrotor parameters. Additionally, the RL-based controller out-performs a traditional positional PID controller with optimized gains in this task, while remaining agnostic to different simulation parameters.