pwc-archive/papers-with-abstracts huggingface dataset:
Fast High-Quality Enhanced Imaging Algorithm for Layered Dielectric Targets Based on MMW MIMO-SAR System
Authors: Xu Chen, Guangsheng Yu, Zhian Yuan, Hao Wu, Yilin Jiang, Ying Wang, Bin Deng, Limin Guo
Date: 2024-11-22 00:00:00
Tasks: Computational Efficiency, Image Reconstruction

Millimeter-wave (MMW) multiple-input multiple-output synthetic aperture radar (MIMO-SAR) system is a technology that can achieve high resolution, high frame rate, and all-weather imaging and has received extensive attention in the non-destructive testing and internal imaging applications of layered dielectric targets. However, the non-ideal scattering effect caused by dielectric materials can significantly deteriorate the imaging quality when using the existing MIMO-SAR fast algorithms. This paper proposes a rapid, high-quality dielectric target-enhanced imaging algorithm for a new universal non-uniform MIMO-SAR system. The algorithm builds on the existing non-uniform MIMO-SAR dielectric target frequency-domain algorithm (DT-FDA) by constructing a forward sensing operator and incorporating it into the alternating direction method of multipliers (ADMM) framework. This approach avoids large matrix operations while maintaining computational efficiency. By integrating an optimal regularization parameter search, the algorithm enhances the image reconstruction quality of dielectric internal structures or defects. Experimental results show the proposed algorithm outperforms IBP and DT-FDA, achieving better focusing, sidelobe suppression, and 3D imaging accuracy. It yields the lowest image entropy (8.864) and significantly improves efficiency (imaging time: 15.29 s vs. 23295.3 s for IBP).
mmWave Radar for Sit-to-Stand Analysis: A Comparative Study with Wearables and Kinect
Authors: Shuting Hu, Peggy Ackun, Xiang Zhang, Siyang Cao, Jennifer Barton, Melvin G. Hector, Mindy J. Fain, Nima Toosizadeh
Date: 2024-11-22 00:00:00
Tasks: Pose Estimation, Privacy Preserving, STS

This study explores a novel approach for analyzing Sit-to-Stand (STS) movements using millimeter-wave (mmWave) radar technology. The goal is to develop a non-contact sensing, privacy-preserving, and all-day operational method for healthcare applications, including fall risk assessment. We used a 60GHz mmWave radar system to collect radar point cloud data, capturing STS motions from 45 participants. By employing a deep learning pose estimation model, we learned the human skeleton from Kinect built-in body tracking and applied Inverse Kinematics (IK) to calculate joint angles, segment STS motions, and extract commonly used features in fall risk assessment. Radar extracted features were then compared with those obtained from Kinect and wearable sensors. The results demonstrated the effectiveness of mmWave radar in capturing general motion patterns and large joint movements (e.g., trunk). Additionally, the study highlights the advantages and disadvantages of individual sensors and suggests the potential of integrated sensor technologies to improve the accuracy and reliability of motion analysis in clinical and biomedical research settings.
LightLLM: A Versatile Large Language Model for Predictive Light Sensing
Authors: Jiawei Hu, Hong Jia, Mahbub Hassan, Lina Yao, Brano Kusy, Wen Hu
Date: 2024-11-20 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model

We propose LightLLM, a model that fine tunes pre-trained large language models (LLMs) for light-based sensing tasks. It integrates a sensor data encoder to extract key features, a contextual prompt to provide environmental information, and a fusion layer to combine these inputs into a unified representation. This combined input is then processed by the pre-trained LLM, which remains frozen while being fine-tuned through the addition of lightweight, trainable components, allowing the model to adapt to new tasks without altering its original parameters. This approach enables flexible adaptation of LLM to specialized light sensing tasks with minimal computational overhead and retraining effort. We have implemented LightLLM for three light sensing tasks: light-based localization, outdoor solar forecasting, and indoor solar estimation. Using real-world experimental datasets, we demonstrate that LightLLM significantly outperforms state-of-the-art methods, achieving 4.4x improvement in localization accuracy and 3.4x improvement in indoor solar estimation when tested in previously unseen environments. We further demonstrate that LightLLM outperforms ChatGPT-4 with direct prompting, highlighting the advantages of LightLLM's specialized architecture for sensor data fusion with textual prompts.
Finding One's Bearings in the Hyperparameter Landscape of a Wide-Kernel Convolutional Fault Detector
Authors: Dan Hudson, Jurgen van den Hoogen, Martin Atzmueller
Date: 2024-11-19 00:00:00
Tasks: Fault Detection

State-of-the-art algorithms are reported to be almost perfect at distinguishing the vibrations arising from healthy and damaged machine bearings, according to benchmark datasets at least. However, what about their application to new data? In this paper, we confirm that neural networks for bearing fault detection can be crippled by incorrect hyperparameterisation, and also that the correct hyperparameter settings can change when transitioning to new data. The paper combines multiple methods to explain the behaviour of the hyperparameters of a wide-kernel convolutional neural network and how to set them. Since guidance already exists for generic hyperparameters like minibatch size, we focus on how to set architecture-specific hyperparameters such as the width of the convolutional kernels, a topic which might otherwise be obscure. We reflect different data properties by fusing information from seven different benchmark datasets, and our results show that the kernel size in the first layer in particular is sensitive to changes in the data. Looking deeper, we use manipulated copies of one dataset in an attempt to spot why the kernel size sometimes needs to change. The relevance of sampling rate is studied by using different levels of resampling, and spectral content is studied by increasingly filtering out high frequencies. We find that, contrary to speculation in earlier work, high-frequency noise is not the main reason why a wide kernel is preferable to a narrow kernel. Finally, we conclude by stating clear guidance on how to set the hyperparameters of our neural network architecture to work effectively on new data.
The Mean-Field Survival Model for Stripe Formation in Zebrafish Exhibits Turing Instability
Authors: Robert Jencks
Date: 2024-11-22 00:00:00

Zebrafish have been used as a model organism in many areas of biology, including the study of pattern formation. The mean-field survival model is a coupled ODE system describing the expected evolution of chromatophores coordinating to form stripes in zebrafish. This paper presents analysis of the model focusing on parameters for the number of cells, length of distant-neighbor interactions, and rates related to birth and death of chromatophores. We derive the conditions on these parameters for a Turing bifurcation to occur and show that the model predicts patterns qualitatively similar to those in nature. In addition to answering questions about this particular model, this paper also serves as a case study for Turing analysis on coupled ODE systems. The qualitative behavior of such coupled ODE models may deviate significantly from continuum limit models. The ability to analyze such systems directly avoids this concern and allows for a more accurate description of the behavior at physically relevant scales.
Minimizing information loss reduces spiking neuronal networks to differential equations
Authors: Jie Chang, Zhuoran Li, Zhongyi Wang, Louis Tao, Zhuo-Cheng Xiao
Date: 2024-11-22 00:00:00

Spiking neuronal networks (SNNs) are widely used in computational neuroscience, from biologically realistic modeling of local cortical networks to phenomenological modeling of the whole brain. Despite their prevalence, a systematic mathematical theory for finite-sized SNNs remains elusive, even for idealized homogeneous networks. The primary challenges are twofold: 1) the rich, parameter-sensitive SNN dynamics, and 2) the singularity and irreversibility of spikes. These challenges pose significant difficulties when relating SNNs to systems of differential equations, leading previous studies to impose additional assumptions or to focus on individual dynamic regimes. In this study, we introduce a Markov approximation of homogeneous SNN dynamics to minimize information loss when translating SNNs into ordinary differential equations. Our only assumption for the Markov approximation is the fast self-decorrelation of synaptic conductances. The system of ordinary differential equations derived from the Markov model effectively captures high-frequency partial synchrony and the metastability of finite-neuron networks produced by interacting excitatory and inhibitory populations. Besides accurately predicting dynamical statistics, such as firing rates, our theory also quantitatively captures the geometry of attractors and bifurcation structures of SNNs. Thus, our work provides a comprehensive mathematical framework that can systematically map parameters of single-neuron physiology, network coupling, and external stimuli to homogeneous SNN dynamics.
Dynamics of an LPAA model for Tribolium Growth: Insights into Population Chaos
Authors: Samantha J. Brozak, Sophia Peralta, Tin Phan, John D. Nagy, Yang Kuang
Date: 2024-11-21 00:00:00

Flour beetles (genus Tribolium) have long been used as a model organism to understand population dynamics in ecological research. A rich and rigorous body of work has cemented flour beetles' place in the field of mathematical biology. One of the most interesting results using flour beetles is the induction of chaos in a laboratory beetle population, in which the well-established LPA (larvae-pupae-adult) model was used to inform the experimental factors which would lead to chaos. However, whether chaos is an intrinsic property of flour beetles remains an open question. Inspired by new experimental data, we extend the LPA model by stratifying the adult population into newly emerged and mature adults and considering cannibalism as a function of mature adults. We fit the model to longitudinal data of larvae, pupae, and adult beetle populations to demonstrate the model's ability to recapitulate the transient dynamics of flour beetles. We present local and global stability results for the trivial and positive steady states and explore bifurcations and limit cycles numerically. Our results suggest that while chaos is a possibility, it is a rare phenomenon within realistic ranges of the parameters obtained from our experiment, and is likely induced by environmental changes connected to media changes and population censusing.
S$^2$ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning
Authors: Mingze Yin, Hanjing Zhou, Jialu Wu, Yiheng Zhu, Yuxuan Zhan, Zitai Kong, Hongxia Xu, Chang-Yu Hsieh, Jintai Chen, Tingjun Hou, Jian Wu
Date: 2024-11-20 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model, Representation Learning

Antibodies safeguard our health through their precise and potent binding to specific antigens, demonstrating promising therapeutic efficacy in the treatment of numerous diseases, including COVID-19. Recent advancements in biomedical language models have shown the great potential to interpret complex biological structures and functions. However, existing antibody specific models have a notable limitation that they lack explicit consideration for antibody structural information, despite the fact that both 1D sequence and 3D structure carry unique and complementary insights into antibody behavior and functionality. This paper proposes Sequence-Structure multi-level pre-trained Antibody Language Model (S$^2$ALM), combining holistic sequential and structural information in one unified, generic antibody foundation model. We construct a hierarchical pre-training paradigm incorporated with two customized multi-level training objectives to facilitate the modeling of comprehensive antibody representations. S$^2$ALM's representation space uncovers inherent functional binding mechanisms, biological evolution properties and structural interaction patterns. Pre-trained over 75 million sequences and 11.7 million structures, S$^2$ALM can be adopted for diverse downstream tasks: accurately predicting antigen-antibody binding affinities, precisely distinguishing B cell maturation stages, identifying antibody crucial binding positions, and specifically designing novel coronavirus-binding antibodies. Remarkably, S$^2$ALM outperforms well-established and renowned baselines and sets new state-of-the-art performance across extensive antibody specific understanding and generation tasks. S$^2$ALM's ability to model comprehensive and generalized representations further positions its potential to advance real-world therapeutic antibody development, potentially addressing unmet academic, industrial, and clinical needs.
M2oE: Multimodal Collaborative Expert Peptide Model
Authors: Zengzhu Guo, Zhiqi Ma
Date: 2024-11-20 00:00:00
Tasks: Drug Design, model

Peptides are biomolecules comprised of amino acids that play an important role in our body. In recent years, peptides have received extensive attention in drug design and synthesis, and peptide prediction tasks help us better search for functional peptides. Typically, we use the primary sequence and structural information of peptides for model encoding. However, recent studies have focused more on single-modal information (structure or sequence) for prediction without multi-modal approaches. We found that single-modal models are not good at handling datasets with less information in that particular modality. Therefore, this paper proposes the M2oE multi-modal collaborative expert peptide model. Based on previous work, by integrating sequence and spatial structural information, employing expert model and Cross-Attention Mechanism, the model's capabilities are balanced and improved. Experimental results indicate that the M2oE model performs excellently in complex task predictions.
JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data
Authors: Apurva Kalia, Yan Zhou Chen, Dilip Krishnan, Soha Hassoun
Date: 2024-11-18 00:00:00
Tasks: Molecule retrieval from MS/MS spectrum, Molecule retrieval from MS/MS spectrum (bonus chemical formulae)

Motivation: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra and in spectra-to-molecular fingerprint prediction (FP), annotation rates remain low. Results: We introduce in this paper a novel paradigm (JESTR) for annotation. Unlike prior approaches that explicitly construct molecular fingerprints or spectra, JESTR leverages the insight that molecules and their corresponding spectra are views of the same data and effectively embeds their representations in a joint space. Candidate structures are ranked based on cosine similarity between the embeddings of query spectrum and each candidate. We evaluate JESTR against mol-to-spec and spec-to-FP annotation tools on three datasets. On average, for rank@[1-5], JESTR outperforms other tools by 23.6%-71.6%. We further demonstrate the strong value of regularization with candidate molecules during training, boosting rank@1 performance by 11.4% and enhancing the model's ability to discern between target and candidate molecules. When comparing JESTR's performance against that of publicly available pretrained models of SIRIUS and CFM-ID on appropriate subsets of MassSpecGym benchmark dataset, JESTR outperforms these tools by 31% and 238%, respectively. Through JESTR, we offer a novel promising avenue towards accurate annotation, therefore unlocking valuable insights into the metabolome.
The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion
Authors: Yingke Ma, Xuetong Zhao, Yaokai Jia, Zhenxian Han, Caixia Yu, Zhuojing Fan, Zhang Zhang, Jingfa Xiao, Wenming Zhao, Yiming Bao, Meili Chen
Date: 2024-11-23 00:00:00
Tasks: Management

The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper highlights noteworthy enhancements to the GWH since the 2021 version, emphasizing substantial advancements in web interfaces for data submission, database functionality updates, and resource integration. Key updates include the reannotation of released prokaryotic genomes, mirroring of genome resources from National Center for Biotechnology Information (NCBI) GenBank and RefSeq, integration of Poxviridae sequences, implementation of an online batch submission system, enhancements to the quality control system, advanced search capabilities, and the introduction of a controlled-access mechanism for human genome data. These improvements collectively augment the ease and security of data submission and access as well as genome data value, thereby fostering heightened convenience and utility for researchers in the genomic field.
Group-wise normalization in differential abundance analysis of microbiome samples
Authors: Dylan Clark-Boucher, Brent A Coull, Harrison T Reeder, Fenglei Wang, Qi Sun, Jacqueline R Starr, Kyu Ha Lee
Date: 2024-11-23 00:00:00

A key challenge in differential abundance analysis of microbial samples is that the counts for each sample are compositional, resulting in biased comparisons of the absolute abundance across study groups. Normalization-based differential abundance analysis methods rely on external normalization factors that account for the compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled at maintaining the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in differential abundance analysis by re-conceptualizing normalization as a group-level task. We present two normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS). G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings, while maintaining the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the differential abundance analysis method MetagenomeSeq. Code for implementing the methods and replicating the analysis can be found at our GitHub page (https://github.com/dclarkboucher/microbiome_groupwise_normalization).
An improved, high yield method for isolating nuclei from individual zebrafish embryos for single-nucleus RNA sequencing
Authors: Clifford Rostomily, Heidi Lee, Amy Tresenrider, Riza Daza, Andrew Mullen, Jay Shendure, David Kimelman, Cole Trapnell
Date: 2024-11-22 00:00:00

Zebrafish are an ideal system to study the effect(s) of chemical, genetic, and environmental perturbations on development due to their high fecundity and fast growth. Recently, single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high-quality nuclei from zebrafish embryos in a 96-well plate format by bead homogenization in a lysis buffer. Through head-to-head sciPlex-RNA-seq experiments, we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.
Leveraging Gene Expression Data and Explainable Machine Learning for Enhanced Early Detection of Type 2 Diabetes
Authors: Aurora Lithe Roy, Md Kamrul Siam, Nuzhat Noor Islam Prova, Sumaiya Jahan, Abdullah Al Maruf
Date: 2024-11-18 00:00:00
Tasks: Explainable artificial intelligence, Explainable Artificial Intelligence (XAI)

Diabetes, particularly Type 2 diabetes (T2D), poses a substantial global health burden, compounded by its associated complications such as cardiovascular diseases, kidney failure, and vision impairment. Early detection of T2D is critical for improving healthcare outcomes and optimizing resource allocation. In this study, we address the gap in early T2D detection by leveraging machine learning (ML) techniques on gene expression data obtained from T2D patients. Our primary objective was to enhance the accuracy of early T2D detection through advanced ML methodologies and increase the model's trustworthiness using the explainable artificial intelligence (XAI) technique. Analyzing the biological mechanisms underlying T2D through gene expression datasets represents a novel research frontier, relatively less explored in previous studies. While numerous investigations have focused on utilizing clinical and demographic data for T2D prediction, the integration of molecular insights from gene expression datasets offers a unique and promising avenue for understanding the pathophysiology of the disease. By employing six ML classifiers on data sourced from NCBI's Gene Expression Omnibus (GEO), we observed promising performance across all models. Notably, the XGBoost classifier exhibited the highest accuracy, achieving 97%. Our study addresses a notable gap in early T2D detection methodologies, emphasizing the importance of leveraging gene expression data and advanced ML techniques.
Functional dissociations versus post-hoc selection: Moving beyond the Stockart et al. (2025) compromise
Authors: Thomas Schmidt, Xin Ying Lee, Maximilian P. Wolkersdorfer
Date: 2024-11-22 00:00:00
Tasks: Sensitivity

Stockart et al. (2025) recommend guidelines for best practices in the field of unconscious cognition. However, they condone the repeatedly criticized technique of excluding trials with high visibility ratings or of participants with high sensitivity for the critical stimulus. Based on standard signal detection theory for discrimination judgments, we show that post-hoc trial selection only isolates points of neutral response bias but remains consistent with uncomfortably high levels of sensitivity. We argue that post-hoc selection constitutes a sampling fallacy that capitalizes on chance, generates regression artifacts, and wrongly ascribes unconscious processing to stimulus conditions that may be far from indiscriminable. As an alternative, we advocate the study of functional dissociations, where direct (D) and indirect (I) measures are conceptualized as spanning up a two-dimensional D-I-space and where single, sensitivity, and double dissociations appear as distinct curve patterns. While Stockart et al.'s recommendations cover only a single line of that space where D is close to zero, functional dissociations can utilize the entire space, circumventing requirements like null visibility and exhaustive reliability, and allowing for the planful measurement of theoretically meaningful functional relationships between experimentally controlled variables.