Supporting effective health and biomedical information retrieval and navigation: A novel facet view interface evaluation

AbstractThere is a need to provide a more effective user interface to facilitate non-domain experts’ health information seeking in authoritative online databases such as MEDLINE. We developed a new topic cluster based information navigation system called SimMed. Instead of offering a list of documents, SimMed presents users with a list of ranked clusters. Topically similar documents are grouped together to provide users with a better overview of the search results and to support exploration of similar literature within a cluster. We conducted an empirical user study to compare SimMed to a traditional document list based search interface. A total of 42 study participants were recruited to use both interfaces for health information exploration search tasks. The results showed that SimMed is more effective in terms of users’ perceived topic knowledge changes and their engagement in user-system interactions. We also developed a new metric to assess users’ efforts to find relevant citations. On average, users need significantly fewer clicks to find relevant information in SimMed than in the baseline system. Comments from study participants indicated that SimMed is more helpful in finding similar citations, providing related medical terms, and presenting better organized search results, particularly when the initial search is unsatisfactory. Findings from the study shed light on future health and biomedical information retrieval system and interface designs

Computational Aspects of Optional P\'{o}lya Tree

Optional P\'{o}lya Tree (OPT) is a flexible non-parametric Bayesian model for density estimation. Despite its merits, the computation for OPT inference is challenging. In this paper we present time complexity analysis for OPT inference and propose two algorithmic improvements. The first improvement, named Limited-Lookahead Optional P\'{o}lya Tree (LL-OPT), aims at greatly accelerate the computation for OPT inference. The second improvement modifies the output of OPT or LL-OPT and produces a continuous piecewise linear density estimate. We demonstrate the performance of these two improvements using simulations

Data-driven and Model-independent Reconstruction of Modified Gravity

In this paper, the modified gravity, which is characterized by the modified factor $\mu$ in the linear matter density perturbation theory, is reconstructed in a completely data-driven and model-independent way via Gaussian process by using currently available cosmic observations, which consist Pantheon+ SNe Ia samples, observed Hubble parameter $H(z)$ and the redshift space distortion $f\sigma_8(z)$ data points. The reconstructed results suggest a time varying $\mu$ at low redshifts. It also implies more complicated modified gravity beyond the simplest general relativity and the Dvali-Gabadadze-Porrati braneworld model is required.Comment: 8 pages, 3 figures, comments welcom

SOL-NeRF:Sunlight Modeling for Outdoor Scene Decomposition and Relighting

Outdoor scenes often involve large-scale geometry and complex unknown lighting conditions, making it difficult to decompose them into geometry, reflectance and illumination. Recently researchers made attempts to decompose outdoor scenes using Neural Radiance Fields (NeRF) and learning-based lighting and shadow representations. However, diverse lighting conditions and shadows in outdoor scenes are challenging for learning-based models. Moreover, existing methods may produce rough geometry and normal reconstruction and introduce notable shading artifacts when the scene is rendered under a novel illumination. To solve the above problems, we propose SOL-NeRF to decompose outdoor scenes with the help of a hybrid lighting representation and a signed distance field geometry reconstruction. We use a single Spherical Gaussian (SG) lobe to approximate the sun lighting, and a first-order Spherical Harmonic (SH) mixture to resemble the sky lighting. This hybrid representation is specifically designed for outdoor settings, and compactly models the outdoor lighting, ensuring robustness and efficiency. The shadow of the direct sun lighting can be obtained by casting the ray against the mesh extracted from the signed distance field, and the remaining shadow can be approximated by Ambient Occlusion (AO). Additionally, sun lighting color prior and a relaxed Manhattan-world assumption can be further applied to boost decomposition and relighting performance. When changing the lighting condition, our method can produce consistent relighting results with correct shadow effects. Experiments conducted on our hybrid lighting scheme and the entire decomposition pipeline show that our method achieves better reconstruction, decomposition, and relighting performance compared to previous methods both quantitatively and qualitatively.</p

Unified Language-Vision Pretraining in LLM with Dynamic Discrete Visual Tokenization

Recently, the remarkable advance of the Large Language Model (LLM) has inspired researchers to transfer its extraordinary reasoning capability to both vision and language data. However, the prevailing approaches primarily regard the visual input as a prompt and focus exclusively on optimizing the text generation process conditioned upon vision content by a frozen LLM. Such an inequitable treatment of vision and language heavily constrains the model's potential. In this paper, we break through this limitation by representing both vision and language in a unified form. Specifically, we introduce a well-designed visual tokenizer to translate the non-linguistic image into a sequence of discrete tokens like a foreign language that LLM can read. The resulting visual tokens encompass high-level semantics worthy of a word and also support dynamic sequence length varying from the image. Coped with this tokenizer, the presented foundation model called LaVIT can handle both image and text indiscriminately under the same generative learning paradigm. This unification empowers LaVIT to serve as an impressive generalist interface to understand and generate multi-modal content simultaneously. Extensive experiments further showcase that it outperforms the existing models by a large margin on massive vision-language tasks. Our code and models will be available at https://github.com/jy0205/LaVIT

Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Ichthyophthirius multifiliis Through Co-Expression and Machine Learning

Ichthyophthirius multifiliis is a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transcriptomic responses in the liver and head kidney and hemato-serological indexes were profiled under I. multifiliis infection and recovery to investigate systemic immuno-physiological characteristics. Several strategies for massive transcriptomic interpretation, such as differentially expressed genes (DEGs), Poisson linear discriminant (PLDA), and weighted gene co-expression network analysis (WGCNA) models were used to investigate the featured genes/pathways while minimizing the disadvantages of individual methods. During the course of infection, 6,097 and 2,931 DEGs were identified in the head kidney and liver, respectively. Markers of protein processing in the endoplasmic reticulum, oxidative phosphorylation, and the proteasome were highly expressed. Likewise, simultaneous ferroptosis and cellular reconstruction was observed, which is strongly linked to multiple organ dysfunction. In contrast, pathways relevant to cellular replication were up-regulated in only the head kidney, while endocytosis- and phagosome-related pathways were notably expressed in the liver. Moreover, interestingly, most immune-relevant pathways (e.g., leukocyte trans-endothelial migration, Fc gamma R-mediated phagocytosis) were highly activated in the liver, but the same pathways in the head kidney were down-regulated. These conflicting results from different organs suggest that interpretation of co-expression among organs is crucial for profiling of systemic responses during infection. The dual-organ transcriptomics approaches presented in this study will greatly contribute to our understanding of multi-organ interactions under I. multifiliis infection from a broader perspective.publishedVersio