Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using data extracted from the STRING database. A TF cascade is a sequence of TFs that regulate each other, forming a directed path in the TF network. We constructed a knowledge graph of 81,488 unique TF cascades, with the longest cascade consisting of 62 TFs. Our results highlight the complex and intricate nature of TF interactions, where multiple TFs work together to regulate gene expression. We also identified 10 TFs with the highest regulatory influence based on centrality measurements, providing valuable information for researchers interested in studying specific TFs. Furthermore, our pathway enrichment analysis revealed significant enrichment of various pathways and functional categories, including those involved in cancer and other diseases, as well as those involved in development, differentiation, and cell signaling. The enriched pathways identified in this study may have potential as targets for therapeutic intervention in diseases associated with dysregulation of transcription factors. We have released the dataset, knowledge graph, and graphML methods for the TF cascades, and created a website to display the results, which can be accessed by researchers interested in using this dataset. Our study provides a valuable resource for understanding the complex network of interactions between TFs and their regulatory roles in cellular processes.
We propose a 4-dimensional 2-ary amplitude ring-switched modulation format with 64 symbols, which is denoted as 4D-2A-RS64 encoded over two polarization tributaries to improve the transmission performance over long-haul optical fibers in the presence of the non-linear Kerr effect. At a spectral efficiency of 6 bits per 4D, simulation results show that this format outperforms the polarization division multiplexed (PDM) 8QAM-star modulation as well as the 4D-2A-8PSK over links without inline dispersion management. We evaluate the performance for a WDM transmission of $11\times90~\mathrm{Gbaud}$ channels over a multi-span SSMF link. For an achievable information rate of $4.8\mathrm{bit/s/Hz}$, the maximum transmission distance is improved by $10.6\%$ (400 km) and $4\%$ (160 km) compared to PDM-8QAM-star and 4D-2A-8PSK respectively. The achieved gains are composed of a linear part and a non-linear part, respectively from the improved Euclidean-distance distribution and the constant power property of the 4D modulation. The geometric shaping of the proposed scheme is easy to implement and is robust to Mach-Zehnder modulator (MZM) imbalances and quantization errors stemming from the finite digital-to-analog converter (DAC) resolution. This robustness is compared to the one of other geometric-shaped non-linearity tolerant 4D schemes such as the 4D-2A-8PSK and the 4D-64PRS that can be both outperformed by our scheme in severe conditions.
Text-to-image diffusion models have remarkably excelled in producing diverse, high-quality, and photo-realistic images. This advancement has spurred a growing interest in incorporating specific identities into generated content. Most current methods employ an inversion approach to embed a target visual concept into the text embedding space using a single reference image. However, the newly synthesized faces either closely resemble the reference image in terms of facial attributes, such as expression, or exhibit a reduced capacity for identity preservation. Text descriptions intended to guide the facial attributes of the synthesized face may fall short, owing to the intricate entanglement of identity information with identity-irrelevant facial attributes derived from the reference image. To address these issues, we present the novel use of the extended StyleGAN embedding space $\mathcal{W}_+$, to achieve enhanced identity preservation and disentanglement for diffusion models. By aligning this semantically meaningful human face latent space with text-to-image diffusion models, we succeed in maintaining high fidelity in identity preservation, coupled with the capacity for semantic editing. Additionally, we propose new training objectives to balance the influences of both prompt and identity conditions, ensuring that the identity-irrelevant background remains unaffected during facial attribute modifications. Extensive experiments reveal that our method adeptly generates personalized text-to-image outputs that are not only compatible with prompt descriptions but also amenable to common StyleGAN editing directions in diverse settings. Our source code will be available at \url{https://github.com/csxmli2016/w-plus-adapter}.
Recently, video text detection, tracking, and recognition in natural scenes are becoming very popular in the computer vision community. However, most existing algorithms and benchmarks focus on common text cases (e.g., normal size, density) and single scenario, while ignoring extreme video text challenges, i.e., dense and small text in various scenarios. In this paper, we establish a video text reading benchmark, named DSText V2, which focuses on Dense and Small text reading challenges in the video with various scenarios. Compared with the previous datasets, the proposed dataset mainly include three new challenges: 1) Dense video texts, a new challenge for video text spotters to track and read. 2) High-proportioned small texts, coupled with the blurriness and distortion in the video, will bring further challenges. 3) Various new scenarios, e.g., Game, Sports, etc. The proposed DSText V2 includes 140 video clips from 7 open scenarios, supporting three tasks, i.e., video text detection (Task 1), video text tracking (Task 2), and end-to-end video text spotting (Task 3). In this article, we describe detailed statistical information of the dataset, tasks, evaluation protocols, and the results summaries. Most importantly, a thorough investigation and analysis targeting three unique challenges derived from our dataset are provided, aiming to provide new insights. Moreover, we hope the benchmark will promise video text research in the community. DSText v2 is built upon DSText v1, which was previously introduced to organize the ICDAR 2023 competition for dense and small video text.
Explainable Artificial Intelligence is a concept aimed at making complex algorithms transparent to users through a uniform solution. Researchers have highlighted the importance of integrating domain specific contexts to develop explanations tailored to end users. In this study, we focus on the Schufa housing scoring system in Germany and investigate how users information needs and expectations for explanations vary based on their roles. Using the speculative design approach, we asked business information students to imagine user interfaces that provide housing credit score explanations from the perspectives of both tenants and landlords. Our preliminary findings suggest that although there are general needs that apply to all users, there are also conflicting needs that depend on the practical realities of their roles and how credit scores affect them. We contribute to Human centered XAI research by proposing future research directions that examine users explanatory needs considering their roles and agencies.
Federated learning (FL) is a distributed learning paradigm that allows multiple decentralized clients to collaboratively learn a common model without sharing local data. Although local data is not exposed directly, privacy concerns nonetheless exist as clients' sensitive information can be inferred from intermediate computations. Moreover, such information leakage accumulates substantially over time as the same data is repeatedly used during the iterative learning process. As a result, it can be particularly difficult to balance the privacy-accuracy trade-off when designing privacy-preserving FL algorithms. In this paper, we introduce Upcycled-FL, a novel federated learning framework with first-order approximation applied at every even iteration. Under this framework, half of the FL updates incur no information leakage and require much less computation. We first conduct the theoretical analysis on the convergence (rate) of Upcycled-FL, and then apply perturbation mechanisms to preserve privacy. Experiments on real-world data show that Upcycled-FL consistently outperforms existing methods over heterogeneous data, and significantly improves privacy-accuracy trade-off while reducing 48% of the training time on average.
The impact of non-deterministic outputs from Large Language Models (LLMs) is not well examined for financial text understanding tasks. Through a compelling case study on investing in the US equity market via news sentiment analysis, we uncover substantial variability in sentence-level sentiment classification results, underscoring the innate volatility of LLM outputs. These uncertainties cascade downstream, leading to more significant variations in portfolio construction and return. While tweaking the temperature parameter in the language model decoder presents a potential remedy, it comes at the expense of stifled creativity. Similarly, while ensembling multiple outputs mitigates the effect of volatile outputs, it demands a notable computational investment. This work furnishes practitioners with invaluable insights for adeptly navigating uncertainty in the integration of LLMs into financial decision-making, particularly in scenarios dictated by non-deterministic information.
This paper details the work of the University of Groningen for the BabyLM Challenge. We follow the idea that, like babies, language models should be introduced to simpler concepts first and build off of that knowledge to understand more complex concepts. We examine this strategy of simple-then-complex through a variety of lenses, namely context size, vocabulary, and overall linguistic complexity of the data. We find that only one, context size, is truly beneficial to training a language model. However this simple change to context size gives us improvements of 2 points on average on (Super)GLUE tasks, 1 point on MSGS tasks, and 12\% on average on BLiMP tasks. Our context-limited model outperforms the baseline that was trained on 10$\times$ the amount of data.
Geographic location is essential for modeling tasks in fields ranging from ecology to epidemiology to the Earth system sciences. However, extracting relevant and meaningful characteristics of a location can be challenging, often entailing expensive data fusion or data distillation from global imagery datasets. To address this challenge, we introduce Satellite Contrastive Location-Image Pretraining (SatCLIP), a global, general-purpose geographic location encoder that learns an implicit representation of locations from openly available satellite imagery. Trained location encoders provide vector embeddings summarizing the characteristics of any given location for convenient usage in diverse downstream tasks. We show that SatCLIP embeddings, pretrained on globally sampled multi-spectral Sentinel-2 satellite data, can be used in various predictive tasks that depend on location information but not necessarily satellite imagery, including temperature prediction, animal recognition in imagery, and population density estimation. Across tasks, SatCLIP embeddings consistently outperform embeddings from existing pretrained location encoders, ranging from models trained on natural images to models trained on semantic context. SatCLIP embeddings also help to improve geographic generalization. This demonstrates the potential of general-purpose location encoders and opens the door to learning meaningful representations of our planet from the vast, varied, and largely untapped modalities of geospatial data.
Camouflaged objects adaptively fit their color and texture with the environment, which makes them indistinguishable from the surroundings. Current methods revealed that high-level semantic features can highlight the differences between camouflaged objects and the backgrounds. Consequently, they integrate high-level semantic features with low-level detailed features for accurate camouflaged object detection (COD). Unlike previous designs for multi-level feature fusion, we state that enhancing low-level features is more impending for COD. In this paper, we propose an overlapped window cross-level attention (OWinCA) to achieve the low-level feature enhancement guided by the highest-level features. By sliding an aligned window pair on both the highest- and low-level feature maps, the high-level semantics are explicitly integrated into the low-level details via cross-level attention. Additionally, it employs an overlapped window partition strategy to alleviate the incoherence among windows, which prevents the loss of global information. These adoptions enable the proposed OWinCA to enhance low-level features by promoting the separability of camouflaged objects. The associated proposed OWinCANet fuses these enhanced multi-level features by simple convolution operation to achieve the final COD. Experiments conducted on three large-scale COD datasets demonstrate that our OWinCANet significantly surpasses the current state-of-the-art COD methods.