Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein pathways are key drivers of embryogenesis and physiological processes. Comprehending their diverse behaviors is essential for tackling diseases, including cancer, as well as for engineering novel biological constructs. Despite the availability of extensive mathematical models represented in Systems Biology Markup Language (SBML), researchers face significant challenges in exploring the full spectrum of behaviors and optimizing interventions to efficiently shape those behaviors. Existing tools designed for simulation of biological network models are not tailored to facilitate interventions on network dynamics nor to facilitate automated discovery. Leveraging recent developments in machine learning (ML), this paper introduces SBMLtoODEjax, a lightweight library designed to seamlessly integrate SBML models with ML-supported pipelines, powered by JAX. SBMLtoODEjax facilitates the reuse and customization of SBML-based models, harnessing JAX's capabilities for efficient parallel simulations and optimization, with the aim to accelerate research in biological network analysis.
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What makes a presupposition of an utterance -- information taken for granted by its speaker -- different from other pragmatic inferences such as an entailment is projectivity (e.g., the negative sentence the boy did not stop shedding tears presupposes the boy had shed tears before). The projectivity may vary depending on the combination of presupposition triggers and environments. However, prior natural language understanding studies fail to take it into account as they either use no human baseline or include only negation as an entailment-canceling environment to evaluate models' performance. The current study attempts to reconcile these issues. We introduce a new dataset, projectivity of presupposition (PROPRES, which includes 12k premise-hypothesis pairs crossing six triggers involving some lexical variety with five environments. Our human evaluation reveals that humans exhibit variable projectivity in some cases. However, the model evaluation shows that the best-performed model, DeBERTa, does not fully capture it. Our findings suggest that probing studies on pragmatic inferences should take extra care of the human judgment variability and the combination of linguistic items.
Retinal vascular segmentation, is a widely researched subject in biomedical image processing, aims to relieve ophthalmologists' workload when treating and detecting retinal disorders. However, segmenting retinal vessels has its own set of challenges, with prior techniques failing to generate adequate results when segmenting branches and microvascular structures. The neural network approaches used recently are characterized by the inability to keep local and global properties together and the failure to capture tiny end vessels make it challenging to attain the desired result. To reduce this retinal vessel segmentation problem, we propose a full-scale micro-vessel extraction mechanism based on an encoder-decoder neural network architecture, sigmoid smoothing, and an adaptive threshold method. The network consists of of residual, encoder booster, bottleneck enhancement, squeeze, and excitation building blocks. All of these blocks together help to improve the feature extraction and prediction of the segmentation map. The proposed solution has been evaluated using the DRIVE, CHASE-DB1, and STARE datasets, and competitive results are obtained when compared with previous studies. The AUC and accuracy on the DRIVE dataset are 0.9884 and 0.9702, respectively. On the CHASE-DB1 dataset, the scores are 0.9903 and 0.9755, respectively. On the STARE dataset, the scores are 0.9916 and 0.9750, respectively. The performance achieved is one step ahead of what has been done in previous studies, and this results in a higher chance of having this solution in real-life diagnostic centers that seek ophthalmologists attention.
The recently emerging text-to-motion advances have spired numerous attempts for convenient and interactive human motion generation. Yet, existing methods are largely limited to generating body motions only without considering the rich two-hand motions, let alone handling various conditions like body dynamics or texts. To break the data bottleneck, we propose BOTH57M, a novel multi-modal dataset for two-hand motion generation. Our dataset includes accurate motion tracking for the human body and hands and provides pair-wised finger-level hand annotations and body descriptions. We further provide a strong baseline method, BOTH2Hands, for the novel task: generating vivid two-hand motions from both implicit body dynamics and explicit text prompts. We first warm up two parallel body-to-hand and text-to-hand diffusion models and then utilize the cross-attention transformer for motion blending. Extensive experiments and cross-validations demonstrate the effectiveness of our approach and dataset for generating convincing two-hand motions from the hybrid body-and-textual conditions. Our dataset and code will be disseminated to the community for future research.
The past decade has witnessed the rapid development of geospatial artificial intelligence (GeoAI) primarily due to the ground-breaking achievements in deep learning and machine learning. A growing number of scholars from cartography have demonstrated successfully that GeoAI can accelerate previously complex cartographic design tasks and even enable cartographic creativity in new ways. Despite the promise of GeoAI, researchers and practitioners have growing concerns about the ethical issues of GeoAI for cartography. In this paper, we conducted a systematic content analysis and narrative synthesis of research studies integrating GeoAI and cartography to summarize current research and development trends regarding the usage of GeoAI for cartographic design. Based on this review and synthesis, we first identify dimensions of GeoAI methods for cartography such as data sources, data formats, map evaluations, and six contemporary GeoAI models, each of which serves a variety of cartographic tasks. These models include decision trees, knowledge graph and semantic web technologies, deep convolutional neural networks, generative adversarial networks, graph neural networks, and reinforcement learning. Further, we summarize seven cartographic design applications where GeoAI have been effectively employed: generalization, symbolization, typography, map reading, map interpretation, map analysis, and map production. We also raise five potential ethical challenges that need to be addressed in the integration of GeoAI for cartography: commodification, responsibility, privacy, bias, and (together) transparency, explainability, and provenance. We conclude by identifying four potential research directions for future cartographic research with GeoAI: GeoAI-enabled active cartographic symbolism, human-in-the-loop GeoAI for cartography, GeoAI-based mapping-as-a-service, and generative GeoAI for cartography.
This study presents the outcomes of empirical investigations pertaining to human-vehicle interactions involving an autonomous vehicle equipped with both internal and external Human Machine Interfaces (HMIs) within a crosswalk scenario. The internal and external HMIs were integrated with implicit communication techniques, incorporating a combination of gentle and aggressive braking maneuvers within the crosswalk. Data were collected through a combination of questionnaires and quantifiable metrics, including pedestrian decision to cross related to the vehicle distance and speed. The questionnaire responses reveal that pedestrians experience enhanced safety perceptions when the external HMI and gentle braking maneuvers are used in tandem. In contrast, the measured variables demonstrate that the external HMI proves effective when complemented by the gentle braking maneuver. Furthermore, the questionnaire results highlight that the internal HMI enhances passenger confidence only when paired with the aggressive braking maneuver.
Chain-of-thought reasoning, a cognitive process fundamental to human intelligence, has garnered significant attention in the realm of artificial intelligence and natural language processing. However, there still remains a lack of a comprehensive survey for this arena. To this end, we take the first step and present a thorough survey of this research field carefully and widely. We use X-of-Thought to refer to Chain-of-Thought in a broad sense. In detail, we systematically organize the current research according to the taxonomies of methods, including XoT construction, XoT structure variants, and enhanced XoT. Additionally, we describe XoT with frontier applications, covering planning, tool use, and distillation. Furthermore, we address challenges and discuss some future directions, including faithfulness, multi-modal, and theory. We hope this survey serves as a valuable resource for researchers seeking to innovate within the domain of chain-of-thought reasoning.
Believable proxies of human behavior can empower interactive applications ranging from immersive environments to rehearsal spaces for interpersonal communication to prototyping tools. In this paper, we introduce generative agents--computational software agents that simulate believable human behavior. Generative agents wake up, cook breakfast, and head to work; artists paint, while authors write; they form opinions, notice each other, and initiate conversations; they remember and reflect on days past as they plan the next day. To enable generative agents, we describe an architecture that extends a large language model to store a complete record of the agent's experiences using natural language, synthesize those memories over time into higher-level reflections, and retrieve them dynamically to plan behavior. We instantiate generative agents to populate an interactive sandbox environment inspired by The Sims, where end users can interact with a small town of twenty five agents using natural language. In an evaluation, these generative agents produce believable individual and emergent social behaviors: for example, starting with only a single user-specified notion that one agent wants to throw a Valentine's Day party, the agents autonomously spread invitations to the party over the next two days, make new acquaintances, ask each other out on dates to the party, and coordinate to show up for the party together at the right time. We demonstrate through ablation that the components of our agent architecture--observation, planning, and reflection--each contribute critically to the believability of agent behavior. By fusing large language models with computational, interactive agents, this work introduces architectural and interaction patterns for enabling believable simulations of human behavior.
Multimodality Representation Learning, as a technique of learning to embed information from different modalities and their correlations, has achieved remarkable success on a variety of applications, such as Visual Question Answering (VQA), Natural Language for Visual Reasoning (NLVR), and Vision Language Retrieval (VLR). Among these applications, cross-modal interaction and complementary information from different modalities are crucial for advanced models to perform any multimodal task, e.g., understand, recognize, retrieve, or generate optimally. Researchers have proposed diverse methods to address these tasks. The different variants of transformer-based architectures performed extraordinarily on multiple modalities. This survey presents the comprehensive literature on the evolution and enhancement of deep learning multimodal architectures to deal with textual, visual and audio features for diverse cross-modal and modern multimodal tasks. This study summarizes the (i) recent task-specific deep learning methodologies, (ii) the pretraining types and multimodal pretraining objectives, (iii) from state-of-the-art pretrained multimodal approaches to unifying architectures, and (iv) multimodal task categories and possible future improvements that can be devised for better multimodal learning. Moreover, we prepare a dataset section for new researchers that covers most of the benchmarks for pretraining and finetuning. Finally, major challenges, gaps, and potential research topics are explored. A constantly-updated paperlist related to our survey is maintained at //github.com/marslanm/multimodality-representation-learning.
Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.
A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics community.
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