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Apr 17

From shape to fate: making bacterial swarming expansion predictable

Microbial swarming on mucosal surfaces reshapes microbial communities and influences mucosal healing and antibiotic tolerance. Yet even with time-lapse microscopy and deep learning, analyses of swarming colonies remain descriptive and cannot forecast how their fronts reorganize in time. This limitation is significant because the advancing edge determines access to nutrients, host tissue and competing microbes. We recast the expansion of Enterobacter sp. SM3 swarms as a problem of morphological forecasting, and assemble SwarmEvo, a time-lapse dataset represented as boundary-resolved segmentations. TexPol--Net, a texture- and geometry-aware segmentation model, sharpens diffuse edges and preserves fingered fronts, creating a stable substrate for dynamics. On this representation, we develop Morpher, an autoregressive forecasting network with a ``Morphon'' memory that links local curvature to long-range temporal dependencies. Morpher outperforms leading video-prediction models in maintaining front localization and anisotropic branching, and modest segmentation improvements yield noticeably more stable forecasts. Ablations across sequence models, inference strategies and observation ratios show that attention-based architectures with structural memory best preserve dense-finger propagation. By uniting geometry-aware segmentation with morphology-level forecasting, this framework turns swarming expansion into a predictive dynamical system, enabling quantitative interrogation and potential control of microbial collectives during mucosal repair and gut ecosystem engineering.

  • 8 authors
·
Feb 1

Will It Survive? Deciphering the Fate of AI-Generated Code in Open Source

The integration of AI agents as coding assistants into software development has raised questions about the long-term viability of AI agent-generated code. A prevailing hypothesis within the software engineering community suggests this code is "disposable", meaning it is merged quickly but discarded shortly thereafter. If true, organizations risk shifting maintenance burden from generation to post-deployment remediation. We investigate this hypothesis through survival analysis of 201 open-source projects, tracking over 200,000 code units authored by AI agents versus humans. Contrary to the disposable code narrative, agent-authored code survives significantly longer: at the line level, it exhibits a 15.8 percentage-point lower modification rate and 16% lower hazard of modification (HR = 0.842, p < 0.001). However, modification profiles differ. Agent-authored code shows modestly elevated corrective rates (26.3% vs. 23.0%), while human code shows higher adaptive rates. However, the effect sizes are small (Cramér's V = 0.116), and per-agent variation exceeds the agent-human gap. Turning to prediction, textual features can identify modification-prone code (AUC-ROC = 0.671), but predicting when modifications occur remains challenging (Macro F1 = 0.285), suggesting timing depends on external organizational dynamics. The bottleneck for agent-generated code may not be generation quality, but the organizational practices that govern its long-term evolution.

  • 2 authors
·
Jan 23

Accurate Expert Predictions in MoE Inference via Cross-Layer Gate

Large Language Models (LLMs) have demonstrated impressive performance across various tasks, and their application in edge scenarios has attracted significant attention. However, sparse-activated Mixture-of-Experts (MoE) models, which are well suited for edge scenarios, have received relatively little attention due to their high memory demands. Offload-based methods have been proposed to address this challenge, but they face difficulties with expert prediction. Inaccurate expert predictions can result in prolonged inference delays. To promote the application of MoE models in edge scenarios, we propose Fate, an offloading system designed for MoE models to enable efficient inference in resource-constrained environments. The key insight behind Fate is that gate inputs from adjacent layers can be effectively used for expert prefetching, achieving high prediction accuracy without additional GPU overhead. Furthermore, Fate employs a shallow-favoring expert caching strategy that increases the expert hit rate to 99\%. Additionally, Fate integrates tailored quantization strategies for cache optimization and IO efficiency. Experimental results show that, compared to Load on Demand and Expert Activation Path-based method, Fate achieves up to 4.5x and 1.9x speedups in prefill speed and up to 4.1x and 2.2x speedups in decoding speed, respectively, while maintaining inference quality. Moreover, Fate's performance improvements are scalable across different memory budgets.

  • 8 authors
·
Feb 17, 2025

Governance of the AI, by the AI, and for the AI

Over the past half century, there have been several false dawns during which the "arrival" of world-changing artificial intelligence (AI) has been heralded. Tempting fate, the authors believe the age of AI has, indeed, finally arrived. Powerful image generators, such as DALL-E2 and Midjourney have suddenly allowed anyone with access the ability easily to create rich and complex art. In a similar vein, text generators, such as GPT3.5 (including ChatGPT) and BLOOM, allow users to compose detailed written descriptions of many topics of interest. And, it is even possible now for a person without extensive expertise in writing software to use AI to generate code capable of myriad applications. While AI will continue to evolve and improve, probably at a rapid rate, the current state of AI is already ushering in profound changes to many different sectors of society. Every new technology challenges the ability of humanity to govern it wisely. However, governance is usually viewed as both possible and necessary due to the disruption new technology often poses to social structures, industries, the environment, and other important human concerns. In this article, we offer an analysis of a range of interactions between AI and governance, with the hope that wise decisions may be made that maximize benefits and minimize costs. The article addresses two main aspects of this relationship: the governance of AI by humanity, and the governance of humanity by AI. The approach we have taken is itself informed by AI, as this article was written collaboratively by the authors and ChatGPT.

  • 2 authors
·
May 3, 2023

Origin of Phobos and Deimos : Orbital evolution shortly after formation from a potential dislocation

This paper deals with the formation and evolution of Mars' moons, Phobos and Deimos, assuming the dislocation of a larger progenitor as the origin of these moons. The study by Hyodo et al. (2022) argue that under somewhat simplistic modeling, the post-dislocation orbits of Phobos and Deimos inevitably collide within 10,000 years, leading to their mutual annihilation. These findings are based on N-body simulations, accounting for Mars' J_2 and J_4 gravitational perturbations and mutual perturbations between the moons. In this paper, we challenge these findings by extending their work. We incorporate important perturbations such as solar perturbations, Mars' axial precession and nutation, and its deformation along three axes. We also extend some of the hypotheses made by Hyodo et al. (2022) concerning the initial distribution of Phobos and Deimos after the dislocation. Our analysis reveals that including these additional perturbations as well as the possibility of having more than two fragments after the dislocation does not alter the ultimate fate of Phobos and Deimos. The moons still converge towards collision within comparable timescales, supporting Hyodo et al. (2022) conclusions that the dislocation hypothesis under the dynamical scenario developed by Bagheri et al. (2021) has, in the best conditions, about 10\% chance of surviving after the first 100,000 years following their formation.

  • 3 authors
·
Apr 11, 2025

T-RAG: Lessons from the LLM Trenches

Large Language Models (LLM) have shown remarkable language capabilities fueling attempts to integrate them into applications across a wide range of domains. An important application area is question answering over private enterprise documents where the main considerations are data security, which necessitates applications that can be deployed on-prem, limited computational resources and the need for a robust application that correctly responds to queries. Retrieval-Augmented Generation (RAG) has emerged as the most prominent framework for building LLM-based applications. While building a RAG is relatively straightforward, making it robust and a reliable application requires extensive customization and relatively deep knowledge of the application domain. We share our experiences building and deploying an LLM application for question answering over private organizational documents. Our application combines the use of RAG with a finetuned open-source LLM. Additionally, our system, which we call Tree-RAG (T-RAG), uses a tree structure to represent entity hierarchies within the organization. This is used to generate a textual description to augment the context when responding to user queries pertaining to entities within the organization's hierarchy. Our evaluations show that this combination performs better than a simple RAG or finetuning implementation. Finally, we share some lessons learned based on our experiences building an LLM application for real-world use.

  • 3 authors
·
Feb 12, 2024

Enhancing Few-Shot Image Classification through Learnable Multi-Scale Embedding and Attention Mechanisms

In the context of few-shot classification, the goal is to train a classifier using a limited number of samples while maintaining satisfactory performance. However, traditional metric-based methods exhibit certain limitations in achieving this objective. These methods typically rely on a single distance value between the query feature and support feature, thereby overlooking the contribution of shallow features. To overcome this challenge, we propose a novel approach in this paper. Our approach involves utilizing a multi-output embedding network that maps samples into distinct feature spaces. The proposed method extracts feature vectors at different stages, enabling the model to capture both global and abstract features. By utilizing these diverse feature spaces, our model enhances its performance. Moreover, employing a self-attention mechanism improves the refinement of features at each stage, leading to even more robust representations and improved overall performance. Furthermore, assigning learnable weights to each stage significantly improved performance and results. We conducted comprehensive evaluations on the MiniImageNet and FC100 datasets, specifically in the 5-way 1-shot and 5-way 5-shot scenarios. Additionally, we performed cross-domain tasks across eight benchmark datasets, achieving high accuracy in the testing domains. These evaluations demonstrate the efficacy of our proposed method in comparison to state-of-the-art approaches. https://github.com/FatemehAskari/MSENet

  • 3 authors
·
Sep 12, 2024

Fanar: An Arabic-Centric Multimodal Generative AI Platform

We present Fanar, a platform for Arabic-centric multimodal generative AI systems, that supports language, speech and image generation tasks. At the heart of Fanar are Fanar Star and Fanar Prime, two highly capable Arabic Large Language Models (LLMs) that are best in the class on well established benchmarks for similar sized models. Fanar Star is a 7B (billion) parameter model that was trained from scratch on nearly 1 trillion clean and deduplicated Arabic, English and Code tokens. Fanar Prime is a 9B parameter model continually trained on the Gemma-2 9B base model on the same 1 trillion token set. Both models are concurrently deployed and designed to address different types of prompts transparently routed through a custom-built orchestrator. The Fanar platform provides many other capabilities including a customized Islamic Retrieval Augmented Generation (RAG) system for handling religious prompts, a Recency RAG for summarizing information about current or recent events that have occurred after the pre-training data cut-off date. The platform provides additional cognitive capabilities including in-house bilingual speech recognition that supports multiple Arabic dialects, voice and image generation that is fine-tuned to better reflect regional characteristics. Finally, Fanar provides an attribution service that can be used to verify the authenticity of fact based generated content. The design, development, and implementation of Fanar was entirely undertaken at Hamad Bin Khalifa University's Qatar Computing Research Institute (QCRI) and was sponsored by Qatar's Ministry of Communications and Information Technology to enable sovereign AI technology development.

  • 42 authors
·
Jan 18, 2025

Fanar 2.0: Arabic Generative AI Stack

We present Fanar 2.0, the second generation of Qatar's Arabic-centric Generative AI platform. Sovereignty is a first-class design principle: every component, from data pipelines to deployment infrastructure, was designed and operated entirely at QCRI, Hamad Bin Khalifa University. Fanar 2.0 is a story of resource-constrained excellence: the effort ran on 256 NVIDIA H100 GPUs, with Arabic having only ~0.5% of web data despite 400 million native speakers. Fanar 2.0 adopts a disciplined strategy of data quality over quantity, targeted continual pre-training, and model merging to achieve substantial gains within these constraints. At the core is Fanar-27B, continually pre-trained from a Gemma-3-27B backbone on a curated corpus of 120 billion high-quality tokens across three data recipes. Despite using 8x fewer pre-training tokens than Fanar 1.0, it delivers substantial benchmark improvements: Arabic knowledge (+9.1 pts), language (+7.3 pts), dialects (+3.5 pts), and English capability (+7.6 pts). Beyond the core LLM, Fanar 2.0 introduces a rich stack of new capabilities. FanarGuard is a state-of-the-art 4B bilingual moderation filter for Arabic safety and cultural alignment. The speech family Aura gains a long-form ASR model for hours-long audio. Oryx vision family adds Arabic-aware image and video understanding alongside culturally grounded image generation. An agentic tool-calling framework enables multi-step workflows. Fanar-Sadiq utilizes a multi-agent architecture for Islamic content. Fanar-Diwan provides classical Arabic poetry generation. FanarShaheen delivers LLM-powered bilingual translation. A redesigned multi-layer orchestrator coordinates all components through intent-aware routing and defense-in-depth safety validation. Taken together, Fanar 2.0 demonstrates that sovereign, resource-constrained AI development can produce systems competitive with those built at far greater scale.

  • 37 authors
·
Mar 17