Recent developments in the Internet of Bio-Nano Things (IoBNT) are laying the groundwork for innovative applications across the healthcare sector. Nanodevices designed to operate within the body, managed remotely via the internet, are envisioned to promptly detect and actuate on potential diseases. In this vision, an inherent challenge arises due to the limited capabilities of individual nanosensors; specifically, nanosensors must communicate with one another to collaborate as a cluster. Aiming to research the boundaries of the clustering capabilities, this survey emphasizes data-driven communication strategies in molecular communication (MC) channels as a means of linking nanosensors. Relying on the flexibility and robustness of machine learning (ML) methods to tackle the dynamic nature of MC channels, the MC research community frequently refers to neural network (NN) architectures. This interdisciplinary research field encompasses various aspects, including the use of NNs to facilitate communication in MC environments, their implementation at the nanoscale, explainable approaches for NNs, and dataset generation for training. Within this survey, we provide a comprehensive analysis of fundamental perspectives on recent trends in NN architectures for MC, the feasibility of their implementation at the nanoscale, applied explainable artificial intelligence (XAI) techniques, and the accessibility of datasets along with best practices for their generation. Additionally, we offer open-source code repositories that illustrate NN-based methods to support reproducible research for key MC scenarios. Finally, we identify emerging research challenges, such as robust NN architectures, biologically integrated NN modules, and scalable training strategies.
Large-scale Earth system datasets, from high-resolution remote sensing imagery to spatiotemporal climate model outputs, exhibit characteristics analogous to those of standard videos. Their inherent spatial, temporal, and spectral redundancies can thus be readily exploited by established video compression techniques. Here, we present xarrayvideo, a Python library for compressing multichannel spatiotemporal datasets by encoding them as videos. Our approach achieves compression ratios of up to 250x while maintaining high fidelity by leveraging standard, well-optimized video codecs through ffmpeg. We demonstrate the library's effectiveness on four real-world multichannel spatiotemporal datasets: DynamicEarthNet (very high resolution Planet images), DeepExtremeCubes (high resolution Sentinel-2 images), ERA5 (weather reanalysis data), and the SimpleS2 dataset (high resolution multichannel Sentinel-2 images), achieving Peak Signal-to-Noise Ratios (PSNRs) of 55.86, 40.60, 46.58, and 43.23 dB at 0.1 bits per pixel per band (bpppb) and 65.91, 54.28, 62.90, and 55.04 dB at 1 bpppb. We are redistributing two of these datasets, DeepExtremeCubes (2.3 Tb) and DynamicEarthNet (525 Gb), in the machine-learning-ready and cloud-ready TACO format through HuggingFace at significantly reduced sizes (270 Gb and 8.5 Gb, respectively) without compromising quality (PSNR 55.77-56.65 and 60.15). No performance loss is observed when the compressed versions of these datasets are used in their respective deep learning-based downstream tasks (next step reflectance prediction and landcover segmentation). In conclusion, xarrayvideo presents an efficient solution for handling the rapidly growing size of Earth observation datasets, making advanced compression techniques accessible and practical to the Earth science community. The library is available for use at https://github.com/IPL-UV/xarrayvideo
Ensuring persona fidelity in large language models (LLMs) is essential for maintaining coherent and engaging human-AI interactions. However, LLMs often exhibit Out-of-Character (OOC) behavior, where generated responses deviate from an assigned persona, leading to inconsistencies that affect model reliability. Existing evaluation methods typically assign single scores to entire responses, struggling to capture subtle persona misalignment, particularly in long-form text generation. To address this limitation, we propose an atomic-level evaluation framework that quantifies persona fidelity at a finer granularity. Our three key metrics measure the degree of persona alignment and consistency within and across generations. Our approach enables a more precise and realistic assessment of persona fidelity by identifying subtle deviations that real users would encounter. Through our experiments, we demonstrate that our framework effectively detects persona inconsistencies that prior methods overlook. By analyzing persona fidelity across diverse tasks and personality types, we reveal how task structure and persona desirability influence model adaptability, highlighting challenges in maintaining consistent persona expression.
We propose Legato, a new end-to-end transformer model for optical music recognition (OMR). Legato is the first large-scale pretrained OMR model capable of recognizing full-page or multi-page typeset music scores and the first to generate documents in ABC notation, a concise, human-readable format for symbolic music. Bringing together a pretrained vision encoder with an ABC decoder trained on a dataset of more than 214K images, our model exhibits the strong ability to generalize across various typeset scores. We conduct experiments on a range of datasets and demonstrate that our model achieves state-of-the-art performance. Given the lack of a standardized evaluation for end-to-end OMR, we comprehensively compare our model against the previous state of the art using a diverse set of metrics.
We present DuetGen, a novel framework for generating interactive two-person dances from music. The key challenge of this task lies in the inherent complexities of two-person dance interactions, where the partners need to synchronize both with each other and with the music. Inspired by the recent advances in motion synthesis, we propose a two-stage solution: encoding two-person motions into discrete tokens and then generating these tokens from music. To effectively capture intricate interactions, we represent both dancers' motions as a unified whole to learn the necessary motion tokens, and adopt a coarse-to-fine learning strategy in both the stages. Our first stage utilizes a VQ-VAE that hierarchically separates high-level semantic features at a coarse temporal resolution from low-level details at a finer resolution, producing two discrete token sequences at different abstraction levels. Subsequently, in the second stage, two generative masked transformers learn to map music signals to these dance tokens: the first producing high-level semantic tokens, and the second, conditioned on music and these semantic tokens, producing the low-level tokens. We train both transformers to learn to predict randomly masked tokens within the sequence, enabling them to iteratively generate motion tokens by filling an empty token sequence during inference. Through the hierarchical masked modeling and dedicated interaction representation, DuetGen achieves the generation of synchronized and interactive two-person dances across various genres. Extensive experiments and user studies on a benchmark duet dance dataset demonstrate state-of-the-art performance of DuetGen in motion realism, music-dance alignment, and partner coordination.
Direct volume rendering (DVR) is a fundamental technique for visualizing volumetric data, with transfer functions (TFs) playing a crucial role in extracting meaningful structures. However, designing effective TFs remains unintuitive due to the semantic gap between user intent and TF parameter space. Researchers have developed numerous TF optimization methods to bridge this gap. However, existing methods still face two challenges: large exploration space and weak generalizability. To address these issues, we propose What You Think is What You Get (WYTWYG) framework, which leveraging Multi-model Large Language Models (MLLMs) to guide the TF optimization based on user intent. Specifically, we first introduce a novel TF optimization approach comprising two core components: (1) an evolution-based explorer for effective exploration of the TF space, and (2) a volume rendering quality evaluator based on MLLMs to provide generalizable visual guidance. We further propose a TF interactive design system based on this approach. We demonstrate the general applicability of our framework through three case studies, and validate the effectiveness of each component through extensive experiments. Our code is available at: https://github.com/wyysteelhead/TFevolve.
This paper introduces Decoupled Supervised Learning with Information Regularization (DeInfoReg), a novel approach that transforms a long gradient flow into multiple shorter ones, thereby mitigating the vanishing gradient problem. Integrating a pipeline strategy, DeInfoReg enables model parallelization across multiple GPUs, significantly improving training throughput. We compare our proposed method with standard backpropagation and other gradient flow decomposition techniques. Extensive experiments on diverse tasks and datasets demonstrate that DeInfoReg achieves superior performance and better noise resistance than traditional BP models and efficiently utilizes parallel computing resources. The code for reproducibility is available at: https://github.com/ianzih/Decoupled-Supervised-Learning-for-Information-Regularization/.
Deploying quantized deep neural network (DNN) models with resource adaptation capabilities on ubiquitous Internet of Things (IoT) devices to provide high-quality AI services can leverage the benefits of compression and meet multi-scenario resource requirements. However, existing dynamic/mixed precision quantization requires retraining or special hardware, whereas post-training quantization (PTQ) has two limitations for resource adaptation: (i) The state-of-the-art PTQ methods only provide one fixed bitwidth model, which makes it challenging to adapt to the dynamic resources of IoT devices; (ii) Deploying multiple PTQ models with diverse bitwidths consumes large storage resources and switching overheads. To this end, this paper introduces a resource-friendly post-training integer-nesting quantization, i.e., NestQuant, for on-device quantized model switching on IoT devices. The proposed NestQuant incorporates the integer weight decomposition, which bit-wise splits quantized weights into higher-bit and lower-bit weights of integer data types. It also contains a decomposed weights nesting mechanism to optimize the higher-bit weights by adaptive rounding and nest them into the original quantized weights. In deployment, we can send and store only one NestQuant model and switch between the full-bit/part-bit model by paging in/out lower-bit weights to adapt to resource changes and reduce consumption. Experimental results on the ImageNet-1K pretrained DNNs demonstrated that the NestQuant model can achieve high performance in top-1 accuracy, and reduce in terms of data transmission, storage consumption, and switching overheads. In particular, the ResNet-101 with INT8 nesting INT6 can achieve 78.1% and 77.9% accuracy for full-bit and part-bit models, respectively, and reduce switching overheads by approximately 78.1% compared with diverse bitwidths PTQ models.
The recent shift in Generative AI (GenAI) applications from cloud-only environments to end-user devices introduces new challenges in resource management, system efficiency, and user experience. This paper presents ConsumerBench, a comprehensive benchmarking framework designed to evaluate the system efficiency and response time of GenAI models running on end-user devices. Unlike existing benchmarks that assume exclusive model access on dedicated GPUs, ConsumerBench simulates realistic multi-application scenarios executing concurrently on constrained hardware. Furthermore, ConsumerBench supports customizable workflows that simulate complex tasks requiring coordination among multiple applications. ConsumerBench captures both application-level metrics, including latency and Service Level Objective (SLO) attainment, and system-level metrics like CPU/GPU utilization and memory bandwidth. Through extensive experiments, ConsumerBench reveals inefficiencies in resource sharing, unfair scheduling under greedy allocation, and performance pitfalls of static model server configurations. The paper also provides practical insights for model developers and system designers, highlighting the benefits of custom kernels tailored to consumer-grade GPU architectures and the value of implementing SLO-aware scheduling strategies.
Scalp electroencephalography (EEG) and intracranial EEG (iEEG) are vital for epilepsy diagnosis and treatment. Their unified analysis offers the potential to harness the complementary strengths of each modality but is challenging due to variations in recording montages, amplitude and signal-to-noise ratio (SNR), and frequency components. To address the aforementioned challenges, this paper introduces EpiNT, a novel Transformer-based pre-trained model for unified EEG and iEEG analysis. EpiNT employs channel-independent modeling with masked autoencoders (MAE) and vector quantization (VQ), along with a frequency domain mapping quantizer to capture crucial frequency features. Pre-trained on over 2,700 hours of multi-modal clinical neurophysiological data from 1,199 patients, EpiNT outperformed both randomly initialized models and other pre-trained methods on six downstream classification tasks, demonstrating robust representation learning capabilities. This work presents a promising approach for unified epilepsy neurophysiology analysis.
In unsupervised combinatorial optimization (UCO), during training, one aims to have continuous decisions that are promising in a probabilistic sense for each training instance, which enables end-to-end training on initially discrete and non-differentiable problems. At the test time, for each test instance, starting from continuous decisions, derandomization is typically applied to obtain the final deterministic decisions. Researchers have developed more and more powerful test-time derandomization schemes to enhance the empirical performance and the theoretical guarantee of UCO methods. However, we notice a misalignment between training and testing in the existing UCO methods. Consequently, lower training losses do not necessarily entail better post-derandomization performance, even for the training instances without any data distribution shift. Empirically, we indeed observe such undesirable cases. We explore a preliminary idea to better align training and testing in UCO by including a differentiable version of derandomization into training. Our empirical exploration shows that such an idea indeed improves training-test alignment, but also introduces nontrivial challenges into training.
It has been observed that transformers with greater depth (that is, more layers) have more capabilities, but can we establish formally which capabilities are gained with greater depth? We answer this question with a theoretical proof followed by an empirical study. First, we consider transformers that round to fixed precision except inside attention. We show that this subclass of transformers is expressively equivalent to the programming language C-RASP and this equivalence preserves depth. Second, we prove that deeper C-RASP programs are more expressive than shallower C-RASP programs, implying that deeper transformers are more expressive than shallower transformers (within the subclass mentioned above). These results are established by studying a form of temporal logic with counting operators, which was shown equivalent to C-RASP in previous work. Finally, we provide empirical evidence that our theory predicts the depth required for transformers without positional encodings to length-generalize on a family of sequential dependency tasks.
Training LLMs on decentralized and wimpy computation nodes, e.g., multiple on-spot instances, lowers the training cost and enables model democratization. The inevitable challenge here is the churn of nodes due to failures and the operator's scheduling policies, leading to losing a stage - a part of the model. The conventional approaches to recover from failures are to either use checkpointing, where periodically a copy of the entire model is sent to an additional storage, or redundant computation. These approaches yield significant communication and/or computation overhead even in non-failure cases and scale poorly in settings with large models. In this paper, we propose, CheckFree, an efficient recovery method where a failing stage is substituted by a weighted average of the closest neighboring stages. In contrast to the state of the art, CheckFree requires no additional computation or storage. However, because of the nature of averaging neighbouring stages, it can only recover failures of intermediate stages. We further extend our method to CheckFree+ with out-of-order pipeline execution to tolerate crashes of the first and last stages. Thanks to out-of-order pipelining, behaviour of those stages is mimicked by their neighboring ones, which allows CheckFree+ to recover them by simply copying the weights from the immediate neighbour. To be able to recover the (de)embedding layers, CheckFree+ copies those layers to the neighboring stages, which requires relatively small storage overhead. We extensively evaluate our method on LLaMa models of model sizes from 124M to 1.5B with varying failure frequencies. In the case of low and medium failure rates (5-10%), CheckFree and CheckFree+ outperform both checkpointing and redundant computation in terms of convergence in wall-clock time by over 12%. Both of our proposals can be run via our code available at: https://github.com/gensyn-ai/CheckFree.
People are increasingly seeking healthcare information from large language models (LLMs) via interactive chatbots, yet the nature and inherent risks of these conversations remain largely unexplored. In this paper, we filter large-scale conversational AI datasets to achieve HealthChat-11K, a curated dataset of 11K real-world conversations composed of 25K user messages. We use HealthChat-11K and a clinician-driven taxonomy for how users interact with LLMs when seeking healthcare information in order to systematically study user interactions across 21 distinct health specialties. Our analysis reveals insights into the nature of how and why users seek health information, such as common interactions, instances of incomplete context, affective behaviors, and interactions (e.g., leading questions) that can induce sycophancy, underscoring the need for improvements in the healthcare support capabilities of LLMs deployed as conversational AI. Code and artifacts to retrieve our analyses and combine them into a curated dataset can be found here: https://github.com/yahskapar/HealthChat
Large Language Models (LLMs) have shown promise in accelerating the scientific research pipeline. A key capability for this process is the ability to generate novel research ideas, and prior studies have found settings in which LLM-generated research ideas were judged as more novel than human-expert ideas. However, a good idea should not simply appear to be novel, it should also result in better research after being executed. To test whether AI-generated ideas lead to better research outcomes, we conduct an execution study by recruiting 43 expert researchers to execute randomly-assigned ideas, either written by experts or generated by an LLM. Each expert spent over 100 hours implementing the idea and wrote a 4-page short paper to document the experiments. All the executed projects are then reviewed blindly by expert NLP researchers. Comparing the review scores of the same ideas before and after execution, the scores of the LLM-generated ideas decrease significantly more than expert-written ideas on all evaluation metrics (novelty, excitement, effectiveness, and overall; p < 0.05), closing the gap between LLM and human ideas observed at the ideation stage. When comparing the aggregated review scores from the execution study, we even observe that for many metrics there is a flip in rankings where human ideas score higher than LLM ideas. This ideation-execution gap highlights the limitations of current LLMs in generating truly effective research ideas and the challenge of evaluating research ideas in the absence of execution outcomes.
Protein structure prediction models such as AlphaFold3 (AF3) push the frontier of biomolecular modeling by incorporating science-informed architectural changes to the transformer architecture. However, these advances come at a steep system cost, introducing: compute- and memory-intensive operators, 2D attention mechanisms, and retrieval-augmented data pipelines, which collectively hinder the scalability of AF3 training. In this work, we present MegaFold, a cross-platform system to accelerate AF3 training. MegaFold tackles key bottlenecks through ahead-of-time caching to eliminate GPU idle time from the retrieval-augmented data pipeline, Triton-based kernels for memory-efficient EvoAttention on heterogeneous devices, and deep fusion for common and critical small operators in AF3. Evaluation on both NVIDIA H200 and AMD MI250 GPUs shows that MegaFold reduces peak memory usage of AF3 training by up to 1.23$\times$ and improves per-iteration training time by up-to 1.73$\times$ and 1.62$\times$ respectively. More importantly, MegaFold enables training on 1.35$\times$ longer sequence lengths compared to PyTorch baselines without running out-of-memory, significantly improving the scalability of modern protein folding models. We open source our code at https://github.com/Supercomputing-System-AI-Lab/MegaFold/.
Recent advances in graph databases (GDBs) have been driving interest in large-scale analytics, yet current systems fail to support higher-order (HO) interactions beyond first-order (one-hop) relations, which are crucial for tasks such as subgraph counting, polyadic modeling, and HO graph learning. We address this by introducing a new class of systems, higher-order graph databases (HO-GDBs) that use lifting and lowering paradigms to seamlessly extend traditional GDBs with HO. We provide a theoretical analysis of OLTP and OLAP queries, ensuring correctness, scalability, and ACID compliance. We implement a lightweight, modular, and parallelizable HO-GDB prototype that offers native support for hypergraphs, node-tuples, subgraphs, and other HO structures under a unified API. The prototype scales to large HO OLTP & OLAP workloads and shows how HO improves analytical tasks, for example enhancing accuracy of graph neural networks within a GDB by 44%. Our work ensures low latency and high query throughput, and generalizes both ACID-compliant and eventually consistent systems.
We introduce a new dataset and algorithm for fast and efficient coastal distance calculations from Anywhere on Earth (AoE). Existing global coastal datasets are only available at coarse resolution (e.g. 1-4 km) which limits their utility. Publicly available satellite imagery combined with computer vision enable much higher precision. We provide a global coastline dataset at 10 meter resolution, a 100+ fold improvement in precision over existing data. To handle the computational challenge of querying at such an increased scale, we introduce a new library: Layered Iterative Geospatial Hierarchical Terrain-Oriented Unified Search Engine (Lighthouse). Lighthouse is both exceptionally fast and resource-efficient, requiring only 1 CPU and 2 GB of RAM to achieve millisecond online inference, making it well suited for real-time applications in resource-constrained environments.
Detecting harmful content is a crucial task in the landscape of NLP applications for Social Good, with hate speech being one of its most dangerous forms. But what do we mean by hate speech, how can we define it, and how does prompting different definitions of hate speech affect model performance? The contribution of this work is twofold. At the theoretical level, we address the ambiguity surrounding hate speech by collecting and analyzing existing definitions from the literature. We organize these definitions into a taxonomy of 14 Conceptual Elements-building blocks that capture different aspects of hate speech definitions, such as references to the target of hate (individual or groups) or of the potential consequences of it. At the experimental level, we employ the collection of definitions in a systematic zero-shot evaluation of three LLMs, on three hate speech datasets representing different types of data (synthetic, human-in-the-loop, and real-world). We find that choosing different definitions, i.e., definitions with a different degree of specificity in terms of encoded elements, impacts model performance, but this effect is not consistent across all architectures.
Ensuring the trustworthiness of graph neural networks (GNNs) as black-box models requires effective explanation methods. Existing GNN explanations typically apply input perturbations to identify subgraphs that are responsible for the occurrence of the final output of GNNs. However, such approaches lack finer-grained, layer-wise analysis of how intermediate representations contribute to the final result, capabilities that are crucial for model diagnosis and architecture optimization. This paper introduces SliceGX, a novel GNN explanation approach that generates explanations at specific GNN layers in a progressive manner. Given a GNN M, a set of selected intermediate layers, and a target layer, SliceGX automatically segments M into layer blocks ("model slice") and discovers high-quality explanatory subgraphs in each layer block that clarifies the occurrence of output of M at the targeted layer. Although finding such layer-wise explanations is computationally challenging, we develop efficient algorithms and optimization techniques that incrementally generate and maintain these subgraphs with provable approximation guarantees. Additionally, SliceGX offers a SPARQL-like query interface, providing declarative access and search capacities for the generated explanations. Through experiments on large real-world graphs and representative GNN architectures, we verify the effectiveness and efficiency of SliceGX, and illustrate its practical utility in supporting model debugging.