Understanding and extracting structured insights from unstructured documents remains a foundational challenge in industrial NLP. While Large Language Models (LLMs) enable zero-shot extraction, traditional pipelines often fail to handle multi-document packets, complex reasoning, and strict compliance requirements. We present IDP (Intelligent Document Processing) Accelerator, a framework enabling agentic AI for end-to-end document intelligence with four key components: (1) DocSplit, a novel benchmark dataset and multimodal classifier using BIO tagging to segment complex document packets; (2) configurable Extraction Module leveraging multimodal LLMs to transform unstructured content into structured data; (3) Agentic Analytics Module, compliant with the Model Context Protocol (MCP) providing data access through secure, sandboxed code execution; and (4) Rule Validation Module replacing deterministic engines with LLM-driven logic for complex compliance checks. The interactive demonstration enables users to upload document packets, visualize classification results, and explore extracted data through an intuitive web interface. We demonstrate effectiveness across industries, highlighting a
While Central Pattern Generators (CPGs) and Multi-Layer Perceptrons (MLP) are widely used paradigms in robot control, few systematic studies have been performed on the relative merits of large parameter spaces. In contexts where input and output spaces are small and performance is bounded, having more parameters to optimize may actively hinder the learning process instead of empowering it. To empirically measure this, we submit a given robot morphology, with limited proprioceptive capabilities, to controller optimization under two bio-inspired paradigms (CPGs and MLPs) with evolutionary- and reinforcement- trainer protocols. By varying parameter spaces across multiple reward functions, we observe that shallow MLPs and densely connected CPGs result in better performance when compared to deeper MLPs or Actor-Critic architectures. To account for the relationship between said performance and the number of parameters, we introduce a Parameter Impact metric which demonstrates that the additional parameters required by the reinforcement technique do not translate into better performance, thus favouring evolutionary strategies.
Traditional network architectures suffer from severe protocol ossification and structural fragility due to their reliance on static, human-defined rules that fail to adapt to the emergent edge cases and probabilistic reasoning of modern autonomous agents. To address these limitations, this paper proposes DarwinNet, a bio-inspired, self-evolving network architecture that transitions communication protocols from a \textit{design-time} static paradigm to a \textit{runtime} growth paradigm. DarwinNet utilizes a tri-layered framework-comprising an immutable physical anchor (L0), a WebAssembly-based fluid cortex (L1), and an LLM-driven Darwin cortex (L2)-to synthesize high-level business intents into executable bytecode through a dual-loop \textit{Intent-to-Bytecode} (I2B) mechanism. We introduce the Protocol Solidification Index (PSI) to quantify the evolutionary maturity of the system as it collapses from high-latency intelligent reasoning (Slow Thinking) toward near-native execution (Fast Thinking). Validated through a reliability growth framework based on the Crow-AMSAA model, experimental results demonstrate that DarwinNet achieves anti-fragility by treating environmental anomalies
All-atom molecular simulation serves as a quintessential ``computational microscope'' for understanding the machinery of life, yet it remains fundamentally limited by the trade-off between quantum-mechanical (QM) accuracy and biological scale. We present UBio-MolFM, a universal foundation model framework specifically engineered to bridge this gap. UBio-MolFM introduces three synergistic innovations: (1) UBio-Mol26, a large bio-specific dataset constructed via a multi-fidelity ``Two-Pronged Strategy'' that combines systematic bottom-up enumeration with top-down sampling of native protein environments (up to 1,200 atoms); (2) E2Former-V2, a linear-scaling equivariant transformer that integrates Equivariant Axis-Aligned Sparsification (EAAS) and Long-Short Range (LSR) modeling to capture non-local physics with up to ~4x higher inference throughput in our large-system benchmarks; and (3) a Three-Stage Curriculum Learning protocol that transitions from energy initialization to energy-force consistency, with force-focused supervision to mitigate energy offsets. Rigorous benchmarking across microscopic forces and macroscopic observables -- including liquid water structure, ionic solvation
Tactile sensing is essential for robotic manipulation, prosthetics and assistive technologies, yet neuromorphic tactile datasets remain limited compared to their visual counterparts. We introduce STEMNIST, a large-scale neuromorphic tactile dataset extending ST-MNIST from 10 digits to 35 alphanumeric classes (uppercase letters A--Z and digits 1--9), providing a challenging benchmark for event-based haptic recognition. The dataset comprises 7,700 samples collected from 34 participants using a custom \(16\times 16\) tactile sensor array operating at 120 Hz, encoded as 1,005,592 spike events through adaptive temporal differentiation. Following EMNIST's visual character recognition protocol, STEMNIST addresses the critical gap between simplified digit classification and real-world tactile interaction scenarios requiring alphanumeric discrimination. Baseline experiments using conventional CNNs (90.91% test accuracy) and spiking neural networks (89.16%) establish performance benchmarks. The dataset's event-based format, unrestricted spatial variability and rich temporal structure makes it suitable for testing neuromorphic hardware and bio-inspired learning algorithms. STEMNIST enables re
Background: The potential of large language models (LLMs) to automate and support pharmacoepidemiologic study design is an emerging area of interest, yet their reliability remains insufficiently characterized. General-purpose LLMs often display inaccuracies, while the comparative performance of specialized biomedical LLMs in this domain remains unknown. Methods: This study evaluated general-purpose LLMs (GPT-4o and DeepSeek-R1) versus biomedically fine-tuned LLMs (QuantFactory/Bio-Medical-Llama-3-8B-GGUF and Irathernotsay/qwen2-1.5B-medical_qa-Finetune) using 46 protocols (2018-2024) from the HMA-EMA Catalogue and Sentinel System. Performance was assessed across relevance, logic of justification, and ontology-code agreement across multiple coding systems using Least-to-Most (LTM) and Active Prompting strategies. Results: GPT-4o and DeepSeek-R1 paired with LTM prompting achieved the highest relevance and logic of justification scores, with GPT-4o-LTM reaching a median relevance score of 4 in 8 of 9 questions for HMA-EMA protocols. Biomedical LLMs showed lower relevance overall and frequently generated insufficient justification. All LLMs demonstrated limited proficiency in ontology-
Advanced manufacturing with new bio-derived materials can be achieved faster and more economically with first-principle-based artificial intelligence and machine learning (AI/ML)-derived models and process optimization. Not only is this motivated by increased industry profitability, but it can also be optimized to reduce waste generation, energy consumption, and gas emissions through additive manufacturing (AM) and AI/ML-directed self-driving laboratory (SDL) process optimization. From this perspective, the benefits of using 3D printing technology to manufacture durable, sustainable materials will enable high-value reuse and promote a better circular economy. Using AI/ML workflows at different levels, it is possible to optimize the synthesis and adaptation of new bio-derived materials with self-correcting 3D printing methods, and in-situ characterization. Working with training data and hypotheses derived from Large Language Models (LLMs) and algorithms, including ML-optimized simulation, it is possible to demonstrate more field convergence. The combination of SDL and AI/ML Workflows can be the norm for improved use of biobased and renewable materials towards advanced manufacturing.
Concurrent advances across fields such as organoid technology, Microelectrode Arrays (MEAs), neuromorphic computing, and machine learning have given rise to a groundbreaking research paradigm: Synthetic Biological Intelligence (SBI). SBI refers to engineered systems in which living Biological Neural Networks (BNNs) are interfaced with hardware and software to perform task-oriented information processing in a closed loop. This cutting-edge technology, while still in its infancy, has the potential to deliver highly efficient performance across both computing capabilities and energy consumption. The early stage of this field underscores the need for reliable multi-scale and cross-domain interaction interfaces to support applications in robotics, biomedicine, signal processing, and neuroscience research. The hitherto lack of commercially available SBI platforms has slowed the development, as the conditions to produce a testbed are expensive and cumbersome. The introduction of standardized, platform- and cloud-integrated BNNs has been a crucial catalyst for the scientific community, improving the accessibility of SBI and leading the way to further developments. In this survey, we summar
Large language models (LLMs) are rapidly acquiring capabilities relevant to biological research, from literature synthesis to interpretation of experimental data. Increasingly, LLM agents can also perform in silico biology tasks that previously required experienced human biologists. These emerging AI capabilities offer new opportunities for scientific discovery and biomedical advances, but they also shift the landscape of biosecurity risks. To address this, we introduce the Agentic Bio-Capabilities Benchmark (ABC-Bench), a suite of tasks to measure agentic biosecurity-relevant capabilities. ABC-Bench evaluates LLM agents on both benign and dual-use biology tasks: writing code to operate liquid handling robots, designing DNA fragments for in vitro assembly, and evading DNA synthesis screening. These tasks require a combination of biology and software expertise. All tested LLM agents outperformed the median expert human baseliner on all three tasks. Agents performed highly on tasks drawing on published knowledge and well-documented protocols, and more weakly on a task requiring novel bioinformatics reasoning. In three wet-lab validation experiments, we found that OpenAI's o4-mini-hig
Antagonistic artificial muscles can decouple joint torque and stiffness, but contact transients often degrade this independence. We present a unified real-time framework applicable across pneumatic, electrohydraulic, and dielectric elastomer artificial muscle families: a separable Padé force model with a minimal two-state dynamic wrapper, a cascaded inverse-dynamics controller in co-contraction/bias coordinates, and a bio-inspired depth-adaptive interaction policy that schedules stiffness based on penetration depth. The controller runs in under 1 ms per control tick and demonstrates independent torque and stiffness tracking, including a fixed-torque stiffness-step test that preserves torque regulation through stiffness transitions. In a coupled impedance contact protocol simulated across soft-to-rigid environments, comparing depth-adaptive stiffness to fixed-stiffness baselines reveals a shock/load versus stability tradeoff. These results provide a control-oriented foundation for musculoskeletal antagonistic robots to execute adaptive impedance behaviors in dynamic interactions.
Emergency speech recognition systems exhibit systematic performance degradation on non-standard English varieties, creating a critical gap in services for Caribbean populations. We present TRIDENT (Transcription and Routing Intelligence for Dispatcher-Empowered National Triage), a three-layer dispatcher-support architecture designed to structure emergency call inputs for human application of established triage protocols (the ESI for routine operations and START for mass casualty events), even when automatic speech recognition fails. The system combines Caribbean-accent-tuned ASR, local entity extraction via large language models, and bio-acoustic distress detection to provide dispatchers with three complementary signals: transcription confidence, structured clinical entities, and vocal stress indicators. Our key insight is that low ASR confidence, rather than representing system failure, serves as a valuable queue prioritization signal -- particularly when combined with elevated vocal distress markers indicating a caller in crisis whose speech may have shifted toward basilectal registers. A complementary insight drives the entity extraction layer: trained responders and composed by
The Internet of Bio-Nano Things (IoBNT) requires mobile nanomachines that navigate complex fluids while exchanging molecular signals under external supervision. We introduce the chemo-hydrodynamic transceiver, a unified model for catalytic Janus particles in which an external optical control simultaneously drives molecular emission and active self-propulsion. Unlike common abstractions that decouple mobility and communication, we derive a stochastic channel model that captures their physicochemical coupling and shows that actuation-induced distance jitter can dominate the received-signal variance, yielding a fundamental trade-off: stronger actuation increases emission but can sharply reduce reliability through motion-induced fading. Numerical results reveal a unimodal reliability profile with a critical actuation level beyond which the signal-to-noise ratio collapses, and an optimal control level that scales approximately linearly with link distance. Compared with Brownian-mobility baselines, the model exposes a pronounced estimation gap: neglecting active motility noise can underestimate the bit error probability by orders of magnitude. These findings provide physical-layer guidel
This paper presents a protocol for enhancement of life time of WBAN network as well other protocol related issues such as throughput, path loss, and residual energy. Bio-sensors are used for deployment on human body. Poisson distribution and equilibrium model techniques have been used for attaining the required results. Multi-hop network topology and random network node deployment used to achieve minimum energy consumption and longer network lifetime.
In this paper, we present the principles of designing new self-organising and autonomous management protocol to govern the dynamics of bio-inspired decentralized firewall architecture based on Biological Regularity Networks. The new architecture called Firewall Regulatory Networks (FRN) exhibits the following features (1) automatic rule policy configuration with provable utility-risk appetite guarantee, (2) resilient response for changing risks or new service requirements, and (3) globally optimized access control policy reconciliation. We present the FRN protocol and formalize the constraints to synthesize the undetermined components in the protocol to produce interactions that can achieve these objectives. We illustrate the feasibility of the FRN architecture in multiple case studies.
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have supported speedup, polymer simulation protocols continue to face significant challenges in the on-demand generation of realistic 3D atomic structures that respect conformational diversity. Generative algorithms for 3D structures of inorganic crystals, bio-polymers, and small molecules exist, but have not addressed synthetic polymers because of challenges in representation and dataset constraints. In this work, we introduce polyGen, the first generative model designed specifically for polymer structures from minimal inputs such as the repeat unit chemistry alone. polyGen combines graph-based encodings with a latent diffusion transformer using positional biased attention for realistic conformation generation. Given the limited dataset of 3,855 DFT-optimized polymer structures, we incorporate joint training with small molecule data to enhance generation quality. We also establish structure matching criteria to benchmark our approach on this novel prob
According to the European Union's Habitat Directive, habitat monitoring plays a critical role in response to the escalating problems posed by biodiversity loss and environmental degradation. Scree habitats, hosting unique and often endangered species, face severe threats from climate change due to their high-altitude nature. Traditionally, their monitoring has required highly skilled scientists to conduct extensive fieldwork in remote, potentially hazardous locations, making the process resource-intensive and time-consuming. This paper presents a novel approach for scree habitat monitoring using a legged robot to assist botanists in data collection and species identification. Specifically, we deployed the ANYmal C robot in the Italian Alpine bio-region in two field campaigns spanning two years and leveraged deep learning to detect and classify key plant species of interest. Our results demonstrate that agile legged robots can navigate challenging terrains and increase the frequency and efficiency of scree monitoring. When paired with traditional phytosociological surveys performed by botanists, this robotics-assisted protocol not only streamlines field operations but also enhances
Digital ecological art represents an emergent frontier where biological media converge with virtual environments. This study examines the paradigm shift from anthropocentric to plant-centered artistic narratives within the metaverse, contextualizing how digital platforms transform ecological expression. However, current frameworks fail to systematically guide artists in leveraging plant agency for digital symbiosis that transcends human-centered creation. We propose the Biocentric-Creation Transformation Ideology (BCTI) framework and validate it through multimodal case studies spanning bio-art, NFTs, and VR ecosystems (2013-2023). Our analysis reveals: (1) Metaverse ecosystems enable unprecedented plant-algorithm co-creation, with biological artworks increasing by 133% in premier archives (2020 vs 2013); (2) Digital symbiosis manifests through blockchain DAOs where plants govern human-plant collaborations; (3) Algorithmic photosynthesis in VR environments reshapes ecological aesthetics through real-time biodata translation. The BCTI framework advances ecological art theory by systematizing the transition from representation to plant-centered agency, offering artists a blueprint for
Anomalous heat diffusion is investigated for biological tissues displaying a fractal structure and long-term thermal memory, which is modeled via a fractional derivative. For increasing values of the fractional derivation order, the tissue temperature displays three kinds of bio-heat regimes: damped (or sub-diffusive), critical damping and under-damped oscillations. The temperature profiles depend on the fractal dimension of the tissue but notably also on a parameter related to its topology: the spectral dimension. The parametric analysis reveals that these two parameters have antagonistic effects on the pseudo period of the temperature oscillations and their amplitudes. We discuss how our results might impact some treatment protocols.
The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Ac
We report a model for hyperthermia therapies based on heat diffusion in a biological tissue containing a topological defect. Biological tissues behave like active liquid crystals with the presence of topological defects which are likely to anchor tumors during the metastatic phase of cancer evolution and the therapy challenge is to destroy the cancer cells without damaging surrounding healthy tissues. The defect creates an effective non-Euclidean geometry for low-energy excitations, modifying the bio-heat equation. Applications to protocols of thermal ablation for various biological tissues (liver, prostate, and skin) is analyzed and discussed.