CreoPep: A Universal Deep Learning Framework for Target-Specific Peptide Design and Optimization

Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural variants and the labor-intensive nature of traditional optimization strategies. Here, we present CreoPep, a deep learning-based conditional generative framework that integrates masked language modeling with a progressive masking scheme to design high-affinity peptide mutants while uncovering novel structural motifs. CreoPep employs an integrative augmentation pipeline, combining FoldX-based energy screening with temperature-controlled multinomial sampling, to generate structurally and functionally diverse peptides that retain key pharmacological properties. We validate this approach by designing conotoxin inhibitors targeting the $\alpha$7 nicotinic acetylcholine receptor, achieving submicromolar potency in electrophysiological assays. Structural analysis reveals that CreoPep-generated variants engage in both conserved and novel binding modes, including disulfide-deficient forms, thus expanding beyond conventional design paradigms. Overall, CreoPep offers a robust and generalizable platform that bridges computational peptide design with experimental validation, accelerating the discovery of next-generation peptide therapeutics.

Solla: Towards a Speech-Oriented LLM That Hears Acoustic Context

Large Language Models (LLMs) have recently shown remarkable ability to process not only text but also multimodal inputs such as speech and audio. However, most existing models primarily focus on analyzing input signals using text instructions, overlooking scenarios in which speech instructions and audio are mixed and serve as inputs to the model. To address these challenges, we introduce Solla, a novel framework designed to understand speech-based questions and hear the acoustic context concurrently. Solla incorporates an audio tagging module to effectively identify and represent audio events, as well as an ASR-assisted prediction method to improve comprehension of spoken content. To rigorously evaluate Solla and other publicly available models, we propose a new benchmark dataset called SA-Eval, which includes three tasks: audio event classification, audio captioning, and audio question answering. SA-Eval has diverse speech instruction with various speaking styles, encompassing two difficulty levels, easy and hard, to capture the range of real-world acoustic conditions. Experimental results show that Solla performs on par with or outperforms baseline models on both the easy and hard test sets, underscoring its effectiveness in jointly understanding speech and audio.

Identifying Trustworthiness Challenges in Deep Learning Models for Continental-Scale Water Quality Prediction

Water quality is foundational to environmental sustainability, ecosystem resilience, and public health. Deep learning models, particularly Long Short-Term Memory (LSTM) networks, offer transformative potential for large-scale water quality prediction and scientific insights generation. However, their widespread adoption in high-stakes decision-making, such as pollution mitigation and equitable resource allocation, is prevented by unresolved trustworthiness challenges including fairness, uncertainty, interpretability, robustness, generalizability, and reproducibility. In this work, we present the first comprehensive evaluation of trustworthiness in a continental-scale multi-task LSTM model predicting 20 water quality variables (encompassing physical/chemical processes, geochemical weathering, and nutrient cycling) across 482 U.S. basins. Our investigation uncovers systematic patterns of model performance disparities linked to basin characteristics, the inherent complexity of biogeochemical processes, and variable predictability, emphasizing critical performance fairness concerns. We further propose methodological frameworks for quantitatively evaluating critical aspects of trustworthiness, including uncertainty, interpretability, and robustness, identifying key limitations that could challenge reliable real-world deployment. This work serves as a timely call to action for advancing trustworthy data-driven methods for water resources management and provides a pathway to offering critical insights for researchers, decision-makers, and practitioners seeking to leverage artificial intelligence (AI) responsibly in environmental management.

Benchmarking Chinese Medical LLMs: A Medbench-based Analysis of Performance Gaps and Hierarchical Optimization Strategies

The evaluation and improvement of medical large language models (LLMs) are critical for their real-world deployment, particularly in ensuring accuracy, safety, and ethical alignment. Existing frameworks inadequately dissect domain-specific error patterns or address cross-modal challenges. This study introduces a granular error taxonomy through systematic analysis of top 10 models on MedBench, categorizing incorrect responses into eight types: Omissions, Hallucination, Format Mismatch, Causal Reasoning Deficiency, Contextual Inconsistency, Unanswered, Output Error, and Deficiency in Medical Language Generation. Evaluation of 10 leading models reveals vulnerabilities: despite achieving 0.86 accuracy in medical knowledge recall, critical reasoning tasks show 96.3% omission, while safety ethics evaluations expose alarming inconsistency (robustness score: 0.79) under option shuffled. Our analysis uncovers systemic weaknesses in knowledge boundary enforcement and multi-step reasoning. To address these, we propose a tiered optimization strategy spanning four levels, from prompt engineering and knowledge-augmented retrieval to hybrid neuro-symbolic architectures and causal reasoning frameworks. This work establishes an actionable roadmap for developing clinically robust LLMs while redefining evaluation paradigms through error-driven insights, ultimately advancing the safety and trustworthiness of AI in high-stakes medical environments.

TCM-3CEval: A Triaxial Benchmark for Assessing Responses from Large Language Models in Traditional Chinese Medicine

Large language models (LLMs) excel in various NLP tasks and modern medicine, but their evaluation in traditional Chinese medicine (TCM) is underexplored. To address this, we introduce TCM3CEval, a benchmark assessing LLMs in TCM across three dimensions: core knowledge mastery, classical text understanding, and clinical decision-making. We evaluate diverse models, including international (e.g., GPT-4o), Chinese (e.g., InternLM), and medical-specific (e.g., PLUSE). Results show a performance hierarchy: all models have limitations in specialized subdomains like Meridian & Acupoint theory and Various TCM Schools, revealing gaps between current capabilities and clinical needs. Models with Chinese linguistic and cultural priors perform better in classical text interpretation and clinical reasoning. TCM-3CEval sets a standard for AI evaluation in TCM, offering insights for optimizing LLMs in culturally grounded medical domains. The benchmark is available on Medbench's TCM track, aiming to assess LLMs' TCM capabilities in basic knowledge, classic texts, and clinical decision-making through multidimensional questions and real cases.

Active operator learning with predictive uncertainty quantification for partial differential equations

In this work, we develop a method for uncertainty quantification in deep operator networks (DeepONets) using predictive uncertainty estimates calibrated to model errors observed during training. The uncertainty framework operates using a single network, in contrast to existing ensemble approaches, and introduces minimal overhead during training and inference. We also introduce an optimized implementation for DeepONet inference (reducing evaluation times by a factor of five) to provide models well-suited for real-time applications. We evaluate the uncertainty-equipped models on a series of partial differential equation (PDE) problems, and show that the model predictions are unbiased, non-skewed, and accurately reproduce solutions to the PDEs. To assess how well the models generalize, we evaluate the network predictions and uncertainty estimates on in-distribution and out-of-distribution test datasets. We find the predictive uncertainties accurately reflect the observed model errors over a range of problems with varying complexity; simpler out-of-distribution examples are assigned low uncertainty estimates, consistent with the observed errors, while more complex out-of-distribution examples are properly assigned higher uncertainties. We also provide a statistical analysis of the predictive uncertainties and verify that these estimates are well-aligned with the observed error distributions at the tail-end of training. Finally, we demonstrate how predictive uncertainties can be used within an active learning framework to yield improvements in accuracy and data-efficiency for outer-loop optimization procedures.

COAST: Intelligent Time-Adaptive Neural Operators

We introduce Causal Operator with Adaptive Solver Transformer (COAST), a novel neural operator learning method that leverages a causal language model (CLM) framework to dynamically adapt time steps. Our method predicts both the evolution of a system and its optimal time step, intelligently balancing computational efficiency and accuracy. We find that COAST generates variable step sizes that correlate with the underlying system intrinsicities, both within and across dynamical systems. Within a single trajectory, smaller steps are taken in regions of high complexity, while larger steps are employed in simpler regions. Across different systems, more complex dynamics receive more granular time steps. Benchmarked on diverse systems with varied dynamics, COAST consistently outperforms state-of-the-art methods, achieving superior performance in both efficiency and accuracy. This work underscores the potential of CLM-based intelligent adaptive solvers for scalable operator learning of dynamical systems.

ST$^3$: Accelerating Multimodal Large Language Model by Spatial-Temporal Visual Token Trimming

Multimodal large language models (MLLMs) enhance their perceptual capabilities by integrating visual and textual information. However, processing the massive number of visual tokens incurs a significant computational cost. Existing analysis of the MLLM attention mechanisms remains shallow, leading to coarse-grain token pruning strategies that fail to effectively balance speed and accuracy. In this paper, we conduct a comprehensive investigation of MLLM attention mechanisms with LLaVA. We find that numerous visual tokens and partial attention computations are redundant during the decoding process. Based on this insight, we propose Spatial-Temporal Visual Token Trimming ($\textbf{ST}^{3}$), a framework designed to accelerate MLLM inference without retraining. $\textbf{ST}^{3}$ consists of two primary components: 1) Progressive Visual Token Pruning (\textbf{PVTP}), which eliminates inattentive visual tokens across layers, and 2) Visual Token Annealing (\textbf{VTA}), which dynamically reduces the number of visual tokens in each layer as the generated tokens grow. Together, these techniques deliver around $\mathbf{2\times}$ faster inference with only about $\mathbf{30\%}$ KV cache memory compared to the original LLaVA, while maintaining consistent performance across various datasets. Crucially, $\textbf{ST}^{3}$ can be seamlessly integrated into existing pre-trained MLLMs, providing a plug-and-play solution for efficient inference.

SALMONN-omni: A Codec-free LLM for Full-duplex Speech Understanding and Generation

Full-duplex multimodal large language models (LLMs) provide a unified framework for addressing diverse speech understanding and generation tasks, enabling more natural and seamless human-machine conversations. Unlike traditional modularised conversational AI systems, which separate speech recognition, understanding, and text-to-speech generation into distinct components, multimodal LLMs operate as single end-to-end models. This streamlined design eliminates error propagation across components and fully leverages the rich non-verbal information embedded in input speech signals. We introduce SALMONN-omni, a codec-free, full-duplex speech understanding and generation model capable of simultaneously listening to its own generated speech and background sounds while speaking. To support this capability, we propose a novel duplex spoken dialogue framework incorporating a ``thinking'' mechanism that facilitates asynchronous text and speech generation relying on embeddings instead of codecs (quantized speech and audio tokens). Experimental results demonstrate SALMONN-omni's versatility across a broad range of streaming speech tasks, including speech recognition, speech enhancement, and spoken question answering. Additionally, SALMONN-omni excels at managing turn-taking, barge-in, and echo cancellation scenarios, establishing its potential as a robust prototype for full-duplex conversational AI systems. To the best of our knowledge, SALMONN-omni is the first codec-free model of its kind. A full technical report along with model checkpoints will be released soon.

DeepONet as a Multi-Operator Extrapolation Model: Distributed Pretraining with Physics-Informed Fine-Tuning

We propose a novel fine-tuning method to achieve multi-operator learning through training a distributed neural operator with diverse function data and then zero-shot fine-tuning the neural network using physics-informed losses for downstream tasks. Operator learning effectively approximates solution operators for PDEs and various PDE-related problems, yet it often struggles to generalize to new tasks. To address this, we investigate fine-tuning a pretrained model, while carefully selecting an initialization that enables rapid adaptation to new tasks with minimal data. Our approach combines distributed learning to integrate data from various operators in pre-training, while physics-informed methods enable zero-shot fine-tuning, minimizing the reliance on downstream data. We investigate standard fine-tuning and Low-Rank Adaptation fine-tuning, applying both to train complex nonlinear target operators that are difficult to learn only using random initialization. Through comprehensive numerical examples, we demonstrate the advantages of our approach, showcasing significant improvements in accuracy. Our findings provide a robust framework for advancing multi-operator learning and highlight the potential of transfer learning techniques in this domain.