Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned proteins, which poses a major computational bottleneck. In this paper, we develop a near-linear time method to estimate these rate matrices from multiple sequence alignments (MSAs) alone, thereby speeding up computation by orders of magnitude. Our method relies on a near-linear time cherry reconstruction algorithm which we call FastCherries and it can be easily applied to MSAs with millions of sequences. On both simulated and real data, we demonstrate the speed and accuracy of our method as applied to the classical model of protein evolution. By leveraging the unprecedented scalability of our method, we develop a new, rich phylogenetic model called SiteRM, which can estimate a general site-specific rate matrix for each column of an MSA. Remarkably, in variant effect prediction for both clinical and deep mutational scanning data in ProteinGym, we show that despite being an independent-sites model, our SiteRM model outperforms large protein language models that learn complex residue-residue interactions between different sites. We attribute our increased performance to conceptual advances in our probabilistic treatment of evolutionary data and our ability to handle extremely large MSAs. We anticipate that our work will have a lasting impact across both statistical phylogenetics and computational variant effect prediction.

LLM agents have demonstrated remarkable performance across various applications, primarily due to their advanced capabilities in reasoning, utilizing external knowledge and tools, calling APIs, and executing actions to interact with environments. Current agents typically utilize a memory module or a retrieval-augmented generation (RAG) mechanism, retrieving past knowledge and instances with similar embeddings from knowledge bases to inform task planning and execution. However, the reliance on unverified knowledge bases raises significant concerns about their safety and trustworthiness. To uncover such vulnerabilities, we propose a novel red teaming approach AgentPoison, the first backdoor attack targeting generic and RAG-based LLM agents by poisoning their long-term memory orRAG knowledge base. In particular, we form the trigger generation process as a constrained optimization to optimize backdoor triggers by mapping the triggered instances to a unique embedding space, so as to ensure that whenever a user instruction contains the optimized backdoor trigger, the malicious demonstrations are retrieved from the poisoned memory or knowledge base with high probability.

In a rapidly evolving job market, skill demand forecasting is crucial as it enables policymakers and businesses to anticipate and adapt to changes, ensuring that workforce skills align with market needs, thereby enhancing productivity and competitiveness. Additionally, by identifying emerging skill requirements, it directs individuals towards relevant training and education opportunities, promoting continuous self-learning and development. However, the absence of comprehensive datasets presents a significant challenge, impeding research and the advancement of this field. To bridge this gap, we present Job-SDF, a dataset designed to train and benchmark job-skill demand forecasting models. Based on millions of public job advertisements collected from online recruitment platforms, this dataset encompasses monthly recruitment demand.Our dataset uniquely enables evaluating skill demand forecasting models at various granularities, including occupation, company, and regional levels. We benchmark a range of models on this dataset, evaluating their performance in standard scenarios, in predictions focused on lower value ranges, and in the presence of structural breaks, providing new insights for further research.

The cortico-spinal neural pathway is fundamental for motor control and movement execution, and in humans it is typically studied using concurrent electroencephalography (EEG) and electromyography (EMG) recordings. However, current approaches for capturing high-level and contextual connectivity between these recordings have important limitations. Here, we present a novel application of statistical dependence estimators based on orthonormal decomposition of density ratios to model the relationship between cortical and muscle oscillations. Our method extends from traditional scalar-valued measures by learning eigenvalues, eigenfunctions, and projection spaces of density ratios from realizations of the signal, addressing the interpretability, scalability, and local temporal dependence of cortico-muscular connectivity. We experimentally demonstrate that eigenfunctions learned from cortico-muscular connectivity can accurately classify movements and subjects. Moreover, they reveal channel and temporal dependencies that confirm the activation of specific EEG channels during movement.

In the realm of big data and digital healthcare, Electronic Health Records (EHR) have become a rich source of information with the potential to improve patient care and medical research. In recent years, machine learning models have proliferated for analyzing EHR data to predict patients' future health conditions. Among them, some studies advocate for multi-task learning (MTL) to jointly predict multiple target diseases for improving the prediction performance over single task learning. Nevertheless, current MTL frameworks for EHR data have significant limitations due to their heavy reliance on human experts to identify task groups for joint training and design model architectures. To reduce human intervention and improve the framework design, we propose an automated approach named AutoDP, which can search for the optimal configuration of task grouping and architectures simultaneously. To tackle the vast joint search space encompassing task combinations and architectures, we employ surrogate model-based optimization, enabling us to efficiently discover the optimal solution. Experimental results on real-world EHR data demonstrate the efficacy of the proposed AutoDP framework. It achieves significant performance improvements over both hand-crafted and automated state-of-the-art methods, also maintains a feasible search cost at the same time.

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently, there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present Slice-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). Our dataset can be found here. Slice-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

Pearl Abyss, the game's developer, issued a lengthy apology on X and detailed its corrective actions. The developer behind the open-world RPG Crimson Desert has issued an official apology after players discovered several instances of AI-generated art in the game. Pearl Abyss posted on X that it released the game with some 2D visual props that were made with experimental AI generative tools and forgot to replace them before launch. We would like to address questions regarding the use of AI in Crimson Desert. During development, some 2D visual props were created as part of early-stage iteration using experimental AI generative tools.

Motion-to-music and music-to-motion have been studied separately, each attracting substantial research interest within their respective domains. The interaction between human motion and music is a reflection of advanced human intelligence, and establishing a unified relationship between them is particularly important. However, to date, there has been no work that considers them jointly to explore the modality alignment within. To bridge this gap, we propose a novel framework, termed MoMu-Diffusion, for long-term and synchronous motion-music generation. Firstly, to mitigate the huge computational costs raised by long sequences, we propose a novel Bidirectional Contrastive Rhythmic Variational Auto-Encoder (BiCoR-VAE) that extracts the modality-aligned latent representations for both motion and music inputs. Subsequently, leveraging the aligned latent spaces, we introduce a multi-modal diffusion Transformer model and a cross-guidance sampling strategy to enable various generation tasks, including cross-modal, multi-modal, and variable-length generation. Extensive experiments demonstrate that MoMu-Diffusion surpasses recent state-of-the-art methods both qualitatively and quantitatively, and can synthesize realistic, diverse, long-term, and beat-matched music or motion sequences. The generated motion-music samples are available at https://momu-diffusion.github.io/.

Federated Learning (FL) has emerged as a promising paradigm for collaborative machine learning, while preserving user data privacy. Despite its potential, standard FL algorithms lack support for diverse heterogeneous device prototypes, which vary significantly in model and dataset sizes---from small IoT devices to large workstations. This limitation is only partially addressed by existing knowledge distillation (KD) techniques, which often fail to transfer knowledge effectively across a broad spectrum of device prototypes with varied capabilities. This failure primarily stems from two issues: the dilution of informative logits from more capable devices by those from less capable ones, and the use of a single integrated logits as the distillation target across all devices, which neglects their individual learning capacities and and the unique contributions of each device. To address these challenges, we introduce TAKFL, a novel KD-based framework that treats the knowledge transfer from each device prototype's ensemble as a separate task, independently distilling each to preserve its unique contributions and avoid dilution. TAKFL also incorporates a KD-based self-regularization technique to mitigate the issues related to the noisy and unsupervised ensemble distillation process. To integrate the separately distilled knowledge, we introduce an adaptive task arithmetic knowledge integration process, allowing each student model to customize the knowledge integration for optimal performance.

To protect deep neural networks (DNNs) from adversarial attacks, adversarial training (AT) is developed by incorporating adversarial examples (AEs) into model training. Recent studies show that adversarial attacks disproportionately impact the patterns within the phase of the sample's frequency spectrum---typically containing crucial semantic information---more than those in the amplitude, resulting in the model's erroneous categorization of AEs. We find that, by mixing the amplitude of training samples' frequency spectrum with those of distractor images for AT, the model can be guided to focus on phase patterns unaffected by adversarial perturbations. As a result, the model's robustness can be improved. Unfortunately, it is still challenging to select appropriate distractor images, which should mix the amplitude without affecting the phase patterns.