Audio-language pretraining holds promise for general-purpose audio understanding, yet remains underexplored compared to its vision counterpart. While vision-language models like CLIP serve as widely adopted foundations, existing audio-language models primarily excel at retrieval tasks with limited adoption as general-purpose encoders. We identify three key barriers: limited large-scale audio-text corpora, insufficient caption diversity, and lack of systematic exploration and evaluation. To this end, we introduce CaptionStew, a 10.7M caption dataset aggregating diverse open-source audio-text corpora across multiple domains and captioning styles. Using this resource, we conduct the first comprehensive evaluation comparing contrastive and captioning objectives for audio representation learning across speech, music, and environmental sound tasks. Our results demonstrate that audio-language pretraining yields competitive, transferable representations. Through systematic data-scaling experiments, we reveal complementary objective strengths: contrastive learning achieves superior data efficiency at smaller scales, while captioning demonstrates better scalability on language-involved audio understanding tasks. We also find that common supervised initialization practices provide diminishing returns at scale, challenging current approaches. These findings establish audio-language pretraining as a viable pathway toward general-purpose audio representations, guiding future research. To accelerate progress, we release data preparation recipes, training protocols, and pretrained models, paving the way toward universal audio understanding. Early advances relied on supervised learning, where models trained on labeled corpora were adapted to related downstream tasks or transferred across domains (Kong et al., 2020; Chen et al., 2022a; Snyder et al., 2018; Desplanques et al., 2020).

Precise prognostic stratification of colorectal cancer (CRC) remains a major clinical challenge due to its high heterogeneity. The conventional TNM staging system is inadequate for personalized medicine. We aimed to develop and validate a novel multiple instance learning model TDAM-CRC using histopathological whole-slide images for accurate prognostic prediction and to uncover its underlying molecular mechanisms. We trained the model on the TCGA discovery cohort (n=581), validated it in an independent external cohort (n=1031), and further we integrated multi-omics data to improve model interpretability and identify novel prognostic biomarkers. The results demonstrated that the TDAM-CRC achieved robust risk stratification in both cohorts. Its predictive performance significantly outperformed the conventional clinical staging system and multiple state-of-the-art models. The TDAM-CRC risk score was confirmed as an independent prognostic factor in multivariable analysis. Multi-omics analysis revealed that the high-risk subtype is closely associated with metabolic reprogramming and an immunosuppressive tumor microenvironment. Through interaction network analysis, we identified and validated Mitochondrial Ribosomal Protein L37 (MRPL37) as a key hub gene linking deep pathomic features to clinical prognosis. We found that high expression of MRPL37, driven by promoter hypomethylation, serves as an independent biomarker of favorable prognosis. Finally, we constructed a nomogram incorporating the TDAM-CRC risk score and clinical factors to provide a precise and interpretable clinical decision-making tool for CRC patients. Our AI-driven pathological model TDAM-CRC provides a robust tool for improved CRC risk stratification, reveals new molecular targets, and facilitates personalized clinical decision-making.

ESM-1v is pre-trained to output the probability for each possible amino acid at a masked position. At each position, we introduce a mask token and record the model's predicted In all cases, we assume an additive model when multiple mutations are present in a sequence. For example, if mutations are introduced at positions 3 and 6, then M = {3, 6}. This method performs best among the four. ESM-1v and MSA Transformer amortize compute cost into a single expensive pre-training run.

Inverse halftoning is a technique used to recover realistic images from ancient prints ( e.g., photographs, newspapers, books). The rise of deep learning has led to the gradual incorporation of neural network designs into inverse halftoning methods.

Proteins are traditionally optimized through the costly construction and measurement of many mutants. Active Learning-assisted Directed Evolution (ALDE) alleviates that cost by predicting the best improvements and iteratively testing mutants to inform predictions. However, existing ALDE methods face a critical limitation: selecting the highest-predicted mutants in each round yields homogeneous training data insufficient for accurate prediction models in subsequent rounds. Here we present FolDE, an ALDE method designed to maximize end-of-campaign success. In simulations across 20 protein targets, FolDE discovers 23% more top 10% mutants than the best baseline ALDE method (p=0.005) and is 55% more likely to find top 1% mutants. FolDE achieves this primarily through naturalness-based warm-starting, which augments limited activity measurements with protein language model outputs to improve activity prediction. We also introduce a constant-liar batch selector, which improves batch diversity; this is important in multi-mutation campaigns but had limited effect in our benchmarks. The complete workflow is freely available as open-source software, making efficient protein optimization accessible to any laboratory.

Mixture-of-Experts (MoE) has become a popular architecture for scaling large models. However, the rapidly growing scale outpaces model training on a single DC, driving a shift toward a more flexible, cross-DC training paradigm. Under this, Expert Parallelism (EP) of MoE faces significant scalability issues due to the limited cross-DC bandwidth. Specifically, existing EP optimizations attempt to overlap data communication and computation, which has little benefit in low-bandwidth scenarios due to a much longer data communication time. Therefore, the trends of cross-DC EP scaling is fast becoming a critical roadblock to the continued growth of MoE models. To address this, we propose HybridEP, a modeling-guided framework to optimize EP under constrained bandwidth. Our key idea is to dynamically transform the spatial placement of experts to reduce data communication traffic and frequency, thereby minimizing EP's communication overheads. However, it is non-trivial to find the optimal solution because it complicates the original communication pattern by mixing data and expert communication. We therefore build a stream-based model to determine the optimal transmission ratio. Guided by this, we incorporate two techniques: (1) domain-based partition to construct the mapping between hybrid patterns and specific communication topology at GPU level, and (2) parameter-efficient migration to further refine this topology by reducing expert transmission overhead and enlarging the domain size. Combining all these designs, HybridEP can be considered as a more general EP with better scalability. Experimental results show that HybridEP outperforms existing state-of-the-art MoE training systems by up to 5.6x under constrained bandwidth. We further compare HybridEP and EP on large-scale simulations. HybridEP achieves up to 1.45x speedup with 1k DCs under different bandwidths.