In addition, we introduce a simple baseline, "RDumb", that periodically resets the

In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which are crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics technologies provide unprecedented opportunities to systematically infer and analyze CCC from these omics data, either by integrating prior knowledge of ligand-receptor interactions (LRIs) or through de novo approaches. A variety of computational methods have been developed, focusing on methodological innovations, accurate modeling of complex signaling mechanisms, and investigation of broader biological questions. These advances have greatly enhanced our ability to analyze CCC and generate biological hypotheses. Here, we introduce the biological mechanisms and modeling strategies of CCC, and provide a focused overview of more than 140 computational methods for inferring CCC from single-cell and spatial transcriptomic data, emphasizing the diversity in methodological frameworks and biological questions. Finally, we discuss the current challenges and future opportunities in this rapidly evolving field.

AI researchers and practitioners increasingly apply large language models (LLMs) to what we call reasoning-intensive regression (RiR), i.e., deducing subtle numerical scores from text. Unlike standard language regression tasks, e.g., for sentiment or similarity, RiR often appears instead in ad-hoc problems such as rubric-based scoring, modeling dense rewards in complex environments, or domain-specific retrieval, where much deeper analysis of context is required while only limited task-specific training data and computation are available. We cast four realistic problems as RiR tasks to establish an initial benchmark, and use that to test our hypothesis that prompting frozen LLMs and finetuning Transformer encoders via gradient descent will both often struggle in RiR. We then propose MENTAT, a simple and lightweight method that combines batch-reflective prompt optimization with neural ensemble learning. MENTAT achieves up to 65% improvement over both baselines, though substantial room remains for future advances in RiR.

We propose a self-supervised machine learning (SSML) framework for multi-fidelity learning and extended predictive soil spectroscopy based on latent space embeddings. A self-supervised representation was pretrained with the large MIR spectral library and the Variational Autoencoder algorithm to obtain a compressed latent space for generating spectral embeddings. At this stage, only unlabeled spectral data were used, allowing us to leverage the full spectral database and the availability of scan repeats for augmented training. We also leveraged and froze the trained MIR decoder for a spectrum conversion task by plugging it into a NIR encoder to learn the mapping between NIR and MIR spectra in an attempt to leverage the predictive capabilities contained in the large MIR library with a low cost portable NIR scanner. This was achieved by using a smaller subset of the KSSL library with paired NIR and MIR spectra. Downstream machine learning models were then trained to map between original spectra, predicted spectra, and latent space embeddings for nine soil properties. The performance of was evaluated independently of the KSSL training data using a gold-standard test set, along with regression goodness-of-fit metrics. Compared to baseline models, the proposed SSML and its embeddings yielded similar or better accuracy in all soil properties prediction tasks. Predictions derived from the spectrum conversion (NIR to MIR) task did not match the performance of the original MIR spectra but were similar or superior to predictive performance of NIR-only models, suggesting the unified spectral latent space can effectively leverage the larger and more diverse MIR dataset for prediction of soil properties not well represented in current NIR libraries.

Accurate retrieval of vegetation biophysical variables from satellite imagery is crucial for ecosystem monitoring and agricultural management. In this work, we propose a physics-informed Transformer-VAE architecture to invert the PROSAIL radiative transfer model for simultaneous estimation of key canopy parameters from Sentinel-2 data. Unlike previous hybrid approaches that require real satellite images for self-supevised training. Our model is trained exclusively on simulated data, yet achieves performance on par with state-of-the-art methods that utilize real imagery. The Transformer-VAE incorporates the PROSAIL model as a differentiable physical decoder, ensuring that inferred latent variables correspond to physically plausible leaf and canopy properties. We demonstrate retrieval of leaf area index (LAI) and canopy chlorophyll content (CCC) on real-world field datasets (FRM4Veg and BelSAR) with accuracy comparable to models trained with real Sentinel-2 data. Our method requires no in-situ labels or calibration on real images, offering a cost-effective and self-supervised solution for global vegetation monitoring. The proposed approach illustrates how integrating physical models with advanced deep networks can improve the inversion of RTMs, opening new prospects for large-scale, physically-constrained remote sensing of vegetation traits.

We introduce the first formal large-scale assessment of the utility of traditional chemical functional groups as used in chemical explanations. Our assessment employs a fundamental principle from computational learning theory: a good explanation of data should also compress the data. We introduce an unsupervised learning algorithm based on the Minimum Message Length (MML) principle that searches for substructures that compress around three million biologically relevant molecules. We demonstrate that the discovered substructures contain most human-curated functional groups as well as novel larger patterns with more specific functions. We also run our algorithm on 24 specific bioactivity prediction datasets to discover dataset-specific functional groups. Fingerprints constructed from dataset-specific functional groups are shown to significantly outperform other fingerprint representations, including the MACCS and Morgan fingerprint, when training ridge regression models on bioactivity regression tasks.

In addition, we introduce a simple baseline, "RDumb", that periodically resets the

Human engagement estimation in conversational scenarios is essential for applications such as adaptive tutoring, remote healthcare assessment, and socially aware human--computer interaction. Engagement is a dynamic, multimodal signal conveyed by facial expressions, speech, gestures, and behavioral cues over time. In this work we introduce DA-Mamba, a dialogue-aware multimodal architecture that replaces attention-heavy dialogue encoders with Mamba-based selective state-space processing to achieve linear time and memory complexity while retaining expressive cross-modal reasoning. We design a Mamba dialogue-aware selective state-space model composed of three core modules: a Dialogue-Aware Encoder, and two Mamba-based fusion mechanisms: Modality-Group Fusion and Partner-Group Fusion, these modules achieve expressive dialogue understanding. Extensive experiments on three standard benchmarks (NoXi, NoXi-Add, and MPIIGI) show that DA-Mamba surpasses prior state-of-the-art (SOTA) methods in concordance correlation coefficient (CCC), while reducing training time and peak memory; these gains enable processing much longer sequences and facilitate real-time deployment in resource-constrained, multi-party conversational settings. The source code will be available at: https://github.com/kksssssss-ssda/MMEA.