Modeling stochastic and irregularly sampled time series is a challenging problem found in a wide range of applications, especially in medicine. Neural stochastic differential equations (Neural SDEs) are an attractive modeling technique for this problem, which parameterize the drift and diffusion terms of an SDE with neural networks. However, current algorithms for training Neural SDEs require backpropagation through the SDE dynamics, greatly limiting their scalability and stability.

Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks.

Foundation models (FMs) have emerged as a powerful paradigm, enabling a diverse range of data analytics and knowledge discovery tasks across scientific fields. Inspired by the success of FMs, particularly large language models, researchers have recently begun to explore spatio-temporal foundation models (STFMs) to improve adaptability and generalization across a wide spectrum of spatio-temporal (ST) tasks. Despite rapid progress, a systematic investigation of trajectory foundation models (TFMs), a crucial subclass of STFMs, is largely lacking. This tutorial addresses this gap by offering a comprehensive overview of recent advances in TFMs, including a taxonomy of existing methodologies and a critical analysis of their strengths and limitations. In addition, the tutorial highlights open challenges and outlines promising research directions to advance spatio-temporal general intelligence through the development of robust, responsible, and transferable TFMs.

Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.

Modeling stochastic and irregularly sampled time series is a challenging problem found in a wide range of applications, especially in medicine. Neural stochastic differential equations (Neural SDEs) are an attractive modeling technique for this problem, which parameterize the drift and diffusion terms of an SDE with neural networks. However, current algorithms for training Neural SDEs require backpropagation through the SDE dynamics, greatly limiting their scalability and stability. To address this, we propose Trajectory Flow Matching (TFM), which trains a Neural SDE in a simulation-free manner, bypassing backpropagation through the dynamics. TFM leverages the flow matching technique from generative modeling to model time series.

Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM (scCello). We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training.

Telecom networks are becoming increasingly complex, with diversified deployment scenarios, multi-standards, and multi-vendor support. The intricate nature of the telecom network ecosystem presents challenges to effectively manage, operate, and optimize networks. To address these hurdles, Artificial Intelligence (AI) has been widely adopted to solve different tasks in telecom networks. However, these conventional AI models are often designed for specific tasks, rely on extensive and costly-to-collect labeled data that require specialized telecom expertise for development and maintenance. The AI models usually fail to generalize and support diverse deployment scenarios and applications. In contrast, Foundation Models (FMs) show effective generalization capabilities in various domains in language, vision, and decision-making tasks. FMs can be trained on multiple data modalities generated from the telecom ecosystem and leverage specialized domain knowledge. Moreover, FMs can be fine-tuned to solve numerous specialized tasks with minimal task-specific labeled data and, in some instances, are able to leverage context to solve previously unseen problems. At the dawn of 6G, this paper investigates the potential opportunities of using FMs to shape the future of telecom technologies and standards. In particular, the paper outlines a conceptual process for developing Telecom FMs (TFMs) and discusses emerging opportunities for orchestrating specialized TFMs for network configuration, operation, and maintenance. Finally, the paper discusses the limitations and challenges of developing and deploying TFMs.

Recent studies have demonstrated the potential to control paraphrase generation, such as through syntax, which has broad applications in various downstream tasks. However, these methods often require detailed parse trees or syntactic exemplars, countering human-like paraphrasing behavior in language use. Furthermore, an inference gap exists, as control specifications are only available during training but not during inference. In this work, we propose a new setup for controlled paraphrase generation. Specifically, we represent user intent as action tokens, embedding and concatenating them with text embeddings, thus flowing together into a self-attention encoder for representation fusion. To address the inference gap, we introduce an optional action token as a placeholder that encourages the model to determine the appropriate action independently when users' intended actions are not provided. Experimental results show that our method successfully enables precise action-controlled paraphrasing and preserves or even enhances performance compared to conventional uncontrolled methods when actions are not given. Our findings promote the concept of action-controlled paraphrasing for a more user-centered design.

Time domain identification is studied in this paper for parameters of a continuous-time multi-input multi-output descriptor system, with these parameters affecting system matrices through a linear fractional transformation. Sampling is permitted to be slow and non-uniform, and there are no necessities to satisfy the Nyquist frequency. This model can be used to described the behaviors of a networked dynamic system, and the obtained results can be straightforwardly applied to a state-space model. An explicit formula is obtained respectively for the transient and steady-state response of the system stimulated by an arbitrary signal. Some relations have been derived between the system steady-state response and its transfer function matrix. A parametric estimation algorithm is suggested.

Blockchains deploy Transaction Fee Mechanisms (TFMs) to determine which user transactions to include in blocks and determine their payments (i.e., transaction fees). Increasing demand and scarce block resources have led to high user transaction fees. As these blockchains are a public resource, it may be preferable to reduce these transaction fees. To this end, we introduce Transaction Fee Redistribution Mechanisms (TFRMs) -- redistributing VCG payments collected from such TFM as rebates to minimize transaction fees. Classic redistribution mechanisms (RMs) achieve this while ensuring Allocative Efficiency (AE) and User Incentive Compatibility (UIC). Our first result shows the non-triviality of applying RM in TFMs. More concretely, we prove that it is impossible to reduce transaction fees when (i) transactions that are not confirmed do not receive rebates and (ii) the miner can strategically manipulate the mechanism. Driven by this, we propose \emph{Robust} TFRM (\textsf{R-TFRM}): a mechanism that compromises on an honest miner's individual rationality to guarantee strictly positive rebates to the users. We then introduce \emph{robust} and \emph{rational} TFRM (\textsf{R}$^2$\textsf{-TFRM}) that uses trusted on-chain randomness that additionally guarantees miner's individual rationality (in expectation) and strictly positive rebates. Our results show that TFRMs provide a promising new direction for reducing transaction fees in public blockchains.