Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

In recent years, generative models have achieved remarkable performance across diverse applications, including image generation, text synthesis, audio creation, video generation, and data augmentation. Diffusion models have emerged as superior alternatives to Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) by addressing their limitations, such as training instability, mode collapse, and poor representation of multimodal distributions. This success has spurred widespread research interest. In the domain of tabular data, diffusion models have begun to showcase similar advantages over GANs and VAEs, achieving significant performance breakthroughs and demonstrating their potential for addressing unique challenges in tabular data modeling. However, while domains like images and time series have numerous surveys summarizing advancements in diffusion models, there remains a notable gap in the literature for tabular data. Despite the increasing interest in diffusion models for tabular data, there has been little effort to systematically review and summarize these developments. This lack of a dedicated survey limits a clear understanding of the challenges, progress, and future directions in this critical area. This survey addresses this gap by providing a comprehensive review of diffusion models for tabular data. Covering works from June 2015, when diffusion models emerged, to December 2024, we analyze nearly all relevant studies, with updates maintained in a \href{https://github.com/Diffusion-Model-Leiden/awesome-diffusion-models-for-tabular-data}{GitHub repository}. Assuming readers possess foundational knowledge of statistics and diffusion models, we employ mathematical formulations to deliver a rigorous and detailed review, aiming to promote developments in this emerging and exciting area.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Personalized news headline generation, aiming at generating user-specific headlines based on readers' preferences, burgeons a recent flourishing research direction. Existing studies generally inject a user interest embedding into an encoderdecoder headline generator to make the output personalized, while the factual consistency of headlines is inadequate to be verified. In this paper, we propose a framework Fact-Preserved Personalized News Headline Generation (short for FPG), to prompt a tradeoff between personalization and consistency. In FPG, the similarity between the candidate news to be exposed and the historical clicked news is used to give different levels of attention to key facts in the candidate news, and the similarity scores help to learn a fact-aware global user embedding. Besides, an additional training procedure based on contrastive learning is devised to further enhance the factual consistency of generated headlines. Extensive experiments conducted on a real-world benchmark PENS validate the superiority of FPG, especially on the tradeoff between personalization and factual consistency.

Predicting multiple functions labeled with Enzyme Commission (EC) numbers from the enzyme sequence is of great significance but remains a challenge due to its sparse multi-label classification nature, i.e., each enzyme is typically associated with only a few labels out of more than 6000 possible EC numbers. However, existing machine learning algorithms generally learn a fixed global representation for each enzyme to classify all functions, thereby they lack interpretability and the fine-grained information of some function-specific local residue fragments may be overwhelmed. Here we present an attention-based framework, namely ProtDETR (Protein Detection Transformer), by casting enzyme function prediction as a detection problem. It uses a set of learnable functional queries to adaptatively extract different local representations from the sequence of residue-level features for predicting different EC numbers. ProtDETR not only significantly outperforms existing deep learning-based enzyme function prediction methods, but also provides a new interpretable perspective on automatically detecting different local regions for identifying different functions through cross-attentions between queries and residue-level features. The development of genome sequencing technologies has unveiled a vast collection of protein sequences, but detailed functional annotations are only available for a very small number of them [2]. Evaluating the functions of protein sequences via wet experiments is time-consuming, labor-intensive, and expensive, underscoring the critical need for computational methods to predict protein functions. This is particularly acute in the study of enzymes, which catalyze various biological reactions and are central to understanding metabolic processes. For the most widely-used EC number classification scheme, each class of enzyme function is assigned an EC number, which is a four-level hierarchy reflecting the intricate organization of enzyme functions.

While large language models (LLMs) excel in many domains, their complexity and scale challenge deployment in resource-limited environments. Current compression techniques, such as parameter pruning, often fail to effectively utilize the knowledge from pruned parameters. To address these challenges, we propose Manifold-Based Knowledge Alignment and Layer Merging Compression (MKA), a novel approach that uses manifold learning and the Normalized Pairwise Information Bottleneck (NPIB) measure to merge similar layers, reducing model size while preserving essential performance. We evaluate MKA on multiple benchmark datasets and various LLMs. Our findings show that MKA not only preserves model performance but also achieves substantial compression ratios, outperforming traditional pruning methods. Moreover, when coupled with quantization, MKA delivers even greater compression. Specifically, on the MMLU dataset using the Llama3-8B model, MKA achieves a compression ratio of 43.75% with a minimal performance decrease of only 2.82\%. The proposed MKA method offers a resource-efficient and performance-preserving model compression technique for LLMs.

In the Retrieval-Augmented Generation (RAG) system, advanced Large Language Models (LLMs) have emerged as effective Query Likelihood Models (QLMs) in an unsupervised way, which re-rank documents based on the probability of generating the query given the content of a document. However, directly prompting LLMs to approximate QLMs inherently is biased, where the estimated distribution might diverge from the actual document-specific distribution. In this study, we introduce a novel framework, $\mathrm{UR^3}$, which leverages Bayesian decision theory to both quantify and mitigate this estimation bias. Specifically, $\mathrm{UR^3}$ reformulates the problem as maximizing the probability of document generation, thereby harmonizing the optimization of query and document generation probabilities under a unified risk minimization objective. Our empirical results indicate that $\mathrm{UR^3}$ significantly enhances re-ranking, particularly in improving the Top-1 accuracy. It benefits the QA tasks by achieving higher accuracy with fewer input documents.

Due to the empirical success of reinforcement learning, an increasing number of students study the subject. However, from our practical teaching experience, we see students entering the field (bachelor, master and early PhD) often struggle. On the one hand, textbooks and (online) lectures provide the fundamentals, but students find it hard to translate between equations and code. On the other hand, public codebases do provide practical examples, but the implemented algorithms tend to be complex, and the underlying test environments contain multiple reinforcement learning challenges at once. Although this is realistic from a research perspective, it often hinders educational conceptual understanding. To solve this issue we introduce EduGym, a set of educational reinforcement learning environments and associated interactive notebooks tailored for education. Each EduGym environment is specifically designed to illustrate a certain aspect/challenge of reinforcement learning (e.g., exploration, partial observability, stochasticity, etc.), while the associated interactive notebook explains the challenge and its possible solution approaches, connecting equations and code in a single document. An evaluation among RL students and researchers shows 86% of them think EduGym is a useful tool for reinforcement learning education. All notebooks are available from https://sites.google.com/view/edu-gym/home, while the full software package can be installed from https://github.com/RLG-Leiden/edugym.

Text-to-motion generation has gained increasing attention, but most existing methods are limited to generating short-term motions that correspond to a single sentence describing a single action. However, when a text stream describes a sequence of continuous motions, the generated motions corresponding to each sentence may not be coherently linked. Existing long-term motion generation methods face two main issues. Firstly, they cannot directly generate coherent motions and require additional operations such as interpolation to process the generated actions. Secondly, they generate subsequent actions in an autoregressive manner without considering the influence of future actions on previous ones. To address these issues, we propose a novel approach that utilizes a past-conditioned diffusion model with two optional coherent sampling methods: Past Inpainting Sampling and Compositional Transition Sampling. Past Inpainting Sampling completes subsequent motions by treating previous motions as conditions, while Compositional Transition Sampling models the distribution of the transition as the composition of two adjacent motions guided by different text prompts. Our experimental results demonstrate that our proposed method is capable of generating compositional and coherent long-term 3D human motions controlled by a user-instructed long text stream. The code is available at \href{https://github.com/yangzhao1230/PCMDM}{https://github.com/yangzhao1230/PCMDM}.