GENERator: A Long-Context Generative Genomic Foundation Model

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Optimizing Knowledge Integration in Retrieval-Augmented Generation with Self-Selection

Retrieval-Augmented Generation (RAG), which integrates external knowledge into Large Language Models (LLMs), has proven effective in enabling LLMs to produce more accurate and reliable responses. However, it remains a significant challenge how to effectively integrate external retrieved knowledge with internal parametric knowledge in LLMs. In this work, we propose a novel Self-Selection RAG framework, where the LLM is made to select from pairwise responses generated with internal parametric knowledge solely and with external retrieved knowledge together to achieve enhanced accuracy. To this end, we devise a Self-Selection-RGP method to enhance the capabilities of the LLM in both generating and selecting the correct answer, by training the LLM with Direct Preference Optimization (DPO) over a curated Retrieval Generation Preference (RGP) dataset. Experimental results with two open-source LLMs (i.e., Llama2-13B-Chat and Mistral-7B) well demonstrate the superiority of our approach over other baseline methods on Natural Questions (NQ) and TrivialQA datasets.

Large Language Models for Recommendation with Deliberative User Preference Alignment

While recent advancements in aligning Large Language Models (LLMs) with recommendation tasks have shown great potential and promising performance overall, these aligned recommendation LLMs still face challenges in complex scenarios. This is primarily due to the current alignment approach focusing on optimizing LLMs to generate user feedback directly, without incorporating deliberation. To overcome this limitation and develop more reliable LLMs for recommendations, we propose a new Deliberative Recommendation task, which incorporates explicit reasoning about user preferences as an additional alignment goal. We then introduce the Deliberative User Preference Alignment framework, designed to enhance reasoning capabilities by utilizing verbalized user feedback in a step-wise manner to tackle this task. The framework employs collaborative step-wise experts and tailored training strategies for each expert. Experimental results across three real-world datasets demonstrate the rationality of the deliberative task formulation and the superior performance of the proposed framework in improving both prediction accuracy and reasoning quality.

Efficient Multi-Agent System Training with Data Influence-Oriented Tree Search

Monte Carlo Tree Search (MCTS) based methods provide promising approaches for generating synthetic data to enhance the self-training of Large Language Model (LLM) based multi-agent systems (MAS). These methods leverage Q-values to estimate individual agent contributions. However, relying solely on Q-values to identify informative data may misalign with the data synthesis objective, as the focus should be on selecting data that best enhances model training. To address this discrepancy, we propose Data Influence-oriented Tree Search (DITS), a novel framework that incorporates influence scores to guide both tree search and data selection. By leveraging influence scores, we effectively identify the most impactful data for system improvement, thereby enhancing model performance. Furthermore, we derive influence score estimation methods tailored for non-differentiable metrics, significantly reducing computational overhead by utilizing inference computations. Extensive experiments on eight multi-agent datasets demonstrate the robustness and effectiveness of the proposed methods. Notably, our findings reveal that allocating more inference resources to estimate influence scores, rather than Q-values, during data synthesis can more effectively and efficiently enhance model training.

Leveraging Memory Retrieval to Enhance LLM-based Generative Recommendation

Leveraging Large Language Models (LLMs) to harness user-item interaction histories for item generation has emerged as a promising paradigm in generative recommendation. However, the limited context window of LLMs often restricts them to focusing on recent user interactions only, leading to the neglect of long-term interests involved in the longer histories. To address this challenge, we propose a novel Automatic Memory-Retrieval framework (AutoMR), which is capable of storing long-term interests in the memory and extracting relevant information from it for next-item generation within LLMs. Extensive experimental results on two real-world datasets demonstrate the effectiveness of our proposed AutoMR framework in utilizing long-term interests for generative recommendation.

Disentangling Reasoning Tokens and Boilerplate Tokens For Language Model Fine-tuning

When using agent-task datasets to enhance agent capabilities for Large Language Models (LLMs), current methodologies often treat all tokens within a sample equally. However, we argue that tokens serving different roles - specifically, reasoning tokens versus boilerplate tokens (e.g., those governing output format) - differ significantly in importance and learning complexity, necessitating their disentanglement and distinct treatment. To address this, we propose a novel Shuffle-Aware Discriminator (SHAD) for adaptive token discrimination. SHAD classifies tokens by exploiting predictability differences observed after shuffling input-output combinations across samples: boilerplate tokens, due to their repetitive nature among samples, maintain predictability, whereas reasoning tokens do not. Using SHAD, we propose the Reasoning-highlighted Fine-Tuning (RFT) method, which adaptively emphasizes reasoning tokens during fine-tuning, yielding notable performance gains over common Supervised Fine-Tuning (SFT).

Real-Time Personalization for LLM-based Recommendation with Customized In-Context Learning

Frequently updating Large Language Model (LLM)-based recommender systems to adapt to new user interests -- as done for traditional ones -- is impractical due to high training costs, even with acceleration methods. This work explores adapting to dynamic user interests without any model updates by leveraging In-Context Learning (ICL), which allows LLMs to learn new tasks from few-shot examples provided in the input. Using new-interest examples as the ICL few-shot examples, LLMs may learn real-time interest directly, avoiding the need for model updates. However, existing LLM-based recommenders often lose the in-context learning ability during recommendation tuning, while the original LLM's in-context learning lacks recommendation-specific focus. To address this, we propose RecICL, which customizes recommendation-specific in-context learning for real-time recommendations. RecICL organizes training examples in an in-context learning format, ensuring that in-context learning ability is preserved and aligned with the recommendation task during tuning. Extensive experiments demonstrate RecICL's effectiveness in delivering real-time recommendations without requiring model updates. Our code is available at https://github.com/ym689/rec_icl.

FLOW: A Feedback LOop FrameWork for Simultaneously Enhancing Recommendation and User Agents

Agents powered by large language models have shown remarkable reasoning and execution capabilities, attracting researchers to explore their potential in the recommendation domain. Previous studies have primarily focused on enhancing the capabilities of either recommendation agents or user agents independently, but have not considered the interaction and collaboration between recommendation agents and user agents. To address this gap, we propose a novel framework named FLOW, which achieves collaboration between the recommendation agent and the user agent by introducing a feedback loop. Specifically, the recommendation agent refines its understanding of the user's preferences by analyzing the user agent's feedback on previously suggested items, while the user agent leverages suggested items to uncover deeper insights into the user's latent interests. This iterative refinement process enhances the reasoning capabilities of both the recommendation agent and the user agent, enabling more precise recommendations and a more accurate simulation of user behavior. To demonstrate the effectiveness of the feedback loop, we evaluate both recommendation performance and user simulation performance on three widely used recommendation domain datasets. The experimental results indicate that the feedback loop can simultaneously improve the performance of both the recommendation and user agents.

MMDocBench: Benchmarking Large Vision-Language Models for Fine-Grained Visual Document Understanding

Large Vision-Language Models (LVLMs) have achieved remarkable performance in many vision-language tasks, yet their capabilities in fine-grained visual understanding remain insufficiently evaluated. Existing benchmarks either contain limited fine-grained evaluation samples that are mixed with other data, or are confined to object-level assessments in natural images. To holistically assess LVLMs' fine-grained visual understanding capabilities, we propose using document images with multi-granularity and multi-modal information to supplement natural images. In this light, we construct MMDocBench, a benchmark with various OCR-free document understanding tasks for the evaluation of fine-grained visual perception and reasoning abilities. MMDocBench defines 15 main tasks with 4,338 QA pairs and 11,353 supporting regions, covering various document images such as research papers, receipts, financial reports, Wikipedia tables, charts, and infographics. Based on MMDocBench, we conduct extensive experiments using 13 open-source and 3 proprietary advanced LVLMs, assessing their strengths and weaknesses across different tasks and document image types. The benchmark, task instructions, and evaluation code will be made publicly available.

Personalized Image Generation with Large Multimodal Models

Personalized content filtering, such as recommender systems, has become a critical infrastructure to alleviate information overload. However, these systems merely filter existing content and are constrained by its limited diversity, making it difficult to meet users' varied content needs. To address this limitation, personalized content generation has emerged as a promising direction with broad applications. Nevertheless, most existing research focuses on personalized text generation, with relatively little attention given to personalized image generation. The limited work in personalized image generation faces challenges in accurately capturing users' visual preferences and needs from noisy user-interacted images and complex multimodal instructions. Worse still, there is a lack of supervised data for training personalized image generation models. To overcome the challenges, we propose a Personalized Image Generation Framework named Pigeon, which adopts exceptional large multimodal models with three dedicated modules to capture users' visual preferences and needs from noisy user history and multimodal instructions. To alleviate the data scarcity, we introduce a two-stage preference alignment scheme, comprising masked preference reconstruction and pairwise preference alignment, to align Pigeon with the personalized image generation task. We apply Pigeon to personalized sticker and movie poster generation, where extensive quantitative results and human evaluation highlight its superiority over various generative baselines.