Biological Pathway Guided Gene Selection Through Collaborative Reinforcement Learning

Gene selection in high-dimensional genomic data is essential for understanding disease mechanisms and improving therapeutic outcomes. Traditional feature selection methods effectively identify predictive genes but often ignore complex biological pathways and regulatory networks, leading to unstable and biologically irrelevant signatures. Prior approaches, such as Lasso-based methods and statistical filtering, either focus solely on individual gene-outcome associations or fail to capture pathway-level interactions, presenting a key challenge: how to integrate biological pathway knowledge while maintaining statistical rigor in gene selection? To address this gap, we propose a novel two-stage framework that integrates statistical selection with biological pathway knowledge using multi-agent reinforcement learning (MARL). First, we introduce a pathway-guided pre-filtering strategy that leverages multiple statistical methods alongside KEGG pathway information for initial dimensionality reduction. Next, for refined selection, we model genes as collaborative agents in a MARL framework, where each agent optimizes both predictive power and biological relevance. Our framework incorporates pathway knowledge through Graph Neural Network-based state representations, a reward mechanism combining prediction performance with gene centrality and pathway coverage, and collaborative learning strategies using shared memory and a centralized critic component. Extensive experiments on multiple gene expression datasets demonstrate that our approach significantly improves both prediction accuracy and biological interpretability compared to traditional methods.

Weaver: Interweaving SQL and LLM for Table Reasoning

Querying tables with unstructured data is challenging due to the presence of text (or image), either embedded in the table or in external paragraphs, which traditional SQL struggles to process, especially for tasks requiring semantic reasoning. While Large Language Models (LLMs) excel at understanding context, they face limitations with long input sequences. Existing approaches that combine SQL and LLMs typically rely on rigid, predefined work-flows, limiting their adaptability to complex queries. To address these issues, we introduce Weaver , a modular pipeline that dynamically integrates SQL and LLMs for table-based question answering (TableQA). Weaver generates a flexible, step-by-step plan that combines SQL for structured data retrieval with LLMs for semantic processing. By decomposing complex queries into manageable subtasks, Weaver improves accuracy and generalization. Our experiments show that Weaver consistently outperforms state-of-the-art methods across four TableQA datasets, reducing both API calls and error rates.

Brownian Bridge Augmented Surrogate Simulation and Injection Planning for Geological CO$_2$ Storage

Geological CO2 storage (GCS) involves injecting captured CO2 into deep subsurface formations to support climate goals. The effective management of GCS relies on adaptive injection planning to dynamically control injection rates and well pressures to balance both storage safety and efficiency. Prior literature, including numerical optimization methods and surrogate-optimization methods, is limited by real-world GCS requirements of smooth state transitions and goal-directed planning within limited time. To address these limitations, we propose a Brownian Bridge-augmented framework for surrogate simulation and injection planning in GCS and develop two insights: (i) Brownian bridge as a smooth state regularizer for better surrogate simulation; (ii) Brownian bridge as goal-time-conditioned planning guidance for improved injection planning. Our method has three stages: (i) learning deep Brownian bridge representations with contrastive and reconstructive losses from historical reservoir and utility trajectories, (ii) incorporating Brownian bridge-based next state interpolation for simulator regularization, and (iii) guiding injection planning with Brownian utility-conditioned trajectories to generate high-quality injection plans. Experimental results across multiple datasets collected from diverse GCS settings demonstrate that our framework consistently improves simulation fidelity and planning effectiveness while maintaining low computational overhead.

Sculpting Features from Noise: Reward-Guided Hierarchical Diffusion for Task-Optimal Feature Transformation

Feature Transformation (FT) crafts new features from original ones via mathematical operations to enhance dataset expressiveness for downstream models. However, existing FT methods exhibit critical limitations: discrete search struggles with enormous combinatorial spaces, impeding practical use; and continuous search, being highly sensitive to initialization and step sizes, often becomes trapped in local optima, restricting global exploration. To overcome these limitations, DIFFT redefines FT as a reward-guided generative task. It first learns a compact and expressive latent space for feature sets using a Variational Auto-Encoder (VAE). A Latent Diffusion Model (LDM) then navigates this space to generate high-quality feature embeddings, its trajectory guided by a performance evaluator towards task-specific optima. This synthesis of global distribution learning (from LDM) and targeted optimization (reward guidance) produces potent embeddings, which a novel semi-autoregressive decoder efficiently converts into structured, discrete features, preserving intra-feature dependencies while allowing parallel inter-feature generation. Extensive experiments on 14 benchmark datasets show DIFFT consistently outperforms state-of-the-art baselines in predictive accuracy and robustness, with significantly lower training and inference times.

Agentic Feature Augmentation: Unifying Selection and Generation with Teaming, Planning, and Memories

As a widely-used and practical tool, feature engineering transforms raw data into discriminative features to advance AI model performance. However, existing methods usually apply feature selection and generation separately, failing to strive a balance between reducing redundancy and adding meaningful dimensions. To fill this gap, we propose an agentic feature augmentation concept, where the unification of feature generation and selection is modeled as agentic teaming and planning. Specifically, we develop a Multi-Agent System with Long and Short-Term Memory (MAGS), comprising a selector agent to eliminate redundant features, a generator agent to produce informative new dimensions, and a router agent that strategically coordinates their actions. We leverage in-context learning with short-term memory for immediate feedback refinement and long-term memory for globally optimal guidance. Additionally, we employ offline Proximal Policy Optimization (PPO) reinforcement fine-tuning to train the router agent for effective decision-making to navigate a vast discrete feature space. Extensive experiments demonstrate that this unified agentic framework consistently achieves superior task performance by intelligently orchestrating feature selection and generation.

Bridging the Domain Gap in Equation Distillation with Reinforcement Feedback

The data-to-equation (Data2Eqn) task aims to discover interpretable mathematical equations that map observed values to labels, offering physical insights and broad applicability across academic and industrial domains. Genetic programming and traditional deep learning-based approaches suffer from search inefficiency and poor generalization on small task-specific datasets. Foundation models showed promise in this area, but existing approaches suffer from: 1) They are pretrained on general-purpose data distributions, making them less effective for domain-specific tasks; and 2) their training objectives focus on token-level alignment, overlooking mathematical semantics, which can lead to inaccurate equations. To address these issues, we aim to enhance the domain adaptability of foundation models for Data2Eqn tasks. In this work, we propose a reinforcement learning-based finetuning framework that directly optimizes the generation policy of a pretrained model through reward signals derived from downstream numerical fitness. Our method allows the model to adapt to specific and complex data distributions and generate mathematically meaningful equations. Extensive experiments demonstrate that our approach improves both the accuracy and robustness of equation generation under complex distributions.

Continuous Optimization for Feature Selection with Permutation-Invariant Embedding and Policy-Guided Search

Feature selection removes redundant features to enhanc performance and computational efficiency in downstream tasks. Existing works often struggle to capture complex feature interactions and adapt to diverse scenarios. Recent advances in this domain have incorporated generative intelligence to address these drawbacks by uncovering intricate relationships between features. However, two key limitations remain: 1) embedding feature subsets in a continuous space is challenging due to permutation sensitivity, as changes in feature order can introduce biases and weaken the embedding learning process; 2) gradient-based search in the embedding space assumes convexity, which is rarely guaranteed, leading to reduced search effectiveness and suboptimal subsets. To address these limitations, we propose a new framework that can: 1) preserve feature subset knowledge in a continuous embedding space while ensuring permutation invariance; 2) effectively explore the embedding space without relying on strong convex assumptions. For the first objective, we develop an encoder-decoder paradigm to preserve feature selection knowledge into a continuous embedding space. This paradigm captures feature interactions through pairwise relationships within the subset, removing the influence of feature order on the embedding. Moreover, an inducing point mechanism is introduced to accelerate pairwise relationship computations. For the second objective, we employ a policy-based reinforcement learning (RL) approach to guide the exploration of the embedding space. The RL agent effectively navigates the space by balancing multiple objectives. By prioritizing high-potential regions adaptively and eliminating the reliance on convexity assumptions, the RL agent effectively reduces the risk of converging to local optima. Extensive experiments demonstrate the effectiveness, efficiency, robustness and explicitness of our model.

Unsupervised Feature Transformation via In-context Generation, Generator-critic LLM Agents, and Duet-play Teaming

Feature transformation involves generating a new set of features from the original dataset to enhance the data's utility. In certain domains like material performance screening, dimensionality is large and collecting labels is expensive and lengthy. It highly necessitates transforming feature spaces efficiently and without supervision to enhance data readiness and AI utility. However, existing methods fall short in efficient navigation of a vast space of feature combinations, and are mostly designed for supervised settings. To fill this gap, our unique perspective is to leverage a generator-critic duet-play teaming framework using LLM agents and in-context learning to derive pseudo-supervision from unsupervised data. The framework consists of three interconnected steps: (1) Critic agent diagnoses data to generate actionable advice, (2) Generator agent produces tokenized feature transformations guided by the critic's advice, and (3) Iterative refinement ensures continuous improvement through feedback between agents. The generator-critic framework can be generalized to human-agent collaborative generation, by replacing the critic agent with human experts. Extensive experiments demonstrate that the proposed framework outperforms even supervised baselines in feature transformation efficiency, robustness, and practical applicability across diverse datasets.

NAPER: Fault Protection for Real-Time Resource-Constrained Deep Neural Networks

Fault tolerance in Deep Neural Networks (DNNs) deployed on resource-constrained systems presents unique challenges for high-accuracy applications with strict timing requirements. Memory bit-flips can severely degrade DNN accuracy, while traditional protection approaches like Triple Modular Redundancy (TMR) often sacrifice accuracy to maintain reliability, creating a three-way dilemma between reliability, accuracy, and timeliness. We introduce NAPER, a novel protection approach that addresses this challenge through ensemble learning. Unlike conventional redundancy methods, NAPER employs heterogeneous model redundancy, where diverse models collectively achieve higher accuracy than any individual model. This is complemented by an efficient fault detection mechanism and a real-time scheduler that prioritizes meeting deadlines by intelligently scheduling recovery operations without interrupting inference. Our evaluations demonstrate NAPER's superiority: 40% faster inference in both normal and fault conditions, maintained accuracy 4.2% higher than TMR-based strategies, and guaranteed uninterrupted operation even during fault recovery. NAPER effectively balances the competing demands of accuracy, reliability, and timeliness in real-time DNN applications

FastFT: Accelerating Reinforced Feature Transformation via Advanced Exploration Strategies

Feature Transformation is crucial for classic machine learning that aims to generate feature combinations to enhance the performance of downstream tasks from a data-centric perspective. Current methodologies, such as manual expert-driven processes, iterative-feedback techniques, and exploration-generative tactics, have shown promise in automating such data engineering workflow by minimizing human involvement. However, three challenges remain in those frameworks: (1) It predominantly depends on downstream task performance metrics, as assessment is time-consuming, especially for large datasets. (2) The diversity of feature combinations will hardly be guaranteed after random exploration ends. (3) Rare significant transformations lead to sparse valuable feedback that hinders the learning processes or leads to less effective results. In response to these challenges, we introduce FastFT, an innovative framework that leverages a trio of advanced strategies.We first decouple the feature transformation evaluation from the outcomes of the generated datasets via the performance predictor. To address the issue of reward sparsity, we developed a method to evaluate the novelty of generated transformation sequences. Incorporating this novelty into the reward function accelerates the model's exploration of effective transformations, thereby improving the search productivity. Additionally, we combine novelty and performance to create a prioritized memory buffer, ensuring that essential experiences are effectively revisited during exploration. Our extensive experimental evaluations validate the performance, efficiency, and traceability of our proposed framework, showcasing its superiority in handling complex feature transformation tasks.