Mechanistic interpretability of large language models (LLMs) aims to uncover the internal processes of information propagation and reasoning. Sparse autoencoders (SAEs) have demonstrated promise in this domain by extracting interpretable and monosemantic features. However, prior works primarily focus on feature extraction from a single layer, failing to effectively capture activations that span multiple layers. In this paper, we introduce Route Sparse Autoencoder (RouteSAE), a new framework that integrates a routing mechanism with a shared SAE to efficiently extract features from multiple layers. It dynamically assigns weights to activations from different layers, incurring minimal parameter overhead while achieving high interpretability and flexibility for targeted feature manipulation. We evaluate RouteSAE through extensive experiments on Llama-3.2-1B-Instruct. Specifically, under the same sparsity constraint of 64, RouteSAE extracts 22.5% more features than baseline SAEs while achieving a 22.3% higher interpretability score. These results underscore the potential of RouteSAE as a scalable and effective method for LLM interpretability, with applications in feature discovery and model intervention. Our codes are available at https://github.com/swei2001/RouteSAEs.

Transformers' ability to generalize to longer sequences than they have been trained on, known as length extrapolation, degrades as sequence length increases. Most of Relative Positional Encoding (RPE) methods address this problem by either adding constant linear biases or learning general biases, lacking the ability to specialize for different sequences. In this work, inspired by ALiBi, we propose Context-aware Biases for Length Extrapolation (Cable), that learns token-specific biases for each head in decoder-based transformers. Cable learns adaptive, context-aware biases, overcoming the limitations of fixed patterns by adding dynamic biases specific to each token in the sequence. Results show that when tested on a sequence length of 1024, a GPT-3 Medium (334M parameters) with our positional encoding, trained on a sequence length of 512, achieves better perplexity (-0.65) than a similar network with sinusoidal positional encoding trained on a sequence length of 1024. This is achieved with 48% lower memory usage, and only 3.5% higher training time. Furthermore, our method notably improves the extrapolation ability of existing RPE methods on the Edu-FineWeb10B and WikiText-103 datasets. Code is available at: https://github.com/axiomlab/Cable

Large Language Models (LLMs) have made significant progress in open-ended dialogue, yet their inability to retain and retrieve relevant information from long-term interactions limits their effectiveness in applications requiring sustained personalization. External memory mechanisms have been proposed to address this limitation, enabling LLMs to maintain conversational continuity. However, existing approaches struggle with two key challenges. First, rigid memory granularity fails to capture the natural semantic structure of conversations, leading to fragmented and incomplete representations. Second, fixed retrieval mechanisms cannot adapt to diverse dialogue contexts and user interaction patterns. In this work, we propose Reflective Memory Management (RMM), a novel mechanism for long-term dialogue agents, integrating forward- and backward-looking reflections: (1) Prospective Reflection, which dynamically summarizes interactions across granularities-utterances, turns, and sessions-into a personalized memory bank for effective future retrieval, and (2) Retrospective Reflection, which iteratively refines the retrieval in an online reinforcement learning (RL) manner based on LLMs' cited evidence. Experiments show that RMM demonstrates consistent improvement across various metrics and benchmarks. For example, RMM shows more than 10% accuracy improvement over the baseline without memory management on the LongMemEval dataset.

Data watermarking in language models injects traceable signals, such as specific token sequences or stylistic patterns, into copyrighted text, allowing copyright holders to track and verify training data ownership. Previous data watermarking techniques primarily focus on effective memorization after pretraining, while overlooking challenges that arise in other stages of the LLM pipeline, such as the risk of watermark filtering during data preprocessing, or potential forgetting through post-training, or verification difficulties due to API-only access. We propose a novel data watermarking approach that injects coherent and plausible yet fictitious knowledge into training data using generated passages describing a fictitious entity and its associated attributes. Our watermarks are designed to be memorized by the LLM through seamlessly integrating in its training data, making them harder to detect lexically during preprocessing. We demonstrate that our watermarks can be effectively memorized by LLMs, and that increasing our watermarks' density, length, and diversity of attributes strengthens their memorization. We further show that our watermarks remain robust throughout LLM development, maintaining their effectiveness after continual pretraining and supervised finetuning. Finally, we show that our data watermarks can be evaluated even under API-only access via question answering.

Dynamic interactions between entities are prevalent in domains like social platforms, financial systems, healthcare, and e-commerce. These interactions can be effectively represented as time-evolving graphs, where predicting future connections is a key task in applications such as recommendation systems. Temporal Graph Neural Networks (TGNNs) have achieved strong results for such predictive tasks but typically require extensive training data, which is often limited in real-world scenarios. One approach to mitigating data scarcity is leveraging pre-trained models from related datasets. However, direct knowledge transfer between TGNNs is challenging due to their reliance on node-specific memory structures, making them inherently difficult to adapt across datasets. To address this, we introduce a novel transfer approach that disentangles node representations from their associated features through a structured bipartite encoding mechanism. This decoupling enables more effective transfer of memory components and other learned inductive patterns from one dataset to another. Empirical evaluations on real-world benchmarks demonstrate that our method significantly enhances TGNN performance in low-data regimes, outperforming non-transfer baselines by up to 56\% and surpassing existing transfer strategies by 36\%

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Collecting labeled data for machine learning models is often expensive and time-consuming. Active learning addresses this challenge by selectively labeling the most informative observations, but when initial labeled data is limited, it becomes difficult to distinguish genuinely informative points from those appearing uncertain primarily due to noise. Ensemble methods like random forests are a powerful approach to quantifying this uncertainty but do so by aggregating all models indiscriminately. This includes poor performing models and redundant models, a problem that worsens in the presence of noisy data. We introduce UNique Rashomon Ensembled Active Learning (UNREAL), which selectively ensembles only distinct models from the Rashomon set, which is the set of nearly optimal models. Restricting ensemble membership to high-performing models with different explanations helps distinguish genuine uncertainty from noise-induced variation. We show that UNREAL achieves faster theoretical convergence rates than traditional active learning approaches and demonstrates empirical improvements of up to 20% in predictive accuracy across five benchmark datasets, while simultaneously enhancing model interpretability.

Machine learning frameworks for physical problems must capture and enforce physical constraints that preserve the structure of dynamical systems. Many existing approaches achieve this by integrating physical operators into neural networks. While these methods offer theoretical guarantees, they face two key limitations: (i) they primarily model local relations between adjacent time steps, overlooking longer-range or higher-level physical interactions, and (ii) they focus on forward simulation while neglecting broader physical reasoning tasks. We propose the Denoising Hamiltonian Network (DHN), a novel framework that generalizes Hamiltonian mechanics operators into more flexible neural operators. DHN captures non-local temporal relationships and mitigates numerical integration errors through a denoising mechanism. DHN also supports multi-system modeling with a global conditioning mechanism. We demonstrate its effectiveness and flexibility across three diverse physical reasoning tasks with distinct inputs and outputs.

This paper introduces BSPA, a parallel algorithm that leverages beam search to address the two-dimensional strip packing problem. The study begins with a comprehensive review of existing approaches and methodologies, followed by a detailed presentation of the BSPA algorithm. Experimental results demonstrate the effectiveness of the proposed method. To facilitate further research, both the code and datasets are publicly available.

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.