Daily Papers

Memory is becoming core infrastructure for long-horizon LLM agents, yet existing evaluations offer limited guidance on which memory substrate, namely the underlying medium in which memory is represented and stored, should be used under different operating regimes. We present a controlled harness evaluation of memory substrates for memory-augmented agents, covering dense and sparse indices, text records, structural stores, hierarchical stores, refinement-based memories, parametric updates, and activation-compatible context mechanisms. Across three backbone models and four benchmark suites spanning user-centric question answering and agent-centric decision-making, we instrument 26 performance and efficiency metrics under a unified harness. Our results show that no single substrate consistently dominates: broad retrieval benefits long-context factual QA, while excessive retrieval can harm sequential decision-making by shifting attention away from action-critical context. Scalability introduces a further routing axis, as substrates that perform well at moderate history lengths can become costly or brittle at longer horizons. These findings motivate substrate routing as a necessary component of adaptive agent memory systems and provide empirical guidance for designing efficient, reliable, and regime-aware long-term memory for LLM agents. Code will be made available upon acceptance.

Large Language Models (LLMs) have achieved remarkable performance on single-turn tasks, yet their effectiveness deteriorates in multi-turn conversations. We define this phenomenon as cumulative contextual decay - a progressive degradation of contextual integrity caused by attention pollution, dilution, and drift. To address this challenge, we propose Rhea (Role-aware Heuristic Episodic Attention), a novel framework that decouples conversation history into two functionally independent memory modules: (1) an Instructional Memory (IM) that persistently stores high-fidelity global constraints via a structural priority mechanism, and (2) an Episodic Memory (EM) that dynamically manages user-model interactions via asymmetric noise control and heuristic context retrieval. During inference, Rhea constructs a high signal-to-noise context by applying its priority attention: selectively integrating relevant episodic information while always prioritizing global instructions. To validate this approach, experiments on multiple multi-turn conversation benchmarks - including MT-Eval and Long-MT-Bench+ - show that Rhea mitigates performance decay and improves overall accuracy by 1.04 points on a 10-point scale (a 16% relative gain over strong baselines). Moreover, Rhea maintains near-perfect instruction fidelity (IAR > 8.1) across long-horizon interactions. These results demonstrate that Rhea provides a principled and effective framework for building more precise, instruction-consistent conversational LLMs.

The performance of modern language models depends critically on pretraining data composition. Yet existing data selection methods rely on auxiliary classifiers for document scoring or mixture optimization, adding computational overhead and dependence on labeled data. We propose WebGraphMix, a lightweight data selection framework that computes structural centrality scores over the Common Crawl host-level web graph and uses them to vary the proportion of central versus peripheral documents in the pretraining mixture. We hypothesize that central hosts expose models to reusable abstractions, while peripheral hosts encode specialized, long-tail knowledge. WebGraphMix computes centrality scores efficiently at web scale, requiring no model training, labeled data, or downstream supervision. We integrate WebGraphMix into the DataComp-LM pipeline and train models at 400M and 1B parameter scales with 8B and 28B tokens respectively, evaluating on 23 tasks ranging from factual knowledge to symbolic reasoning. Our experiments show that central and peripheral web regions encode complementary capabilities. Mixture combining both at a ratio of 1:1 achieves 41.4% on average, compared to 39.8% for uniform sampling. Combining structural scores with document-level quality classifier scores further improves performance to 43.8%. These findings demonstrate that web graph topology is a meaningful axis for pretraining data curation, capturing information that is largely orthogonal to existing content-based approaches.

Large language models in regulated financial workflows are governed by natural-language policies that the same model interprets, creating a principal--agent failure: outputs can appear compliant without being compliant. Existing evaluation measures task accuracy but not whether governance constrains behaviour at the decision rationale level -- where regulated decisions must be auditable. We introduce five governance metrics that quantify policy compliance at the rationale level and apply them in a synthetic banking domain to compare text-only governance against mechanical enforcement: four primitives operating outside the model's interpretive loop. Under text-only governance, 27% of deferrals carry no decision-relevant information. Mechanical enforcement reduces this rate by 73%, more than doubles deferral information content, and raises task accuracy from MCC~0.43 to 0.88. The improvement is driven by architectural separation: LLM-generated rationales under mechanical enforcement show comparable CDL to text-only governance -- the gain comes from removing clear-cut decisions from the model's control. A causal ablation confirms that each primitive is individually necessary. Our central finding is a governance-task decoupling: under structural stress, text-only governance degrades on both dimensions simultaneously, whereas mechanical enforcement preserves governance quality even as task performance drops. This implies that governance and task evaluation are distinct axes: accuracy is not a sufficient proxy for governance in regulated AI systems.

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

Pre-training methods with contrastive learning objectives have shown remarkable success in dialog understanding tasks. However, current contrastive learning solely considers the self-augmented dialog samples as positive samples and treats all other dialog samples as negative ones, which enforces dissimilar representations even for dialogs that are semantically related. In this paper, we propose SPACE-2, a tree-structured pre-trained conversation model, which learns dialog representations from limited labeled dialogs and large-scale unlabeled dialog corpora via semi-supervised contrastive pre-training. Concretely, we first define a general semantic tree structure (STS) to unify the inconsistent annotation schema across different dialog datasets, so that the rich structural information stored in all labeled data can be exploited. Then we propose a novel multi-view score function to increase the relevance of all possible dialogs that share similar STSs and only push away other completely different dialogs during supervised contrastive pre-training. To fully exploit unlabeled dialogs, a basic self-supervised contrastive loss is also added to refine the learned representations. Experiments show that our method can achieve new state-of-the-art results on the DialoGLUE benchmark consisting of seven datasets and four popular dialog understanding tasks. For reproducibility, we release the code and data at https://github.com/AlibabaResearch/DAMO-ConvAI/tree/main/space-2.

How can a robot efficiently extract a desired object from a shelf when it is fully occluded by other objects? Prior works propose geometric approaches for this problem but do not consider object semantics. Shelves in pharmacies, restaurant kitchens, and grocery stores are often organized such that semantically similar objects are placed close to one another. Can large language models (LLMs) serve as semantic knowledge sources to accelerate robotic mechanical search in semantically arranged environments? With Semantic Spatial Search on Shelves (S^4), we use LLMs to generate affinity matrices, where entries correspond to semantic likelihood of physical proximity between objects. We derive semantic spatial distributions by synthesizing semantics with learned geometric constraints. S^4 incorporates Optical Character Recognition (OCR) and semantic refinement with predictions from ViLD, an open-vocabulary object detection model. Simulation experiments suggest that semantic spatial search reduces the search time relative to pure spatial search by an average of 24% across three domains: pharmacy, kitchen, and office shelves. A manually collected dataset of 100 semantic scenes suggests that OCR and semantic refinement improve object detection accuracy by 35%. Lastly, physical experiments in a pharmacy shelf suggest 47.1% improvement over pure spatial search. Supplementary material can be found at https://sites.google.com/view/s4-rss/home.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

Deployed LLM agents increasingly keep their long-term memory as a filesystem: a directory tree of markdown files that the agent itself reads, writes, and reorganizes through generic file tools. Yet research has largely passed over this medium: prior systems design bespoke memory representations and study retrieval over them, leaving the default's two working assumptions untested: that an agent can keep a growing store organized as memories accumulate, conflict, and go stale, and that this organization pays. We present the first systematic exploration of filesystem-based memory for LLM agents. We formalize the setting as three roles around one memory filesystem: a management agent integrates and organizes incoming content, a search agent answers queries with cited sources, and an execution agent supplies task trajectories that are distilled into skills, unifying declarative memory and skills in a single store. Across long-conversation benchmarks and embodied tasks, we vary memory shape (agent-organized hierarchy, verbatim dump, chunk retrieval), stream scale, tool harness (sandboxed shell, memory-tool-style functions, varied search tooling), and the strengths of the management and search agents, tracking answer quality, cost, and store health as memory grows. What organization reliably buys is search economy: organized stores roughly halve retrieval cost where material is large. Today's agents, however, fall short of the default's promise: in our growth study, organization erodes for all but the strongest management agent, and no agent we measure converts organization itself into better answers. And the model is not the only lever over a store's shape: changing the tool set alone reshapes the store as strongly as swapping the model. The study turns the filesystem default from an assumption into a design space for agent memory.

The growing interest in artificial intelligence has created workloads that require both sequential and random access. At the same time, NVMe-backed storage solutions have emerged, providing caching capability for large columnar datasets in cloud storage. Current columnar storage libraries fall short of effectively utilizing an NVMe device's capabilities, especially when it comes to random access. Historically, this has been assumed an implicit weakness in columnar storage formats, but this has not been sufficiently explored. In this paper, we examine the effectiveness of popular columnar formats such as Apache Arrow, Apache Parquet, and Lance in both random access and full scan tasks against NVMe storage. We argue that effective encoding of a column's structure, such as the repetition and validity information, is the key to unlocking the disk's performance. We show that Parquet, when configured correctly, can achieve over 60x better random access performance than default settings. We also show that this high random access performance requires making minor trade-offs in scan performance and RAM utilization. We then describe the Lance structural encoding scheme, which alternates between two different structural encodings based on data width, and achieves better random access performance without making trade-offs in scan performance or RAM utilization.