arXiv subjects

Ge Liu

Publications and source records attributed to Ge Liu.

At least 37 records · Page 2Linked to original sources

arXiv2026

RouteProfile: Graph-Based Profiling for Cold-Start LLM Routing

LLM routing is increasingly important for selecting suitable models under diverse user needs and deployment constraints, but its practical effectiveness depends on continual adaptation to emerging queries and newly released models. New-LLM integration is particularly challenging, as newly released models lack the query-response-reward interactions required for router training and cannot be profiled as directly as new queries via semantic embeddings. Existing profiles are limited: LLM-generated descriptions are often coarse, while interaction-based embeddings are costly to construct. To address this problem, we propose RouteProfile, a graph-based profiling framework that constructs LLM profiles from public signals in technical reports or model cards, including model family, model description, reported benchmark scores, and benchmark domains. RouteProfile organizes these heterogeneous signals into a graph and studies profile construction along four dimensions: organizational form, representation type, aggregation depth, and learning configuration. We evaluate RouteProfile in training-free cold-start routing and new-LLM integration settings. Experiments show that: (1) structured profiles outperform flat baselines in training-free cold-start routing; (2) model family metadata is more reliable than benchmark domain information; and (3) effective new-LLM integration requires profile-router co-design. Overall, our findings highlight the importance of profile design for enabling routing systems to adapt to the evolving model ecosystem.

cs.NI↗

arXiv2026

Position: The Hidden Costs and Measurement Gaps of Reinforcement Learning with Verifiable Rewards

Reinforcement learning with verifiable rewards (RLVR) is a practical, scalable way to improve large language models on math, code, and other structured tasks. However, we argue that many headline RLVR gains are not yet well validated because reports often conflate policy improvement with three confounds: (i) budget mismatch between RLVR and baseline evaluations, (ii) attempt inflation and calibration drift that convert abstentions into confident answers, and (iii) benchmark data contamination. Using budget-matched reproductions and partial-prompt contamination probes, we find that several widely cited gaps shrink substantially or disappear once budgets, prompts, and dataset versions are matched and contaminated sets are treated as memorization probes rather than evidence of reasoning. This does not mean that RLVR is ineffective, but it implies that current measurements often overstate capability gains and obscure reliability costs. We therefore propose a compact, tax-aware minimum standard for RLVR training and evaluation: budget-matched saturation curves with variance, calibration, and abstention tracking, a judge-robustness stress test when LLM judges are used, and an explicit contamination screen. With these controls, RLVR remains effective and deployable in verifiable domains, but reasoning gains should be treated as provisional without them.

cs.LG↗

arXiv2026

The Many Faces of On-Policy Distillation: Pitfalls, Mechanisms, and Fixes

On-policy distillation (OPD) and on-policy self-distillation (OPSD) have emerged as promising post-training methods for large language models, offering dense token-level supervision on trajectories sampled from the model's own policy. However, existing results on their effectiveness remain mixed: while OP(S)D has shown promise in system prompt and knowledge internalization, recent studies also report instability and degradation. In this work, we present a comprehensive empirical study of when OPD and OPSD work, when they fail, and why. We find that OPD on mathematical reasoning is highly sensitive to teacher choice and loss formulation, whereas OPSD fails in our tested settings due to test-time absence of instance-specific privileged information (PI). In contrast, OPSD is effective when PI represents a shared latent rule, such as a system prompt or alignment preference. We identify three failure mechanisms: (1) distribution mismatch between teacher and student caused by conditioning on student-generated prefixes, (2) optimization instability from biased TopK reverse-KL gradients, and (3) an OPSD-specific limitation where the student learns a PI-free policy that aggregates PI-conditioned teachers, which is insufficient when PI is instance-specific. We further show that stop-gradient TopK objectives, RLVR-adapted teachers, and SFT-stabilized students mitigate these failures.

cs.AI↗

arXiv2026

MemReward: Graph-Based Experience Memory for LLM Reward Prediction with Limited Labels

Reinforcement learning has emerged as a powerful paradigm for improving large language model (LLM) reasoning, where rollouts are sampled from the policy and reward signals computed on those rollouts are used to update the policy. However, in data-scarce scenarios, obtaining ground-truth labels to verify rollouts at scale often requires expensive human annotation or labor-intensive expert verification. For instance, evaluating mathematical proofs demands expert review, and open-ended question answering lacks definitive ground truth. When ground-truth labels are scarce, the effectiveness of reinforcement learning fine-tuning is constrained. Inspired by the success of semi-supervised learning in propagating labels from labeled to unlabeled samples, we propose MemReward, a graph-based experience memory framework that integrates reward propagation directly into online policy optimization. MemReward stores rollouts (thinking processes and final answers) from an initial LLM policy as nodes in a heterogeneous graph connected by similarity and structural edges, over which a GNN propagates rewards from labeled to unlabeled rollouts. To train such a framework, we first warm up the GNN on labeled rollouts to predict rewards via heterogeneous aggregation over query, thinking, and answer nodes. During online RL fine-tuning, unlabeled rollouts are attached to the graph by query similarity, and the GNN predicts their rewards, yielding a hybrid reward acquisition strategy that combines ground-truth and GNN-predicted rewards. Experiments on Qwen2.5-1.5B and 3B in mathematics, question answering, and code generation demonstrate that MemReward, with ground-truth rewards on only 20% of rollouts, achieves 96.6% of Oracle performance on 1.5B and 97.3% on 3B, and closely approaches Oracle on out-of-domain tasks.

cs.LG↗

arXiv2026

Auto-Dreamer: Learning Offline Memory Consolidation for Language Agents

Language agents increasingly operate over streams of related tasks, yet existing memory systems struggle to convert accumulated experience into reusable knowledge. Retrieval-augmented and structured memory methods record per-session observations effectively, but often couple acquisition and consolidation into a single online process, leaving the agent without a global view across sessions to discover recurring patterns, abstract shared procedures, or prune redundant entries. Inspired by complementary learning systems theory, we propose Auto-Dreamer, a learned offline consolidator for language-agent memory. Auto-Dreamer decouples fast per-session memory acquisition from slow cross-session consolidation. Given a selected working region of a typed memory bank, the consolidator treats the region as read-only evidence, performs bounded tool-use to inspect entries and provenance-linked source trajectories, and synthesizes a fresh compact replacement set that abstracts across sessions and supersedes the original region. We train Auto-Dreamer via GRPO, using end-to-end agent performance as the reward signal to learn how to consolidate memories acquired through fast online experience. Trained on ScienceWorld trajectories alone, Auto-Dreamer outperforms fixed, RL-trained, and prompted memory baselines on ScienceWorld by 7 points while using an active memory bank 12$\times$ smaller than the strongest baseline, and continues to lead on held-out ALFWorld and WebArena without retraining -- using 6$\times$ less memory than the strongest baseline on ALFWorld.

cs.CL↗

arXiv2026

Protein Autoregressive Modeling via Multiscale Structure Generation

We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and refining structural details over scales. To achieve this, PAR consists of three key components: (i) multi-scale downsampling operations that represent protein structures across multiple scales during training; (ii) an autoregressive transformer that encodes multi-scale information and produces conditional embeddings to guide structure generation; (iii) a flow-based backbone decoder that generates backbone atoms conditioned on these embeddings. Moreover, autoregressive models suffer from exposure bias, caused by the training and the generation procedure mismatch, and substantially degrades structure generation quality. We effectively alleviate this issue by adopting noisy context learning and scheduled sampling, enabling robust backbone generation. Notably, PAR exhibits strong zero-shot generalization, supporting flexible human-prompted conditional generation and motif scaffolding without requiring fine-tuning. On the unconditional generation benchmark, PAR effectively learns protein distributions and produces backbones of high design quality, and exhibits favorable scaling behavior. Together, these properties establish PAR as a promising framework for protein structure generation.

cs.LG↗

arXiv2026

Retrieval is Cheap, Show Me the Code: Executable Multi-Hop Reasoning for Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) has become a standard approach for knowledge-intensive question answering, but existing systems remain brittle on multi-hop questions, where solving the task requires chaining multiple retrieval and reasoning steps. Key challenges are that current methods represent reasoning through free-form natural language, where intermediate states are implicit, retrieval queries can drift from intended entities, and errors are detected by the same model that produces them making self-reflection an unreliable, ungrounded signal. We observe that multi-hop question answering is a typical form of step-by-step computation, and that this structured process aligns closely with how code-specialized language models are trained to operate. Motivated by this, we introduce \pyrag, a framework that reformulates multi-hop RAG as program synthesis and execution. Instead of free-form reasoning trajectories, \pyrag represents the reasoning process as an executable Python program over retrieval and QA tools, exposing intermediate states as variables, producing deterministic feedback through execution, and yielding an inspectable trace of the entire reasoning process. This formulation further enables compiler-grounded self-repair and execution-driven adaptive retrieval without any additional training. Experiments on five QA benchmarks (PopQA, HotpotQA, 2WikiMultihopQA, MuSiQue, and Bamboogle) show that \pyrag consistently outperforms strong baselines under both training-free and RL-trained settings, with especially large gains on compositional multi-hop datasets. Our code, data and models are publicly available at https://github.com/GasolSun36/PyRAG.

cs.AI↗

arXiv2026

A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion

We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino acid-level sequence design, our approach is fully atomic within a unified multimodal diffusion framework, in which residue identities are inferred solely from atom-level predictions. Built upon the powerful all-atom architecture, A-CODE achieves superior designability for unconditional protein generation, outperforming all existing one-stage and two-stage design models. For binder design, A-CODE rivals and even outperforms existing state-of-the-art two-stage design models and, compared with the existing one-stage co-design model, achieves a drastic tenfold improvement in success rate on hard tasks. The inherent flexibility of our atomic formulation enables, for the first time, seamless adaptation to non-canonical amino acid (ncAA) modeling. Our fully atomic framework establishes a new, versatile foundation for all-atom generative modeling that can be naturally extended to complex biomolecular systems.

q-bio.QM↗

arXiv2026

UniRec: Unified Multimodal Encoding for LLM-Based Recommendations

Large language models have recently shown promise for multimodal recommendation, particularly with text and image inputs. Yet real-world recommendation signals extend far beyond these modalities. To reflect this, we formalize recommendation features into four modalities: text, images, categorical features, and numerical attributes, and highlight the unique challenges this heterogeneity poses for LLMs in understanding multimodal information. In particular, these challenges arise not only across modalities but also within them, as attributes such as price, rating, and time may all be numeric yet carry distinct semantic meanings. Beyond this intra-modality ambiguity, another major challenge is the nested structure of recommendation signals, where user histories are sequences of items, each associated with multiple attributes. To address these challenges, we propose UniRec, a unified multimodal encoder for LLM-based recommendation. UniRec first employs modality-specific encoders to produce consistent embeddings across heterogeneous signals. It then adopts a triplet representation, comprising attribute name, type, and value, to separate schema from raw inputs and preserve semantic distinctions. Finally, a hierarchical Q-Former models the nested structure of user interactions while maintaining their layered organization. Across multiple real-world benchmarks, UniRec outperforms state-of-the-art multimodal and LLM-based recommenders by up to 15%, and extensive ablation studies further validate the contributions of each component.

cs.IR↗

arXiv2026

FARM: Enhancing Molecular Representations with Functional Group Awareness

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key idea behind FARM is the incorporation of functional group (FG) annotations at the atomic level, enabling both FG-enhanced SMILES and FG graphs. In this representation, SMILES strings are enriched with functional group information that identifies the group membership of each atom, while the FG graph captures molecular structure by representing how functional groups are connected. This tokenization injects chemical knowledge into SMILES and expands the effective molecular vocabulary, making the representation more suitable for Transformer-based models and more aligned with natural language structure. FARM learns molecular representations from two complementary perspectives to jointly encode functional and structural information. Masked language modeling on FG-enhanced SMILES captures atom-level features enriched with functional context, while graph neural networks model higher-level molecular topology through functional group connectivity. Contrastive learning is then used to align these two views into a unified embedding space, ensuring that both atom-level detail and functional group structure are jointly represented. We evaluate FARM on the MoleculeNet benchmark and achieve state-of-the-art performance on 8 out of 13 tasks. We further validate its generalization ability on a photostability dataset for quantum mechanical properties. These results demonstrate that FARM improves molecular representation learning, supports strong transfer learning across drug discovery and materials science, and enables broad applications in pharmaceutical research and functional material design.

cs.LG↗

arXiv2026

h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking, occur only under specific local conditions. Most existing approaches represent molecules as atom-level graphs; however, atom-level representations can hardly express higher-order chemical context (e.g., stereochemistry, lone pairs, conjugation). Fragment-based methods (e.g., principal subgraph, predefined functional groups) fail to preserve essential information such as chirality, aromaticity, and ionic states. This work addresses these limitations from two aspects. (i) OverlapBPE tokenization. We propose a novel data-driven molecule tokenization method. Unlike existing approaches, our method allows overlapping fragments, reflecting the inherently fuzzy boundaries of small-molecule substructures and, together with enriched chemical information at the token level, thereby preserving a more complete chemical context. (ii) h-MINT model. OverlapBPE induces many-to-many atom-fragment mappings, which necessitate a new hierarchical architecture. We therefore develop a hierarchical molecular interaction network capable of jointly modeling interactions at both atom and fragment levels. By supporting fragment overlaps, the model naturally accommodates the many-to-many atom-fragment mappings introduced by the OverlapBPE scheme. Extensive evaluation against state-of-the-art methods shows our method improves binding affinity prediction by 2-4% Pearson/Spearman correlation on PDBBind and LBA, enhances virtual screening by 1-3% in key metrics on DUD-E and LIT-PCBA, and achieves the best overall HTS performance on PubChem assays. Further analysis demonstrates that our method effectively captures interactive information while maintaining good generalization.

cs.LG↗

arXiv2026

LangFlow: Continuous Diffusion Rivals Discrete in Language Modeling

Continuous diffusion has been the foundation of high-fidelity, controllable, and few-step generation of many data modalities such as images. However, in language modeling, prior continuous diffusion language models (DLMs) lag behind discrete counterparts due to the sparse data space and the underexplored design space. In this work, we close this gap with LangFlow, the first continuous DLM to rival discrete diffusion, by connecting embedding-space DLMs to Flow Matching via Bregman divergence, alongside three key innovations: (1) we derive a novel ODE-based NLL bound for principled evaluation of continuous flow-based language models; (2) we propose an information-uniform principle for setting the noise schedule, which motivates a learnable noise scheduler based on a Gumbel distribution; and (3) we revise prior training protocols by incorporating self-conditioning, as we find it improves both likelihood and sample quality of embedding-space DLMs with effects substantially different from discrete diffusion. Putting everything together, LangFlow rivals top discrete DLMs on both the perplexity (PPL) and the generative perplexity (Gen. PPL), reaching a PPL of 30.0 on LM1B and 24.6 on OpenWebText. It even exceeds autoregressive baselines in zero-shot transfer on 4 out of 7 benchmarks. LangFlow provides the first clear evidence that continuous diffusion is a promising paradigm for language modeling. Homepage: https://github.com/nealchen2003/LangFlow

cs.CL↗

arXiv2026

Thought-Retriever: Don't Just Retrieve Raw Data, Retrieve Thoughts for Memory-Augmented Agentic Systems

Large language models (LLMs) have transformed AI research thanks to their powerful internal capabilities and knowledge. However, existing LLMs still fail to effectively incorporate the massive external knowledge when interacting with the world. Although retrieval-augmented LLMs are proposed to mitigate the issue, they are still fundamentally constrained by the context length of LLMs, as they can only retrieve top-K raw data chunks from the external knowledge base which often consists of millions of data chunks. Here we propose Thought-Retriever, a novel model-agnostic algorithm that helps LLMs generate output conditioned on arbitrarily long external data, without being constrained by the context length or number of retrieved data chunks. Our key insight is to let an LLM fully leverage its intermediate responses generated when solving past user queries (thoughts), filtering meaningless and redundant thoughts, organizing them in thought memory, and retrieving the relevant thoughts when addressing new queries. This effectively equips LLM-based agents with a self-evolving long-term memory that grows more capable through continuous interaction. Besides algorithmic innovation, we further meticulously prepare a novel benchmark, AcademicEval, which requires an LLM to faithfully leverage ultra-long context to answer queries based on real-world academic papers. Extensive experiments on AcademicEval and two other public datasets validate that Thought-Retriever remarkably outperforms state-of-the-art baselines, achieving an average increase of at least 7.6% in F1 score and 16% in win rate across various tasks. More importantly, we further demonstrate two exciting findings: (1) Thought-Retriever can indeed help LLM self-evolve after solving more user queries; (2) Thought-Retriever learns to leverage deeper thoughts to answer more abstract user queries.

cs.CL↗

arXiv2026

Batched Contextual Reinforcement: A Task-Scaling Law for Efficient Reasoning

Large Language Models employing Chain-of-Thought reasoning achieve strong performance but suffer from excessive token consumption that inflates inference costs. Existing efficiency methods such as explicit length penalties, difficulty estimators, or multi-stage curricula either degrade reasoning quality or require complex training pipelines. We introduce Batched Contextual Reinforcement, a minimalist, single-stage training paradigm that unlocks efficient reasoning through a simple structural modification: training the model to solve N problems simultaneously within a shared context window, rewarded purely by per-instance accuracy. This formulation creates an implicit token budget that yields several key findings: (1) We identify a novel task-scaling law: as the number of concurrent problems N increases during inference, per-problem token usage decreases monotonically while accuracy degrades far more gracefully than baselines, establishing N as a controllable throughput dimension. (2) BCR challenges the traditional accuracy-efficiency trade-off by demonstrating a "free lunch" phenomenon at standard single-problem inference. Across both 1.5B and 4B model families, BCR reduces token usage by 15.8% to 62.6% while consistently maintaining or improving accuracy across five major mathematical benchmarks. (3) Qualitative analyses reveal emergent self-regulated efficiency, where models autonomously eliminate redundant metacognitive loops without explicit length supervision. (4) Crucially, we empirically demonstrate that implicit budget constraints successfully circumvent the adversarial gradients and catastrophic optimization collapse inherent to explicit length penalties, offering a highly stable, constraint-based alternative for length control. These results prove BCR practical, showing simple structural incentives unlock latent high-density reasoning in LLMs.

cs.LG↗

arXiv2026

Flow Matching Meets Biology and Life Science: A Survey

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

cs.LG↗

arXiv2026

mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. Experiments on FDA-approved drugs showed that mCLM is capable of significantly improving chemical functions. mCLM, with only 3B parameters, also achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

cs.AI↗

arXiv2026

Optimal Design for Human Preference Elicitation

Learning of preference models from human feedback has been central to recent advances in artificial intelligence. Motivated by the cost of obtaining high-quality human annotations, we study efficient human preference elicitation for learning preference models. The key idea in our work is to generalize optimal designs, an approach to computing optimal information-gathering policies, to lists of items that represent potential questions with answers. The policy is a distribution over the lists and we elicit preferences from them proportionally to their probabilities. To show the generality of our ideas, we study both absolute and ranking feedback models on items in the list. We design efficient algorithms for both and analyze them. Finally, we demonstrate that our algorithms are practical by evaluating them on existing question-answering problems.

cs.LG↗

arXiv2026

Steer2Adapt: Dynamically Composing Steering Vectors Elicits Efficient Adaptation of LLMs

Activation steering has emerged as a promising approach for efficiently adapting large language models (LLMs) to downstream behaviors. However, most existing steering methods rely on a single static direction per task or concept, making them inflexible under task variation and inadequate for complex tasks that require multiple coordinated capabilities. To address this limitation, we propose STEER2ADAPT, a lightweight framework that adapts LLMs by composing steering vectors rather than learning new ones from scratch. In many domains (e.g., reasoning or safety), tasks share a small set of underlying concept dimensions. STEER2ADAPT captures these dimensions as a reusable, low-dimensional semantic prior subspace, and adapts to new tasks by dynamically discovering a linear combination of basis vectors from only a handful of examples. Experiments across 9 tasks and 3 models in both reasoning and safety domains demonstrate the effectiveness of STEER2ADAPT, achieving an average improvement of 8.2%. Extensive analyses further show that STEER2ADAPT is a data-efficient, stable, and transparent inference-time adaptation method for LLMs.

cs.AI↗