arXiv subjects

Chi Han

Publications and source records attributed to Chi Han.

At least 19 recordsLinked to original sources

arXiv2026

Apodex Discovery: Reality Benchmarks and Environments for Evaluating and Building Discoverative Artificial Intelligence

Apollo did not reach the Moon merely because its engineers could solve difficult equations. It succeeded by turning a distant ambition into a mission architecture of explicit objectives, simulation, verification, and repeated correction. AI now faces a similar transition: frontier models can solve difficult tasks once the problem, tools, and success criteria are specified, yet consequential real-world challenges rarely arrive in an executable or verifiable form. We introduce Apodex Discovery, a framework for building and evaluating discoverative AI through the heavy-duty solver, a system comprising a foundation model, harness, tools, and control policies that pursues extended, stateful, verifiable investigations. It has three core components. First, a problem-scouting process surveyed 561 industries across 16 sectors, assembled 423 high-value real-world problems, and selected 20 for the initial release. Second, a common environment-task-episode abstraction provides data, tools, constraints, feedback, trajectory recording, and verification of intermediate artifacts and final submissions. Third, HDS6 evaluates Tools, Repair, Alternatives, Coherence, Evidence, and Scope independently of final-task success. In AAV capsid design, Apodex surpassed the published state of the art by 7% across viability, tropism, structure prediction, and generative design. In drug repurposing and reformulation, a task-specific biomedical environment improved the mean normalized prediction score of GPT-5.5 and GPT-5.6-sol by 2.5 and 7.6 points over the same closed-book backbone. Controlled ablations show that the fixed TRACES episode interface enables attribution of performance differences to specific solver components. Apodex Discovery moves AI evaluation beyond predefined benchmarks toward verifiable investigations aimed at genuine discovery.

cs.AI↗

arXiv2026

Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference

Modern Protein Language Models (PLMs) apply transformer-based model architectures from natural language processing to biological sequences, predicting a variety of protein functions and properties. However, protein language has key differences from natural language, such as a rich functional space despite a vocabulary of only 20 amino acids. These differences motivate research into how transformer-based architectures operate differently in the protein domain and how we can better leverage PLMs to solve protein-related tasks. In this work, we begin by directly comparing how the distribution of information stored across layers of attention heads differs between the protein and natural language domain. Furthermore, we adapt a simple early-exit technique-originally used in the natural language domain to improve efficiency at the cost of performance-to achieve both increased accuracy and substantial efficiency gains in protein non-structural property prediction by allowing the model to automatically select protein representations from the intermediate layers of the PLMs for the specific task and protein at hand. We achieve performance gains ranging from 0.4 to 7.01 percentage points while simultaneously improving efficiency by over 10 percent across models and non-structural prediction tasks. Our work opens up an area of research directly comparing how language models change behavior when moved into the protein domain and advances language modeling in biological domains.

cs.LG↗

arXiv2026

Neural Synchrony Between Socially Interacting Language Models

Neuroscience has uncovered a fundamental mechanism of our social nature: human brain activity becomes synchronized with others in many social contexts involving interaction. Traditionally, social minds have been regarded as an exclusive property of living beings. Although large language models (LLMs) are widely accepted as powerful approximations of human behavior, with multi-LLM system being extensively explored to enhance their capabilities, it remains controversial whether they can be meaningfully compared to human social minds. In this work, we explore neural synchrony between socially interacting LLMs as an empirical evidence for this debate. Specifically, we introduce neural synchrony during social simulations as a novel proxy for analyzing the sociality of LLMs at the representational level. Through carefully designed experiments, we demonstrate that it reliably reflects both social engagement and temporal alignment in their interactions. Our findings indicate that neural synchrony between LLMs is strongly correlated with their social performance, highlighting an important link between neural synchrony and the social behaviors of LLMs. Our work offers a new perspective to examine the "social minds" of LLMs, highlighting surprising parallels in the internal dynamics that underlie human and LLM social interaction.

cs.CL↗

arXiv2025

Transformers as Multi-task Learners: Decoupling Features in Hidden Markov Models

Transformer based models have shown remarkable capabilities in sequence learning across a wide range of tasks, often performing well on specific task by leveraging input-output examples. Despite their empirical success, a comprehensive theoretical understanding of this phenomenon remains limited. In this work, we investigate the layerwise behavior of Transformers to uncover the mechanisms underlying their multi-task generalization ability. Taking explorations on a typical sequence model, i.e, Hidden Markov Models, which are fundamental to many language tasks, we observe that: first, lower layers of Transformers focus on extracting feature representations, primarily influenced by neighboring tokens; second, on the upper layers, features become decoupled, exhibiting a high degree of time disentanglement. Building on these empirical insights, we provide theoretical analysis for the expressiveness power of Transformers. Our explicit constructions align closely with empirical observations, providing theoretical support for the Transformer's effectiveness and efficiency on sequence learning across diverse tasks.

cs.LG↗

arXiv2025

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↗

arXiv2025

Can Language Models Follow Multiple Turns of Entangled Instructions?

Despite significant achievements in improving the instruction-following capabilities of large language models (LLMs), the ability to process multiple potentially entangled or conflicting instructions remains a considerable challenge. Real-world scenarios often require consistency across multiple instructions over time, such as secret privacy, personal preferences, and prioritization, which demand sophisticated abilities to integrate multiple turns and carefully balance competing objectives when instructions intersect or conflict. This work presents a systematic investigation of LLMs' capabilities in handling multiple turns of instructions, covering three levels of difficulty: (1) retrieving information from instructions, (2) tracking and reasoning across turns, and (3) resolving conflicts among instructions. We construct MultiTurnInstruct~with $\sim$1.1K high-quality multi-turn conversations through the human-in-the-loop approach and result in nine capability categories, including statics and dynamics, reasoning, and multitasking. Our finding reveals an intriguing trade-off between different capabilities. While GPT models demonstrate superior memorization, they show reduced effectiveness in privacy-protection tasks requiring selective information withholding. Larger models exhibit stronger reasoning capabilities but still struggle with resolving conflicting instructions. Importantly, these performance gaps cannot be attributed solely to information loss, as models demonstrate strong BLEU scores on memorization tasks. Still, their attention mechanisms fail to integrate multiple related instructions effectively. These findings highlight critical areas for improvement in complex real-world tasks involving multi-turn instructions. Data and codes are released at https://github.com/Glaciohound/Multi-Turn-Instruct.

cs.CL↗

arXiv2025

Computation Mechanism Behind LLM Position Generalization

Most written natural languages are composed of sequences of words and sentences. Similar to humans, large language models (LLMs) exhibit flexibility in handling textual positions - a phenomenon we term position generalization. They can understand texts with position perturbations and generalize to longer texts than those encountered during training with the latest techniques. These phenomena suggest that LLMs handle positions tolerantly, but how LLMs computationally process positional relevance remains largely unexplored. This work connects the linguistic phenomenon with LLMs' computational mechanisms. We show how LLMs enforce certain computational mechanisms for the aforementioned tolerance in position perturbations. Despite the complex design of the self-attention mechanism, this work reveals that LLMs learn a counterintuitive disentanglement of attention logits. Their values show a 0.959 linear correlation with an approximation of the arithmetic sum of positional relevance and semantic importance. Furthermore, we identify a prevalent pattern in intermediate features, which we prove theoretically enables this effect. The pattern, which is different from how randomly initialized parameters would behave, suggests that it is a learned behavior rather than a natural result of the model architecture. Based on these findings, we provide computational explanations and criteria for LLMs' position flexibilities. This work takes a pioneering step in linking position generalization with modern LLMs' internal mechanisms.

cs.CL↗

arXiv2025

The Law of Knowledge Overshadowing: Towards Understanding, Predicting, and Preventing LLM Hallucination

Hallucination is a persistent challenge in large language models (LLMs), where even with rigorous quality control, models often generate distorted facts. This paradox, in which error generation continues despite high-quality training data, calls for a deeper understanding of the underlying LLM mechanisms. To address it, we propose a novel concept: knowledge overshadowing, where model's dominant knowledge can obscure less prominent knowledge during text generation, causing the model to fabricate inaccurate details. Building on this idea, we introduce a novel framework to quantify factual hallucinations by modeling knowledge overshadowing. Central to our approach is the log-linear law, which predicts that the rate of factual hallucination increases linearly with the logarithmic scale of (1) Knowledge Popularity, (2) Knowledge Length, and (3) Model Size. The law provides a means to preemptively quantify hallucinations, offering foresight into their occurrence even before model training or inference. Built on overshadowing effect, we propose a new decoding strategy CoDa, to mitigate hallucinations, which notably enhance model factuality on Overshadow (27.9%), MemoTrap (13.1%) and NQ-Swap (18.3%). Our findings not only deepen understandings of the underlying mechanisms behind hallucinations but also provide actionable insights for developing more predictable and controllable language models.

cs.CL↗

arXiv2025

SyncMind: Measuring Agent Out-of-Sync Recovery in Collaborative Software Engineering

Software engineering (SE) is increasingly collaborative, with developers working together on shared complex codebases. Effective collaboration in shared environments requires participants -- whether humans or AI agents -- to stay on the same page as their environment evolves. When a collaborator's understanding diverges from the current state -- what we term the out-of-sync challenge -- the collaborator's actions may fail, leading to integration issues. In this work, we introduce SyncMind, a framework that systematically defines the out-of-sync problem faced by large language model (LLM) agents in collaborative software engineering (CSE). Based on SyncMind, we create SyncBench, a benchmark featuring 24,332 instances of agent out-of-sync scenarios in real-world CSE derived from 21 popular GitHub repositories with executable verification tests. Experiments on SyncBench uncover critical insights into existing LLM agents' capabilities and limitations. Besides substantial performance gaps among agents (from Llama-3.1 agent <= 3.33% to Claude-3.5-Sonnet >= 28.18%), their consistently low collaboration willingness (<= 4.86%) suggests fundamental limitations of existing LLM in CSE. However, when collaboration occurs, it positively correlates with out-of-sync recovery success. Minimal performance differences in agents' resource-aware out-of-sync recoveries further reveal their significant lack of resource awareness and adaptability, shedding light on future resource-efficient collaborative systems. Code and data are openly available on our project website: https://xhguo7.github.io/SyncMind/.

cs.SE↗

arXiv2024

LDC: Learning to Generate Research Idea with Dynamic Control

Recent advancements in large language models (LLMs) have demonstrated their potential in automating the scientific research ideation. Existing approaches primarily focus on prompting techniques, often producing ideas misaligned with expert standards - novelty, feasibility, and effectiveness, which are widely recognized by the research community as the three key subdimensions of high-quality ideas. Also, balancing these dimensions remains challenging due to their inherent trade-offs. To address these limitations, we propose the first framework that employs a two-stage approach combining Supervised Fine-Tuning (SFT) and controllable Reinforcement Learning (RL) for the task. In the SFT stage, the model learns foundational patterns from pairs of research papers and their corresponding follow-up ideas. In the RL stage, multi-dimensional reward models guided by fine-grained feedback evaluate and optimize the model across key dimensions. During inference, dimensional controllers coordinated by a sentence-level decoder enable dynamic context-aware steering of the idea generation process. Our framework provides a balanced approach to research idea generation, achieving high-quality outcomes in the experiment by dynamically navigating the trade-offs among novelty, feasibility, and effectiveness.

cs.CL↗

arXiv2024

Schema-Guided Culture-Aware Complex Event Simulation with Multi-Agent Role-Play

Complex news events, such as natural disasters and socio-political conflicts, require swift responses from the government and society. Relying on historical events to project the future is insufficient as such events are sparse and do not cover all possible conditions and nuanced situations. Simulation of these complex events can help better prepare and reduce the negative impact. We develop a controllable complex news event simulator guided by both the event schema representing domain knowledge about the scenario and user-provided assumptions representing case-specific conditions. As event dynamics depend on the fine-grained social and cultural context, we further introduce a geo-diverse commonsense and cultural norm-aware knowledge enhancement component. To enhance the coherence of the simulation, apart from the global timeline of events, we take an agent-based approach to simulate the individual character states, plans, and actions. By incorporating the schema and cultural norms, our generated simulations achieve much higher coherence and appropriateness and are received favorably by participants from a humanitarian assistance organization.

cs.AI↗

arXiv2024

MentalArena: Self-play Training of Language Models for Diagnosis and Treatment of Mental Health Disorders

Mental health disorders are one of the most serious diseases in the world. Most people with such a disease lack access to adequate care, which highlights the importance of training models for the diagnosis and treatment of mental health disorders. However, in the mental health domain, privacy concerns limit the accessibility of personalized treatment data, making it challenging to build powerful models. In this paper, we introduce MentalArena, a self-play framework to train language models by generating domain-specific personalized data, where we obtain a better model capable of making a personalized diagnosis and treatment (as a therapist) and providing information (as a patient). To accurately model human-like mental health patients, we devise Symptom Encoder, which simulates a real patient from both cognition and behavior perspectives. To address intent bias during patient-therapist interactions, we propose Symptom Decoder to compare diagnosed symptoms with encoded symptoms, and dynamically manage the dialogue between patient and therapist according to the identified deviations. We evaluated MentalArena against 6 benchmarks, including biomedicalQA and mental health tasks, compared to 6 advanced models. Our models, fine-tuned on both GPT-3.5 and Llama-3-8b, significantly outperform their counterparts, including GPT-4o. We hope that our work can inspire future research on personalized care. Code is available in https://github.com/Scarelette/MentalArena/tree/main

cs.CL↗

arXiv2024

Towards LifeSpan Cognitive Systems

Building a human-like system that continuously interacts with complex environments -- whether simulated digital worlds or human society -- presents several key challenges. Central to this is enabling continuous, high-frequency interactions, where the interactions are termed experiences. We refer to this envisioned system as the LifeSpan Cognitive System (LSCS). A critical feature of LSCS is its ability to engage in incremental and rapid updates while retaining and accurately recalling past experiences. In this paper we focus on the domain of Large Language Models (LLMs), where we identify two major challenges: (1) Abstraction and Experience Merging, and (2) Long-term Retention with Accurate Recall. These properties are essential for storing new experiences, organizing past experiences, and responding to the environment in ways that leverage relevant historical data. Unlike language models with continual learning, which typically rely on large corpora for fine-tuning and focus on improving performance within specific domains or tasks, LSCS must rapidly and incrementally update with new information from its environment at a high frequency. Existing technologies with the potential of solving the above two major challenges can be classified into four classes based on a conceptual metric called Storage Complexity, which measures the relative space required to store past experiences. Each of these four classes of technologies has its own strengths and limitations while we argue none of them alone can achieve LSCS alone. To this end, we propose a potential instantiation for LSCS that can integrate all four classes of technologies. The new instantiation, serving as a conjecture, operates through two core processes: Absorbing Experiences and Generating Responses.

cs.CL↗

arXiv2024

Prospects for using drones to test formation-flying CubeSat concepts, and other astronomical applications

Drones provide a versatile platform for remote sensing and atmospheric studies. However, strict payload mass limits and intense vibrations have proven obstacles to adoption for astronomy. We present a concept for system-level testing of a long-baseline CubeSat space interferometer using drones, taking advantage of their cm-level xyz station-keeping, 6-dof freedom of movement, large operational environment, access to guide stars for end-to-end testing of optical train and control algorithms, and comparable mass and power requirements. We have purchased two different drone platforms (Aurelia X6 Pro, Freefly Alta X) and present characterization studies of vibrations, flight stability, gps positioning precision, and more. We also describe our progress in sub-system development, including inter-drone laser metrology, realtime gimbal control, and LED beacon tracking. Lastly, we explore whether custom-built drone-borne telescopes could be used for interferometry of bright objects over km-level baselines using vibration-isolation platforms and a small fast delay for fringe-tracking.

astro-ph.IM↗

arXiv2024

Eliminating Position Bias of Language Models: A Mechanistic Approach

Position bias has proven to be a prevalent issue of modern language models (LMs), where the models prioritize content based on its position within the given context. This bias often leads to unexpected model failures and hurts performance, robustness, and reliability across various applications. Our mechanistic analysis attributes the position bias to two components employed in nearly all state-of-the-art LMs: causal attention and relative positional encodings. Based on the analyses, we propose to eliminate position bias (e.g., different retrieved documents' orders in QA affect performance) with a training-free zero-shot approach. Our method changes the causal attention to bidirectional attention between documents and utilizes model attention values to decide the relative orders of documents instead of using the order provided in input prompts, therefore enabling Position-INvariant inferencE (PINE) at the document level. By eliminating position bias, models achieve better performance and reliability in downstream tasks, including LM-as-a-judge, retrieval-augmented QA, molecule generation, and math reasoning. Notably, PINE is especially useful when adapting LMs for evaluating reasoning pairs: it consistently provides 8 to 10 percentage points performance gains, making Llama-3-70B-Instruct perform even better than GPT-4-0125-preview and GPT-4o-2024-08-06 on the RewardBench reasoning set.

cs.CL↗

arXiv2024

LISA: Layerwise Importance Sampling for Memory-Efficient Large Language Model Fine-Tuning

The machine learning community has witnessed impressive advancements since large language models (LLMs) first appeared. Yet, their massive memory consumption has become a significant roadblock to large-scale training. For instance, a 7B model typically requires at least 60 GB of GPU memory with full parameter training, which presents challenges for researchers without access to high-resource environments. Parameter Efficient Fine-Tuning techniques such as Low-Rank Adaptation (LoRA) have been proposed to alleviate this problem. However, in most large-scale fine-tuning settings, their performance does not reach the level of full parameter training because they confine the parameter search to a low-rank subspace. Attempting to complement this deficiency, we investigate the layerwise properties of LoRA on fine-tuning tasks and observe an unexpected but consistent skewness of weight norms across different layers. Utilizing this key observation, a surprisingly simple training strategy is discovered, which outperforms both LoRA and full parameter training in a wide range of settings with memory costs as low as LoRA. We name it Layerwise Importance Sampled AdamW (LISA), a promising alternative for LoRA, which applies the idea of importance sampling to different layers in LLMs and randomly freezes most middle layers during optimization. Experimental results show that with similar or less GPU memory consumption, LISA surpasses LoRA or even full parameter tuning in downstream fine-tuning tasks, where LISA consistently outperforms LoRA by over 10%-35% in terms of MT-Bench score while achieving on-par or better performance in MMLU, AGIEval and WinoGrande. On large models, specifically LLaMA-2-70B, LISA surpasses LoRA on MT-Bench, GSM8K, and PubMedQA, demonstrating its effectiveness across different domains.

cs.LG↗

arXiv2023

Subhalos in Galaxy Clusters: Coherent Accretion and Internal Orbits

Subhalo dynamics in galaxy cluster host halos govern the observed distribution and properties of cluster member galaxies. We use the IllustrisTNG simulation to investigate the accretion and orbits of subhalos found in cluster-size halos. We find that the median change in the major axis direction of cluster-size host halos is approximately $80$ degrees between $a\sim0.1$ and present-day. We identify coherent regions in the angular distribution of subhalo accretion, and $\sim68\%$ of accreted subhalos enter their host halo through $\sim38\%$ of the surface area at the virial radius. The majority of galaxy clusters in the sample have $\sim2$ such coherent regions. We further measure angular orbits of subhalos with respect to the host major axis and use a clustering algorithm to identify distinct orbit modes with varying oscillation timescales. The orbit modes correlate with subhalo accretion conditions. Subhalos in orbit modes with shorter oscillations tend to have lower peak masses and accretion directions somewhat more aligned with the major axis. One orbit mode, exhibiting the least oscillatory behavior, largely consists of subhalos that accrete near the plane perpendicular to the host halo major axis. Our findings are consistent with expectations from inflow from major filament structures and internal dynamical friction: most subhalos accrete through coherent regions, and more massive subhalos experience fewer orbits after accretion. Our work offers a unique quantification of subhalo dynamics that can be connected to how the intracluster medium strips and quenches cluster galaxies.

astro-ph.GA↗

arXiv2023

Large Language Models on Graphs: A Comprehensive Survey

Large language models (LLMs), such as GPT4 and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data is associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data is paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graphs (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-attributed graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we discuss the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

cs.CL↗