Chi Han

Bowen Jin, Gang Liu, Chi Han et al.

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.

Chi Han, Mingxuan Wang, Heng Ji et al.

Having numerous potential applications and great impact, end-to-end speech translation (ST) has long been treated as an independent task, failing to fully draw strength from the rapid advances of its sibling - text machine translation (MT). With text and audio inputs represented differently, the modality gap has rendered MT data and its end-to-end models incompatible with their ST counterparts. In observation of this obstacle, we propose to bridge this representation gap with Chimera. By projecting audio and text features to a common semantic representation, Chimera unifies MT and ST tasks and boosts the performance on ST benchmarks, MuST-C and Augmented Librispeech, to a new state-of-the-art. Specifically, Chimera obtains 27.1 BLEU on MuST-C EN-DE, improving the SOTA by a +1.9 BLEU margin. Further experimental analyses demonstrate that the shared semantic space indeed conveys common knowledge between these two tasks and thus paves a new way for augmenting training resources across modalities. Code, data, and resources are available at https://github.com/Glaciohound/Chimera-ST.

Brian Wang, Bin Feng, Xiaoman Pan et al.

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.

Carl Edwards, Chi Han, Gawon Lee et al.

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. mCLM, with only 3B parameters, 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").

Yifan Hao, Chenlu Ye, Chi Han et al.

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.