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Yijia Zheng

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4 published item(s)

preprint2026arXiv

LatentRAG: Latent Reasoning and Retrieval for Efficient Agentic RAG

Single-step retrieval-augmented generation (RAG) provides an efficient way to incorporate external information for simple question answering tasks but struggles with complex questions. Agentic RAG extends this paradigm by replacing single-step retrieval with a multi-step process, in which the large language model (LLM) acts as a search agent that generates intermediate thoughts and subqueries to iteratively interact with the retrieval system. This iterative process incurs substantial latency due to the autoregressive generation of lengthy thoughts and subqueries. To address this limitation, we propose LatentRAG, a novel framework that shifts both reasoning and retrieval from discrete language space to continuous latent space. Unlike existing explicit methods that generate natural language thoughts or subqueries token-by-token, LatentRAG produces latent tokens for thoughts and subqueries directly from the hidden states in a single forward pass. We align LLMs with dense retrieval models in the latent space, enabling retrieval over latent subquery tokens and supporting end-to-end joint optimization. To improve transparency and encourage semantically meaningful latent representations, we incorporate a parallel latent decoding mechanism that translates latent tokens back into natural language. Extensive experiments on seven benchmark datasets show that LatentRAG achieves performance comparable to explicit agentic RAG methods while reducing inference latency by approximately 90%, substantially narrowing the latency gap with traditional single-step RAG.

preprint2020arXiv

Graph Polish: A Novel Graph Generation Paradigm for Molecular Optimization

Molecular optimization, which transforms a given input molecule X into another Y with desirable properties, is essential in molecular drug discovery. The traditional translating approaches, generating the molecular graphs from scratch by adding some substructures piece by piece, prone to error because of the large set of candidate substructures in a large number of steps to the final target. In this study, we present a novel molecular optimization paradigm, Graph Polish, which changes molecular optimization from the traditional "two-language translating" task into a "single-language polishing" task. The key to this optimization paradigm is to find an optimization center subject to the conditions that the preserved areas around it ought to be maximized and thereafter the removed and added regions should be minimized. We then propose an effective and efficient learning framework T&S polish to capture the long-term dependencies in the optimization steps. The T component automatically identifies and annotates the optimization centers and the preservation, removal and addition of some parts of the molecule, and the S component learns these behaviors and applies these actions to a new molecule. Furthermore, the proposed paradigm can offer an intuitive interpretation for each molecular optimization result. Experiments with multiple optimization tasks are conducted on four benchmark datasets. The proposed T&S polish approach achieves significant advantage over the five state-of-the-art baseline methods on all the tasks. In addition, extensive studies are conducted to validate the effectiveness, explainability and time saving of the novel optimization paradigm.

preprint2013arXiv

An Alternative Explanation of Supernova Ia Data

Before 1998 the universe expansion was thought to be slowing down. After 1998 the universe expansion is thought to be accelerating up. This change of the belief is motivated by the observed brightness of the high redshift supernova Ia fainter than expected. In this paper it is argued that this change of the belief is not necessary. There is a more reasonable explanation for the observed brightness of the supernovae Ia fainter than expected. That is: the universe space filled with the tenuous ionized gas; the Thomson Effect of free electron in the ionized gas caused the observed brightness of the high redshift supernova Ia fainter than expected. The observations of Warm-Hot Intergalactic Medium (WHIM) support this explanation. The universe space filled with tenuous ionized gas explanation will lead to the puzzle of the dark matter and dark energy disappeared simultaneously

preprint2013arXiv

The Propagation of Photons in the Dilute Ionized Gas

The dilute ionized gas is very popular in the Universe. Usually only the Compton interactions, the "Sunyaev-Zel'dovich" effect, were considered while photons propagated in this medium. In this paper the "soft-photon process" is considered. Due to the soft photons emitted during the propagation of a photon in the dilute ionized gas, the main photon (propagating in the original direction) will be redshifted. The formula to calculate this redshift is derived.