We propose RT (Refine Thought), a method that can enhance the semantic rea-soning ability of text embedding models. The method obtains the final semanticrepresentation by running multiple forward passes of the text embedding model.Experiments show that RT achieves significant improvements on semantic reason-ing tasks in BRIGHT and the person job matching benchmark PJBenchmark1, while maintaining consistent performance on general-purpose semantic under-standing tasks such as C-MTEB. Our results indicate that RT is effective becauseit further activates the semantic reasoning ability learned during pretraining bydecoder-only text embedding models(e.g., Qwen3-Embedding-8B). RT canbe seen as a test-time inference method.

This doctoral thesis improves the transfer learning for sequence labeling tasks by adapting pre-trained neural language models. The proposed improvements in transfer learning involve introducing a multi-task model that incorporates an additional signal, a method based on architectural modifications in autoregressive large language models, and a sequence labeling framework for autoregressive large language models utilizing supervised in-context fine-tuning combined with response-oriented adaptation strategies. The first improvement is given in the context of domain transfer for the event trigger detection task. The domain transfer of the event trigger detection task can be improved by incorporating an additional signal obtained from a domain-independent text processing system into a multi-task model. The second improvement involves modifying the model's architecture. For that purpose, a method is proposed to enable bidirectional information flow across layers of autoregressive large language models. The third improvement utilizes autoregressive large language models as text generators through a generative supervised in-context fine-tuning framework. The proposed model, method, and framework demonstrate that pre-trained neural language models achieve their best performance on sequence labeling tasks when adapted through targeted transfer learning paradigms.

Large language models (LLMs) predominantly use autoregressive (AR) approaches, but masked diffusion models (MDMs) are emerging as viable alternatives. A key challenge in comparing AR and MDM paradigms is their typical architectural difference: AR models are often decoder-only, while MDMs have largely been encoder-only. This practice of changing both the modeling paradigm and architecture simultaneously makes direct comparisons unfair, as it's hard to distinguish whether observed differences stem from the paradigm itself or the architectural shift. This research evaluates MDMs within a decoder-only framework to: (1) equitably compare MDM (as Any-Order AR, or AO-AR) and standard AR paradigms. Our investigation suggests that the standard AO-AR objective, which averages over all token permutations, may benefit from refinement, as many permutations appear less informative compared to the language's inherent left-to-right structure. (2) Investigate architectural influences (decoder-only vs. encoder-only) within MDMs. We demonstrate that while encoder-only MDMs model a simpler conditional probability space, decoder-only MDMs can achieve dramatic generation speedups ($\sim25\times$) and comparable perplexity with temperature annealing despite modeling a vastly larger space, highlighting key trade-offs. This work thus decouples core paradigm differences from architectural influences, offering insights for future model design. Code is available at https://github.com/scxue/AO-GPT-MDM.

Existing multilingual neural machine translation (MNMT) approaches mainly focus on improving models with the encoder-decoder architecture to translate multiple languages. However, decoder-only architecture has been explored less in MNMT due to its underperformance when trained on parallel data solely. In this work, we attribute the issue of the decoder-only architecture to its lack of language transfer capability. Specifically, the decoder-only architecture is insufficient in encoding source tokens with the target language features. We propose dividing the decoding process into two stages so that target tokens are explicitly excluded in the first stage to implicitly boost the transfer capability across languages. Additionally, we impose contrastive learning on translation instructions, resulting in improved performance in zero-shot translation. We conduct experiments on TED-19 and OPUS-100 datasets, considering both training from scratch and fine-tuning scenarios. Experimental results show that, compared to the encoder-decoder architecture, our methods not only perform competitively in supervised translations but also achieve improvements of up to 3.39 BLEU, 6.99 chrF++, 3.22 BERTScore, and 4.81 COMET in zero-shot translations.

Large language models (LLMs), known for their exceptional reasoning capabilities, generalizability, and fluency across diverse domains, present a promising avenue for enhancing speech-related tasks. In this paper, we focus on integrating decoder-only LLMs to the task of speech-to-text translation (S2TT). We propose a decoder-only architecture that enables the LLM to directly consume the encoded speech representation and generate the text translation. Additionally, we investigate the effects of different parameter-efficient fine-tuning techniques and task formulation. Our model achieves state-of-the-art performance on CoVoST 2 and FLEURS among models trained without proprietary data. We also conduct analyses to validate the design choices of our proposed model and bring insights to the integration of LLMs to S2TT.

Large language models (LLMs) are emerging as a powerful tool in chemistry across multiple domains. In chemistry, LLMs are able to accurately predict properties, design new molecules, optimize synthesis pathways, and accelerate drug and material discovery. A core emerging idea is combining LLMs with chemistry-specific tools like synthesis planners and databases, leading to so-called "agents." This review covers LLMs' recent history, current capabilities, design, challenges specific to chemistry, and future directions. Particular attention is given to agents and their emergence as a cross-chemistry paradigm. Agents have proven effective in diverse domains of chemistry, but challenges remain. It is unclear if creating domain-specific versus generalist agents and developing autonomous pipelines versus "co-pilot" systems will accelerate chemistry. An emerging direction is the development of multi-agent systems using a human-in-the-loop approach. Due to the incredibly fast development of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

This study aims to use powerful yet efficient decoder-only Decoder-only language models (LMs) have been successfully architecture for blockwise streaming ASR. Speech utterances adopted for speech-processing tasks including automatic speech are processed in a blockwise conformer-based speech subnetwork, recognition (ASR). The LMs have ample expressiveness and and each block produces prompts that represent acoustic perform efficiently. This efficiency is a suitable characteristic information. The prompts are considerably compressed by for streaming applications of ASR. In this work, we propose removing unnecessary frames with the auxiliary CTC greedy to use a decoder-only architecture for blockwise streaming search. The speech subnetwork introduces context embedding ASR. In our approach, speech features are compressed using that is inherited from previous blocks and represents past context CTC output and context embedding using blockwise speech information. This context embedding is also provided to the subnetwork, and are sequentially provided as prompts to the decoder.

Simultaneous Machine Translation (SiMT) generates translation while reading source tokens, essentially producing the target prefix based on the source prefix. To achieve good performance, it leverages the relationship between source and target prefixes to exact a policy to guide the generation of translations. Although existing SiMT methods primarily focus on the Encoder-Decoder architecture, we explore the potential of Decoder-only architecture, owing to its superior performance in various tasks and its inherent compatibility with SiMT. However, directly applying the Decoder-only architecture to SiMT poses challenges in terms of training and inference. To alleviate the above problems, we propose the first Decoder-only SiMT model, named Decoder-only Streaming Transformer (DST). Specifically, DST separately encodes the positions of the source and target prefixes, ensuring that the position of the target prefix remains unaffected by the expansion of the source prefix. Furthermore, we propose a Streaming Self-Attention (SSA) mechanism tailored for the Decoder-only architecture. It is capable of obtaining translation policy by assessing the sufficiency of input source information and integrating with the soft-attention mechanism to generate translations. Experiments demonstrate that our approach achieves state-of-the-art performance on three translation tasks.

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional linguistic boundaries, encompassing specialized linguistic systems developed within various scientific disciplines. This growing interest has led to the advent of scientific LLMs, a novel subclass specifically engineered for facilitating scientific discovery. As a burgeoning area in the community of AI for Science, scientific LLMs warrant comprehensive exploration. However, a systematic and up-to-date survey introducing them is currently lacking. In this paper, we endeavor to methodically delineate the concept of "scientific language", whilst providing a thorough review of the latest advancements in scientific LLMs. Given the expansive realm of scientific disciplines, our analysis adopts a focused lens, concentrating on the biological and chemical domains. This includes an in-depth examination of LLMs for textual knowledge, small molecules, macromolecular proteins, genomic sequences, and their combinations, analyzing them in terms of model architectures, capabilities, datasets, and evaluation. Finally, we critically examine the prevailing challenges and point out promising research directions along with the advances of LLMs. By offering a comprehensive overview of technical developments in this field, this survey aspires to be an invaluable resource for researchers navigating the intricate landscape of scientific LLMs.

Mapping speech tokens to the same feature space as text tokens has become the paradigm for the integration of speech modality into decoder-only large language models (LLMs). An alternative approach is to use an encoder-decoder architecture that incorporates speech features through cross-attention. This approach, however, has received less attention in the literature. In this work, we connect the Whisper encoder with ChatGLM3 and provide in-depth comparisons of these two approaches using Chinese automatic speech recognition (ASR) and name entity recognition (NER) tasks. We evaluate them not only by conventional metrics like the F1 score but also by a novel fine-grained taxonomy of ASR-NER errors. Our experiments reveal that encoder-decoder architecture outperforms decoder-only architecture with a short context, while decoder-only architecture benefits from a long context as it fully exploits all layers of the LLM. By using LLM, we significantly reduced the entity omission errors and improved the entity ASR accuracy compared to the Conformer baseline. Additionally, we obtained a state-of-the-art (SOTA) F1 score of 0.805 on the AISHELL-NER test set by using chain-of-thought (CoT) NER which first infers long-form ASR transcriptions and then predicts NER labels.