This study introduces SLLMBO, an innovative framework leveraging large language models (LLMs) for hyperparameter optimization (HPO), incorporating dynamic search space adaptability, enhanced parameter space exploitation, and a novel LLM-tree-structured parzen estimator (LLM-TPE) sampler. By addressing limitations in recent fully LLM-based methods and traditional bayesian optimization (BO), SLLMBO achieves more robust optimization. This comprehensive benchmarking evaluates multiple LLMs, including GPT-3.5-Turbo, GPT-4o, Claude-Sonnet-3.5, and Gemini-1.5-Flash, extending prior work and establishing SLLMBO as the first framework to benchmark a diverse set of LLMs for HPO. By integrating LLMs' established strengths in parameter initialization with the exploitation abilities demonstrated in this study, alongside TPE's exploration capabilities, the LLM-TPE sampler achieves a balanced exploration-exploitation trade-off, reduces API costs, and mitigates premature early stoppings for more effective parameter searches. Across 14 tabular tasks in classification and regression, the LLM-TPE sampler outperformed fully LLM-based methods and achieved superior results over BO methods in 9 tasks. Testing early stopping in budget-constrained scenarios demonstrated competitive performance, indicating that LLM-based methods generally benefit from extended iterations for optimal results. This work lays the foundation for future research exploring open-source LLMs, reproducibility of LLM results in HPO, and benchmarking SLLMBO on complex datasets, such as image classification, segmentation, and machine translation.
Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties. The emergence of deep learning methods for protein modeling has demonstrated superior results at lower costs compared to traditional approaches such as directed evolution and rational design. In mutation effect prediction, the key to pre-training deep learning models lies in accurately interpreting the complex relationships among protein sequence, structure, and function. This study introduces a retrieval-enhanced protein language model for comprehensive analysis of native properties from sequence and local structural interactions, as well as evolutionary properties from retrieved homologous sequences. The state-of-the-art performance of the proposed ProtREM is validated on over 2 million mutants across 217 assays from an open benchmark (ProteinGym). We also conducted post-hoc analyses of the model's ability to improve the stability and binding affinity of a VHH antibody. Additionally, we designed 10 new mutants on a DNA polymerase and conducted wet-lab experiments to evaluate their enhanced activity at higher temperatures. Both in silico and experimental evaluations confirmed that our method provides reliable predictions of mutation effects, offering an auxiliary tool for biologists aiming to evolve existing enzymes. The implementation is publicly available at https://github.com/tyang816/ProtREM.
Large Language Models (LLMs) have demonstrated strong reasoning abilities, making them suitable for complex tasks such as graph computation. Traditional reasoning steps paradigm for graph problems is hindered by unverifiable steps, limited long-term reasoning, and poor generalization to graph variations. To overcome these limitations, we introduce GCoder, a code-based LLM designed to enhance problem-solving in generalized graph computation problems. Our method involves constructing an extensive training dataset, GraphWild, featuring diverse graph formats and algorithms. We employ a multi-stage training process, including Supervised Fine-Tuning (SFT) and Reinforcement Learning from Compiler Feedback (RLCF), to refine model capabilities. For unseen tasks, a hybrid retrieval technique is used to augment performance. Experiments demonstrate that GCoder outperforms GPT-4o, with an average accuracy improvement of 16.42% across various graph computational problems. Furthermore, GCoder efficiently manages large-scale graphs with millions of nodes and diverse input formats, overcoming the limitations of previous models focused on the reasoning steps paradigm. This advancement paves the way for more intuitive and effective graph problem-solving using LLMs. Code and data are available at here: https://github.com/Bklight999/WWW25-GCoder/tree/master.
FP8 training has emerged as a promising method for improving training efficiency. Existing frameworks accelerate training by applying FP8 computation to linear layers while leaving optimizer states and activations in higher precision, which fails to fully optimize memory usage. This paper introduces COAT (Compressing Optimizer States and Activations for FP8 Training), a novel FP8 training framework designed to significantly reduce memory footprint when training large models. COAT addresses current limitations through two key innovations: (1) Dynamic Range Expansion, which aligns optimizer state distributions more closely with the FP8 representation range, thereby reducing quantization error, and (2) Mixed-Granularity Activation Quantization, which optimizes activation memory using a combination of per-tensor and per-group quantization strategies. Experiments demonstrate that COAT effectively reduces end-to-end training memory footprint by 1.54x compared to BF16 while achieving nearly lossless performance across various tasks, such as Large Language Model pretraining and fine-tuning and Vision Language Model training. COAT also achieves a 1.43x end-to-end training speedup compared to BF16, performing on par with or surpassing TransformerEngine's speedup. COAT enables efficient full-parameter training of large models on fewer GPUs, and facilitates doubling the batch size in distributed training settings, providing a practical solution for scaling large-scale model training. The code is available at https://github.com/NVlabs/COAT.
Humans develop their grammars by making structural generalizations from finite input. We ask how filler-gap dependencies, which share a structural generalization despite diverse surface forms, might arise from the input. We explicitly control the input to a neural language model (NLM) to uncover whether the model posits a shared representation for filler-gap dependencies. We show that while NLMs do have success differentiating grammatical from ungrammatical filler-gap dependencies, they rely on superficial properties of the input, rather than on a shared generalization. Our work highlights the need for specific linguistic inductive biases to model language acquisition.
Long-context models(LCMs) have shown great potential in processing long input sequences(even more than 100M tokens) conveniently and effectively. With significant progress, recent research has pointed out that LCMs can accurately locate token-level salient information within the context. Yet, the generation performance of these LCMs is far from satisfactory and might result in misaligned responses, such as hallucinations. To enhance the generation capability of LCMs, existing works have investigated the effects of data size and quality for both pre-training and instruction tuning. Though achieving meaningful improvement, previous methods fall short in either effectiveness or efficiency. In this paper, we introduce LOGO(Long cOntext aliGnment via efficient preference Optimization), a training strategy that first introduces preference optimization for long-context alignment. To overcome the GPU memory-bound issue caused by the long sequence, LOGO employs a reference-free preference optimization strategy and adopts a position synthesis method to construct the training data. By training with only 0.3B data on a single 8$\times$A800 GPU machine for 16 hours, LOGO allows the Llama-3-8B-Instruct-80K model to achieve comparable performance with GPT-4 in real-world long-context tasks while preserving the model's original capabilities on other tasks, e.g., language modeling and MMLU. Moreover, LOGO can extend the model's context window size while enhancing its generation performance.
Masked diffusion models (MDMs) have shown promise in language modeling, yet their scalability and effectiveness in core language tasks, such as text generation and language understanding, remain underexplored. This paper establishes the first scaling law for MDMs, demonstrating a scaling rate comparable to autoregressive models (ARMs) and a relatively small compute gap. Motivated by their scalability, we train a family of MDMs with up to 1.1 billion (B) parameters to systematically evaluate their performance against ARMs of comparable or larger sizes. Fully leveraging the probabilistic formulation of MDMs, we propose a simple yet effective unsupervised classifier-free guidance that effectively exploits large-scale unpaired data, boosting performance for conditional inference. In language understanding, the 1.1B MDM outperforms the 1.1B TinyLlama model trained on the same data across four of eight zero-shot benchmarks. Notably, it achieves competitive math reasoning ability with the 7B Llama-2 model on the GSM8K dataset. In text generation, MDMs provide a flexible trade-off compared to ARMs utilizing KV-cache: MDMs match the performance of ARMs while being 1.4 times faster or achieving higher quality than ARMs at a higher computational cost. Moreover, MDMs address challenging tasks for ARMs by effectively handling bidirectional reasoning and adapting to temporal shifts in data. Notably, a 1.1B MDM breaks the reverse curse encountered by much larger ARMs with significantly more data and computation, such as 13B Llama-2 and 175B GPT-3. Our code is available at https://github.com/ML-GSAI/SMDM.
The number of large language models (LLMs) with varying parameter scales and vocabularies is increasing. While they deliver powerful performance, they also face a set of common optimization needs to meet specific requirements or standards, such as instruction following or avoiding the output of sensitive information from the real world. However, how to reuse the fine-tuning outcomes of one model to other models to reduce training costs remains a challenge. To bridge this gap, we introduce Cross-model Control (CMC), a method that improves multiple LLMs in one-time training with a portable tiny language model. Specifically, we have observed that the logit shift before and after fine-tuning is remarkably similar across different models. Based on this insight, we incorporate a tiny language model with a minimal number of parameters. By training alongside a frozen template LLM, the tiny model gains the capability to alter the logits output by the LLMs. To make this tiny language model applicable to models with different vocabularies, we propose a novel token mapping strategy named PM-MinED. We have conducted extensive experiments on instruction tuning and unlearning tasks, demonstrating the effectiveness of CMC. Our code is available at https://github.com/wujwyi/CMC.
Training data attribution (TDA) methods aim to attribute model outputs back to specific training examples, and the application of these methods to large language model (LLM) outputs could significantly advance model transparency and data curation. However, it has been challenging to date to apply these methods to the full scale of LLM pretraining. In this paper, we refine existing gradient-based methods to work effectively at scale, allowing us to retrieve influential examples for an 8B-parameter language model from a pretraining corpus of over 160B tokens with no need for subsampling or pre-filtering. Our method combines several techniques, including optimizer state correction, a task-specific Hessian approximation, and normalized encodings, which we find to be critical for performance at scale. In quantitative evaluations on a fact tracing task, our method performs best at identifying examples that influence model predictions, but classical, model-agnostic retrieval methods such as BM25 still perform better at finding passages which explicitly contain relevant facts. These results demonstrate a misalignment between factual *attribution* and causal *influence*. With increasing model size and training tokens, we find that influence more closely aligns with factual attribution. Finally, we examine different types of examples identified as influential by our method, finding that while many directly entail a particular fact, others support the same output by reinforcing priors on relation types, common entities, and names. We release our prompt set and model outputs, along with a web-based visualization tool to explore influential examples for factual predictions, commonsense reasoning, arithmetic, and open-ended generation for an 8B-parameter LLM.
Diffusion Language Models (DLMs) have emerged as a promising new paradigm for text generative modeling, potentially addressing limitations of autoregressive (AR) models. However, current DLMs have been studied at a smaller scale compared to their AR counterparts and lack fair comparison on language modeling benchmarks. Additionally, training diffusion models from scratch at scale remains challenging. Given the prevalence of open-source AR language models, we propose adapting these models to build text diffusion models. We demonstrate connections between AR and diffusion modeling objectives and introduce a simple continual pre-training approach for training diffusion models. Through systematic evaluation on language modeling, reasoning, and commonsense benchmarks, we show that we can convert AR models ranging from 127M to 7B parameters (GPT2 and LLaMA) into diffusion models DiffuGPT and DiffuLLaMA, using less than 200B tokens for training. Our experimental results reveal that these models outperform earlier DLMs and are competitive with their AR counterparts. We release a suite of DLMs (with 127M, 355M, and 7B parameters) capable of generating fluent text, performing in-context learning, filling in the middle without prompt re-ordering, and following instructions \url{https://github.com/HKUNLP/DiffuLLaMA}.
The correct specification of reward models is a well-known challenge in reinforcement learning. Hand-crafted reward functions often lead to inefficient or suboptimal policies and may not be aligned with user values. Reinforcement learning from human feedback is a successful technique that can mitigate such issues, however, the collection of human feedback can be laborious. Recent works have solicited feedback from pre-trained large language models rather than humans to reduce or eliminate human effort, however, these approaches yield poor performance in the presence of hallucination and other errors. This paper studies the advantages and limitations of reinforcement learning from large language model feedback and proposes a simple yet effective method for soliciting and applying feedback as a potential-based shaping function. We theoretically show that inconsistent rankings, which approximate ranking errors, lead to uninformative rewards with our approach. Our method empirically improves convergence speed and policy returns over commonly used baselines even with significant ranking errors, and eliminates the need for complex post-processing of reward functions.
Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.
Knowledge distillation (KD) is widely used to train small, high-performing student language models (LMs) using large teacher LMs. While effective in fine-tuning, KD during pre-training faces challenges in efficiency, flexibility, and effectiveness. Existing methods either incur high computational costs due to online teacher inference, require tokenization matching between teacher and student LMs, or risk losing the difficulty and diversity of the teacher-generated training data. To address these issues, we propose MiniPLM, a KD framework for pre-training LMs by refining the training data distribution with the teacher's knowledge. For efficiency, MiniPLM performs offline teacher LM inference, allowing KD for multiple student LMs without adding training-time costs. For flexibility, MiniPLM operates solely on the training corpus, enabling KD across model families. For effectiveness, MiniPLM leverages the differences between large and small LMs to enhance the difficulty and diversity of the training data, helping student LMs acquire versatile and sophisticated knowledge. Extensive experiments demonstrate that MiniPLM boosts the student LMs' performance on 9 widely used downstream tasks, improves the language modeling capabilities, and reduces pre-training computation. The benefit of MiniPLM extends to large pre-training scales, evidenced by the extrapolation of the scaling curves. Further analysis reveals that MiniPLM supports KD across model families and enhances the utilization of pre-training data. Our model, code, and data are available at https://github.com/thu-coai/MiniPLM.
Users can divulge sensitive information to proprietary LLM providers, raising significant privacy concerns. While open-source models, hosted locally on the user's machine, alleviate some concerns, models that users can host locally are often less capable than proprietary frontier models. Toward preserving user privacy while retaining the best quality, we propose Privacy-Conscious Delegation, a novel task for chaining API-based and local models. We utilize recent public collections of user-LLM interactions to construct a natural benchmark called PUPA, which contains personally identifiable information (PII). To study potential approaches, we devise PAPILLON, a multi-stage LLM pipeline that uses prompt optimization to address a simpler version of our task. Our best pipeline maintains high response quality for 85.5% of user queries while restricting privacy leakage to only 7.5%. We still leave a large margin to the generation quality of proprietary LLMs for future work. Our data and code is available at https://github.com/siyan-sylvia-li/PAPILLON.
The fusion of speech and language in the era of large language models has garnered significant attention. Discrete speech token is often utilized in text-to-speech tasks for speech compression and portability, which is convenient for joint training with text and have good compression efficiency. However, we found that the discrete speech tokenizer still suffers from information loss. Therefore, we propose a simple yet effective continuous speech tokenizer named Cont-SPT, and a text-to-speech model based on continuous speech tokens. Our results show that the speech language model based on the continuous speech tokenizer has better continuity and higher estimated Mean Opinion Scores (MoS). This enhancement is attributed to better information preservation rate of the continuous speech tokenizer across both low and high frequencies in the frequency domain. The code and resources for Cont-SPT can be found in https://github.com/Yixing-Li/Continuous-Speech-Tokenizer
There are already many DNA large language models, but most of them still follow traditional uses, such as extracting sequence features for classification tasks. More innovative applications of large language models, such as prompt engineering, RAG, and zero-shot or few-shot prediction, remain challenging for DNA-based models. The key issue lies in the fact that DNA models and human natural language models are entirely separate; however, techniques like prompt engineering require the use of natural language, thereby significantly limiting the application of DNA large language models. This paper introduces a pre-trained model trained on the GPT-2 network, combining DNA sequences and English text, and uses a unified BPE tokenization method. We then convert classification and other downstream tasks into Alpaca format instruction data, and perform instruction fine-tuning on this pre-trained model to create a fine-tuned model capable of handling multiple tasks. The model has demonstrated its effectiveness in DNA related zero-shot prediction and multitask application. This research provides a highly promising direction for building a unified DNA sequence task framework.
Adsorption energy is a key reactivity descriptor in catalysis, enabling efficient screening for optimal catalysts. However, determining adsorption energy typically requires evaluating numerous adsorbate-catalyst configurations. Current algorithmic approaches rely on exhaustive enumeration of adsorption sites and configurations, which makes the process computationally intensive and does not inherently guarantee the identification of the global minimum energy. In this work, we introduce Adsorb-Agent, a Large Language Model (LLM) agent designed to efficiently identify system-specific stable adsorption configurations corresponding to the global minimum adsorption energy. Adsorb-Agent leverages its built-in knowledge and emergent reasoning capabilities to strategically explore adsorption configurations likely to hold adsorption energy. By reducing the reliance on exhaustive sampling, it significantly decreases the number of initial configurations required while improving the accuracy of adsorption energy predictions. We evaluate Adsorb-Agent's performance across twenty representative systems encompassing a range of complexities. The Adsorb-Agent successfully identifies comparable adsorption energies for 83.7% of the systems and achieves lower energies, closer to the actual global minimum, for 35% of the systems, while requiring significantly fewer initial configurations than conventional methods. Its capability is particularly evident in complex systems, where it identifies lower adsorption energies for 46.7% of systems involving intermetallic surfaces and 66.7% of systems with large adsorbate molecules. These results demonstrate the potential of Adsorb-Agent to accelerate catalyst discovery by reducing computational costs and improving the reliability of adsorption energy predictions.
Effective communication within universities is crucial for addressing the diverse information needs of students, alumni, and external stakeholders. However, existing chatbot systems often fail to deliver accurate, context-specific responses, resulting in poor user experiences. In this paper, we present KatzBot, an innovative chatbot powered by KatzGPT, a custom Large Language Model (LLM) fine-tuned on domain-specific academic data. KatzGPT is trained on two university-specific datasets: 6,280 sentence-completion pairs and 7,330 question-answer pairs. KatzBot outperforms established existing open source LLMs, achieving higher accuracy and domain relevance. KatzBot offers a user-friendly interface, significantly enhancing user satisfaction in real-world applications. The source code is publicly available at \url{https://github.com/AiAI-99/katzbot}.
Colonoscopy is currently one of the most sensitive screening methods for colorectal cancer. This study investigates the frontiers of intelligent colonoscopy techniques and their prospective implications for multimodal medical applications. With this goal, we begin by assessing the current data-centric and model-centric landscapes through four tasks for colonoscopic scene perception, including classification, detection, segmentation, and vision-language understanding. This assessment enables us to identify domain-specific challenges and reveals that multimodal research in colonoscopy remains open for further exploration. To embrace the coming multimodal era, we establish three foundational initiatives: a large-scale multimodal instruction tuning dataset ColonINST, a colonoscopy-designed multimodal language model ColonGPT, and a multimodal benchmark. To facilitate ongoing monitoring of this rapidly evolving field, we provide a public website for the latest updates: https://github.com/ai4colonoscopy/IntelliScope.
We propose a general pipeline to automate the extraction of labels from radiology reports using large language models, which we validate on spinal MRI reports. The efficacy of our labelling method is measured on five distinct conditions: spinal cancer, stenosis, spondylolisthesis, cauda equina compression and herniation. Using open-source models, our method equals or surpasses GPT-4 on a held-out set of reports. Furthermore, we show that the extracted labels can be used to train imaging models to classify the identified conditions in the accompanying MR scans. All classifiers trained using automated labels achieve comparable performance to models trained using scans manually annotated by clinicians. Code can be found at https://github.com/robinyjpark/AutoLabelClassifier.