Computational Protein Science in the Era of Large Language Models (LLMs)

Abstract: Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In the last few decades, Artificial Intelligence (AI) has made significant impacts in computational protein science, leading to notable successes in specific protein modeling tasks. However, those previous AI models still meet limitations, such as the difficulty in comprehending the semantics of protein sequences, and the inability to generalize across a wide range of protein modeling tasks. Recently, LLMs have emerged as a milestone in AI due to their unprecedented language processing & generalization capability. They can promote comprehensive progress in fields rather than solving individual tasks. As a result, researchers have actively introduced LLM techniques in computational protein science, developing protein Language Models (pLMs) that skillfully grasp the foundational knowledge of proteins and can be effectively generalized to solve a diversity of sequence-structure-function reasoning problems. While witnessing prosperous developments, it's necessary to present a systematic overview of computational protein science empowered by LLM techniques. First, we summarize existing pLMs into categories based on their mastered protein knowledge, i.e., underlying sequence patterns, explicit structural and functional information, and external scientific languages. Second, we introduce the utilization and adaptation of pLMs, highlighting their remarkable achievements in promoting protein structure prediction, protein function prediction, and protein design studies. Then, we describe the practical application of pLMs in antibody design, enzyme design, and drug discovery. Finally, we specifically discuss the promising future directions in this fast-growing field.

Wenqi Fan
Yi Zhou
Shijie Wang
Yuyao Yan
Hui Liu
Qian Zhao
Le Song
Qing Li


Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning

Abstract: We address protein structure prediction in the 3D Hydrophobic-Polar lattice model through two novel deep learning architectures. For proteins under 36 residues, our hybrid reservoir-based model combines fixed random projections with trainable deep layers, achieving optimal conformations with 25% fewer training episodes. For longer sequences, we employ a long short-term memory network with multi-headed attention, matching best-known energy values. Both architectures leverage a stabilized Deep Q-Learning framework with experience replay and target networks, demonstrating consistent achievement of optimal conformations while significantly improving training efficiency compared to existing methods.

Giovanny Espitia
Yui Tik Pang
James C. Gumbart


PLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy Prediction

Abstract: Recent advances in topology-based modeling have accelerated progress in physical modeling and molecular studies, including applications to protein-ligand binding affinity. In this work, we introduce the Persistent Laplacian Decision Tree (PLD-Tree), a novel method designed to address the challenging task of predicting protein-protein interaction (PPI) affinities. PLD-Tree focuses on protein chains at binding interfaces and employs the persistent Laplacian to capture topological invariants reflecting critical inter-protein interactions. These topological descriptors, derived from persistent homology, are further enhanced by incorporating evolutionary scale modeling (ESM) from a large language model to integrate sequence-based information. We validate PLD-Tree on two benchmark datasets-PDBbind V2020 and SKEMPI v2 demonstrating a correlation coefficient ($R_p$) of 0.83 under the sophisticated leave-out-protein-out cross-validation. Notably, our approach outperforms all reported state-of-the-art methods on these datasets. These results underscore the power of integrating machine learning techniques with topology-based descriptors for molecular docking and virtual screening, providing a robust and accurate framework for predicting protein-protein binding affinities.


Overview of the First Workshop on Language Models for Low-Resource Languages (LoResLM 2025)

Abstract: The first Workshop on Language Models for Low-Resource Languages (LoResLM 2025) was held in conjunction with the 31st International Conference on Computational Linguistics (COLING 2025) in Abu Dhabi, United Arab Emirates. This workshop mainly aimed to provide a forum for researchers to share and discuss their ongoing work on language models (LMs) focusing on low-resource languages, following the recent advancements in neural language models and their linguistic biases towards high-resource languages. LoResLM 2025 attracted notable interest from the natural language processing (NLP) community, resulting in 35 accepted papers from 52 submissions. These contributions cover a broad range of low-resource languages from eight language families and 13 diverse research areas, paving the way for future possibilities and promoting linguistic inclusivity in NLP.

Hansi Hettiarachchi
Tharindu Ranasinghe
Paul Rayson
Ruslan Mitkov
Mohamed Gaber
Damith Premasiri
Fiona Anting Tan
Lasitha Uyangodage


Open-Source Protein Language Models for Function Prediction and Protein Design

Abstract: Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch requires significant computational resources, limiting their accessibility. To address this, we integrate a PLM into DeepChem, an open-source framework for computational biology and chemistry, to provide a more accessible platform for protein-related tasks. We evaluate the performance of the integrated model on various protein prediction tasks, showing that it achieves reasonable results across benchmarks. Additionally, we present an exploration of generating plastic-degrading enzyme candidates using the model's embeddings and latent space manipulation techniques. While the results suggest that further refinement is needed, this approach provides a foundation for future work in enzyme design. This study aims to facilitate the use of PLMs in research fields like synthetic biology and environmental sustainability, even for those with limited computational resources.

Shivasankaran Vanaja Pandi
Bharath Ramsundar


EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations

Abstract: Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

Nuowei Liu
Changzhi Sun
Tao Ji
Junfeng Tian
Jianxin Tang
Yuanbin Wu
Man Lan


Applications of Knot Theory for the Improvement of the AlphaFold Protein Database

Abstract: AlphaFold, a groundbreaking protein prediction model, has revolutionized protein structure prediction, populating the AlphaFold Protein Database (AFDB) with millions of predicted structures. However, AlphaFold's accuracy in predicting proteins with intricate topologies, such as knots, remains a concern. This study investigates AlphaFold's performance in predicting knotted proteins and explores potential solutions to enhance the AFDB's reliability. Forty-five experimentally verified knotted protein structures from the KnotProt database were compared to their AlphaFold-generated counterparts. Knot analysis was performed using PyKnot, a PyMOL plugin, employing both Gauss codes and Alexander-Briggs knot notations. Results showed 95.6% accuracy in predicting the general shape of knots using Alexander-Briggs notation. However, Gauss code analysis revealed a 55.6% discrepancy, indicating AlphaFold's limitations in accurately representing the intricate orientation and directionality of knots. This Applications of Knot Theory for the improvement of the AlphaFold Protein Database suggests potential inaccuracies in a significant portion of the AFDB's knotted protein structures. The study underscores the need for improved knot representation in AlphaFold and proposes potential solutions, including transitioning to a single-module design or removing incorrectly predicted structures from the AFDB. These findings highlight the importance of continuous refinement for AI-based protein structure prediction tools to ensure the accuracy and reliability of protein databases for research and drug development.


FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Abstract: Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.


KULTURE Bench: A Benchmark for Assessing Language Model in Korean Cultural Context

Abstract: Large language models have exhibited significant enhancements in performance across various tasks. However, the complexity of their evaluation increases as these models generate more fluent and coherent content. Current multilingual benchmarks often use translated English versions, which may incorporate Western cultural biases that do not accurately assess other languages and cultures. To address this research gap, we introduce KULTURE Bench, an evaluation framework specifically designed for Korean culture that features datasets of cultural news, idioms, and poetry. It is designed to assess language models' cultural comprehension and reasoning capabilities at the word, sentence, and paragraph levels. Using the KULTURE Bench, we assessed the capabilities of models trained with different language corpora and analyzed the results comprehensively. The results show that there is still significant room for improvement in the models' understanding of texts related to the deeper aspects of Korean culture.

Xiaonan Wang
Jinyoung Yeo
Joon-Ho Lim
Hansaem Kim

Pacific Asia Conference on Language, Information and Computation


Leveraging Multi-modal Representations to Predict Protein Melting Temperatures

Abstract: Accurately predicting protein melting temperature changes (Delta Tm) is fundamental for assessing protein stability and guiding protein engineering. Leveraging multi-modal protein representations has shown great promise in capturing the complex relationships among protein sequences, structures, and functions. In this study, we develop models based on powerful protein language models, including ESM-2, ESM-3 and AlphaFold, using various feature extraction methods to enhance prediction accuracy. By utilizing the ESM-3 model, we achieve a new state-of-the-art performance on the s571 test dataset, obtaining a Pearson correlation coefficient (PCC) of 0.50. Furthermore, we conduct a fair evaluation to compare the performance of different protein language models in the Delta Tm prediction task. Our results demonstrate that integrating multi-modal protein representations could advance the prediction of protein melting temperatures.

Daiheng Zhang
Yan Zeng
Xinyu Hong
Jinbo Xu


SeqProFT: Sequence-only Protein Property Prediction with LoRA Finetuning

Abstract: Protein language models (PLMs) have demonstrated remarkable capabilities in learning relationships between protein sequences and functions. However, finetuning these large models requires substantial computational resources, often with suboptimal task-specific results. This study investigates how parameter-efficient finetuning via LoRA can enhance protein property prediction while significantly reducing computational demands. By applying LoRA to ESM-2 and ESM-C models of varying sizes and evaluating 10 diverse protein property prediction tasks, we demonstrate that smaller models with LoRA adaptation can match or exceed the performance of larger models without adaptation. Additionally, we integrate contact map information through a multi-head attention mechanism, improving model comprehension of structural features. Our systematic analysis reveals that LoRA finetuning enables faster convergence, better performance, and more efficient resource utilization, providing practical guidance for protein research applications in resource-constrained environments. The code is available at https://github.com/jiankliu/SeqProFT.

IEEE Transactions on Artificial Intelligence


SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction

Abstract: Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and structure information, especially as the protein function is largely determined by its spatial properties. Existing approaches mostly focus on protein sequences or topological structures, while rarely exploiting the spatial properties and ignoring the relevance between sequence and structure information. Moreover, obtaining annotated data to improve protein function prediction is often time-consuming and costly. To this end, this work proposes a novel contrast-aware pre-training framework, called SCOP, for protein function prediction. We first design a simple yet effective encoder to integrate the protein topological and spatial features under the structure view. Then a convolutional neural network is utilized to learn the protein features under the sequence view. Finally, we pretrain SCOP by leveraging two types of auxiliary supervision to explore the relevance between these two views and thus extract informative representations to better predict protein function. Experimental results on four benchmark datasets and one self-built dataset demonstrate that SCOP provides more specific results, while using less pre-training data.

Runze Ma
Chengxin He
Huiru Zheng
Xinye Wang
Haiying Wang
Yidan Zhang
Lei Duan

IEEE International Conference on Bioinformatics and Biomedicine


Efficient Alignment of Large Language Models via Data Sampling

Abstract: LLM alignment ensures that large language models behave safely and effectively by aligning their outputs with human values, goals, and intentions. Aligning LLMs employ huge amounts of data, computation, and time. Moreover, curating data with human feedback is expensive and takes time. Recent research depicts the benefit of data engineering in the fine-tuning and pre-training paradigms to bring down such costs. However, alignment differs from the afore-mentioned paradigms and it is unclear if data efficient alignment is feasible. In this work, we first aim to understand how the performance of LLM alignment scales with data. We find out that LLM alignment performance follows an exponential plateau pattern which tapers off post a rapid initial increase. Based on this, we identify data subsampling as a viable method to reduce resources required for alignment. Further, we propose an information theory-based methodology for efficient alignment by identifying a small high quality subset thereby reducing the computation and time required by alignment. We evaluate the proposed methodology over multiple datasets and compare the results. We find that the model aligned using our proposed methodology outperforms other sampling methods and performs comparable to the model aligned with the full dataset while using less than 10% data, leading to greater than 90% savings in costs, resources, and faster LLM alignment.


InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

Abstract: Protein language models (PLMs) have demonstrated remarkable success in protein modeling and design, yet their internal mechanisms for predicting structure and function remain poorly understood. Here we present a systematic approach to extract and analyze interpretable features from PLMs using sparse autoencoders (SAEs). By training SAEs on embeddings from the PLM ESM-2, we identify up to 2,548 human-interpretable latent features per layer that strongly correlate with up to 143 known biological concepts such as binding sites, structural motifs, and functional domains. In contrast, examining individual neurons in ESM-2 reveals up to 46 neurons per layer with clear conceptual alignment across 15 known concepts, suggesting that PLMs represent most concepts in superposition. Beyond capturing known annotations, we show that ESM-2 learns coherent concepts that do not map onto existing annotations and propose a pipeline using language models to automatically interpret novel latent features learned by the SAEs. As practical applications, we demonstrate how these latent features can fill in missing annotations in protein databases and enable targeted steering of protein sequence generation. Our results demonstrate that PLMs encode rich, interpretable representations of protein biology and we propose a systematic framework to extract and analyze these latent features. In the process, we recover both known biology and potentially new protein motifs. As community resources, we introduce InterPLM (interPLM.ai), an interactive visualization platform for exploring and analyzing learned PLM features, and release code for training and analysis at github.com/ElanaPearl/interPLM.


Concept Bottleneck Language Models For protein design

Abstract: We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept. Our architecture offers three key benefits: i) Control: We can intervene on concept values to precisely control the properties of generated proteins, achieving a 3 times larger change in desired concept values compared to baselines. ii) Interpretability: A linear mapping between concept values and predicted tokens allows transparent analysis of the model's decision-making process. iii) Debugging: This transparency facilitates easy debugging of trained models. Our models achieve pre-training perplexity and downstream task performance comparable to traditional masked protein language models, demonstrating that interpretability does not compromise performance. While adaptable to any language model, we focus on masked protein language models due to their importance in drug discovery and the ability to validate our model's capabilities through real-world experiments and expert knowledge. We scale our CB-pLM from 24 million to 3 billion parameters, making them the largest Concept Bottleneck Models trained and the first capable of generative language modeling.

Aya Abdelsalam Ismail
Tuomas Oikarinen
Amy Wang
Julius Adebayo
Samuel Stanton
Taylor Joren
Joseph Kleinhenz
Allen Goodman
Héctor Corrada Bravo
Kyunghyun Cho
Nathan C. Frey

International Conference on Learning Representations


Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation

Abstract: Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences between LLMs used for NLP, which effectively handle multiple tasks and are available in small sizes, and protein language models that are often specialized for specific tasks and only exist in larger sizes. In this work, we introduce two small protein language models, based on Llama-3-8B and Phi-3-mini, that are capable of both uncontrollable and controllable protein generation. For the uncontrollable generation task, our best model achieves an average pLDDT score of 69.75, demonstrating robust performance in generating viable protein structures. For the controllable generation task, in which the model generates proteins according to properties specified in the prompt, we achieve a remarkable average TM-Score of 0.84, indicating high structural similarity to target proteins. We chose 10 properties, including six classes of enzymes, to extend the capabilities of prior protein language models. Our approach utilizes the Low-Rank Adaptor (LoRA) technique, reducing trainable parameters to just 4% of the original model size, lowering computational requirements. By using a subset of the UniRef50 dataset and small models, we reduced the overall training time by 70% without compromising performance. Notably, Phi-3-mini reduced trainable parameters by 60%, decreasing training cost by 30% compared to Llama 3. Consequently, Phi-3 achieved a comparable TM-Score of 0.81, demonstrating that smaller models can match the performance of larger ones, like Llama 3. We also demonstrate the deployment of our models on the energy efficient ET-SoC-1 chip, significantly improving the TPS/W by a factor of 3.


Training Compute-Optimal Protein Language Models

Abstract: We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for the Masked Language Model~(MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.

Xingyi Cheng
Bo Chen
Pan Li
Jing Gong
Jie Tang
Le Song


Beyond Current Boundaries: Integrating Deep Learning and AlphaFold for Enhanced Protein Structure Prediction from Low-Resolution Cryo-EM Maps

Abstract: Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and graph neural networks (GNNs), have spurred the development of sophisticated map-to-model tools like DeepTracer and ModelAngelo, their efficacy notably diminishes with low-resolution maps beyond 4 Å. To address this shortfall, our research introduces DeepTracer-LowResEnhance, an innovative framework that synergizes a deep learning-enhanced map refinement technique with the power of AlphaFold. This methodology is designed to markedly improve the construction of models from low-resolution cryo-EM maps. DeepTracer-LowResEnhance was rigorously tested on a set of 37 protein cryo-EM maps, with resolutions ranging between 2.5 to 8.4 Å, including 22 maps with resolutions lower than 4 Å. The outcomes were compelling, demonstrating that 95.5\% of the low-resolution maps exhibited a significant uptick in the count of total predicted residues. This denotes a pronounced improvement in atomic model building for low-resolution maps. Additionally, a comparative analysis alongside Phenix's auto-sharpening functionality delineates DeepTracer-LowResEnhance's superior capability in rendering more detailed and precise atomic models, thereby pushing the boundaries of current computational structural biology methodologies.


MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering

Abstract: Studying protein mutations within amino acid sequences holds tremendous significance in life sciences. Protein language models (PLMs) have demonstrated strong capabilities in broad biological applications. However, due to architectural design and lack of supervision, PLMs model mutations implicitly with evolutionary plausibility, which is not satisfactory to serve as explainable and engineerable tools in real-world studies. To address these issues, we present MutaPLM, a unified framework for interpreting and navigating protein mutations with protein language models. MutaPLM introduces a protein delta network that captures explicit protein mutation representations within a unified feature space, and a transfer learning pipeline with a chain-of-thought (CoT) strategy to harvest protein mutation knowledge from biomedical texts. We also construct MutaDescribe, the first large-scale protein mutation dataset with rich textual annotations, which provides cross-modal supervision signals. Through comprehensive experiments, we demonstrate that MutaPLM excels at providing human-understandable explanations for mutational effects and prioritizing novel mutations with desirable properties. Our code, model, and data are open-sourced at https://github.com/PharMolix/MutaPLM.

Yizhen Luo
Zikun Nie
Massimo Hong
Suyuan Zhao
Hao Zhou
Zaiqing Nie


Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers

Abstract: Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built upon selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and up to 30% and 16% improvements on protein downstream tasks compared to Transformer-based ESM-2 when trained with 100B and 1T tokens, respectively. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g., structured state space models) in learning universal protein representations and incorporating molecular interaction contexts contained in biological graphs.

Yingheng Wang
Zichen Wang
Gil Sadeh
Luca Zancato
Alessandro Achille
George Karypis
Huzefa Rangwala


Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model

Abstract: 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.

Yang Tan
Ruilin Wang
Banghao Wu
Liang Hong
Bingxin Zhou


A Survey of Large Language Models for Arabic Language and its Dialects

Abstract: This survey offers a comprehensive overview of Large Language Models (LLMs) designed for Arabic language and its dialects. It covers key architectures, including encoder-only, decoder-only, and encoder-decoder models, along with the datasets used for pre-training, spanning Classical Arabic, Modern Standard Arabic, and Dialectal Arabic. The study also explores monolingual, bilingual, and multilingual LLMs, analyzing their architectures and performance across downstream tasks, such as sentiment analysis, named entity recognition, and question answering. Furthermore, it assesses the openness of Arabic LLMs based on factors, such as source code availability, training data, model weights, and documentation. The survey highlights the need for more diverse dialectal datasets and attributes the importance of openness for research reproducibility and transparency. It concludes by identifying key challenges and opportunities for future research and stressing the need for more inclusive and representative models.

Malak Mashaabi
Shahad Al-Khalifa
Hend Al-Khalifa

ACM Transactions on Asian and Low-Resource Language Information Processing


Structure Language Models for Protein Conformation Generation

Abstract: Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

Jiarui Lu
Xiaoyin Chen
Stephen Zhewen Lu
Chence Shi
Hongyu Guo
Yoshua Bengio
Jian Tang


CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation

Abstract: Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for distinguishing between experimentally resolved and computationally predicted structures, evaluating the reliability of prediction methods, and guiding downstream biological studies. Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of protein structures. CPE-Pro learns the structural information of proteins and captures inter-structural differences to achieve accurate traceability on four data classes, and is expected to be extended to more. Simultaneously, we utilized Foldseek to encode protein structures into "structure-sequences" and trained a protein Structural Sequence Language Model, SSLM. Preliminary experiments demonstrated that, compared to large-scale protein language models pre-trained on vast amounts of amino acid sequences, the "structure-sequence" enables the language model to learn more informative protein features, enhancing and optimizing structural representations. We have provided the code, model weights, and all related materials on https://github.com/GouWenrui/CPE-Pro-main.git.

Wenrui Gou
Wenhui Ge
Yang Tan
Mingchen Li
Guisheng Fan
Huiqun Yu

Interdisciplinary Sciences Computational Life Sciences


Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction

Abstract: In recent years, advances in artificial intelligence (AI) have transformed structural biology, particularly protein structure prediction. Though AI-based methods, such as AlphaFold (AF), often predict single conformations of proteins with high accuracy and confidence, predictions of alternative folds are often inaccurate, low-confidence, or simply not predicted at all. Here, we review three blind spots that alternative conformations reveal about AF-based protein structure prediction. First, proteins that assume conformations distinct from their training-set homologs can be mispredicted. Second, AF overrelies on its training set to predict alternative conformations. Third, degeneracies in pairwise representations can lead to high-confidence predictions inconsistent with experiment. These weaknesses suggest approaches to predict alternative folds more reliably.

Devlina Chakravarty
Myeongsang Lee
Lauren L. Porter


DPLM-2: A Multimodal Diffusion Protein Language Model

Abstract: Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Xinyou Wang
Zaixiang Zheng
Fei Ye
Dongyu Xue
Shujian Huang
Quanquan Gu


Bridging Large Language Models and Graph Structure Learning Models for Robust Representation Learning

Abstract: Graph representation learning, involving both node features and graph structures, is crucial for real-world applications but often encounters pervasive noise. State-of-the-art methods typically address noise by focusing separately on node features with large language models (LLMs) and on graph structures with graph structure learning models (GSLMs). In this paper, we introduce LangGSL, a robust framework that integrates the complementary strengths of pre-trained language models and GSLMs to jointly enhance both node feature and graph structure learning. In LangGSL, we first leverage LLMs to filter noise in the raw data and extract valuable cleaned information as features, enhancing the synergy of downstream models. During the mutual learning phase in LangGSL, the core idea is to leverage the relatively small language model (LM) to process local attributes and generate reliable pseudo-labels and informative node embeddings, which are then integrated into the GSLM's prediction phase. This approach enriches the global context and enhances overall performance. Meanwhile, GSLM refines the evolving graph structure constructed from the LM's output, offering updated labels back to the LM as additional guidance, thus facilitating a more effective mutual learning process. The LM and GSLM work synergistically, complementing each other's strengths and offsetting weaknesses within a variational information-maximizing framework, resulting in enhanced node features and a more robust graph structure. Extensive experiments on diverse graph datasets of varying scales and across different task scenarios demonstrate the scalability and effectiveness of the proposed approach.

Guangxin Su
Yifan Zhu
Wenjie Zhang
Hanchen Wang
Ying Zhang


Model-based Large Language Model Customization as Service

Abstract: Prominent Large Language Model (LLM) services from providers like OpenAI and Google excel at general tasks but often underperform on domain-specific applications. Current customization services for these LLMs typically require users to upload data for fine-tuning, posing significant privacy risks. While differentially private (DP) data synthesis presents a potential alternative, its application commonly results in low effectiveness due to the introduction of excessive noise on data for DP. To overcome this, we introduce Llamdex, a novel framework that facilitates LLM customization as a service, where the client uploads pre-trained domain-specific models rather than data. This client-uploaded model, optionally protected by DP with much lower noise, is inserted into the base LLM via connection modules. Significantly, these connecting modules are trained without requiring sensitive domain data, enabling clients to customize LLM services while preserving data privacy. Experiments demonstrate that Llamdex improves domain-specific accuracy by up to 26% over state-of-the-art private data synthesis methods under identical privacy constraints and, by obviating the need for users to provide domain context within queries, maintains inference efficiency comparable to the original LLM service.

Zhaomin Wu
Jizhou Guo
Junyi Hou
Bingsheng He
Lixin Fan
Qiang Yang

Conference on Empirical Methods in Natural Language Processing


From N-grams to Pre-trained Multilingual Models For Language Identification

Abstract: In this paper, we investigate the use of N-gram models and Large Pre-trained Multilingual models for Language Identification (LID) across 11 South African languages. For N-gram models, this study shows that effective data size selection remains crucial for establishing effective frequency distributions of the target languages, that efficiently model each language, thus, improving language ranking. For pre-trained multilingual models, we conduct extensive experiments covering a diverse set of massively pre-trained multilingual (PLM) models -- mBERT, RemBERT, XLM-r, and Afri-centric multilingual models -- AfriBERTa, Afro-XLMr, AfroLM, and Serengeti. We further compare these models with available large-scale Language Identification tools: Compact Language Detector v3 (CLD V3), AfroLID, GlotLID, and OpenLID to highlight the importance of focused-based LID. From these, we show that Serengeti is a superior model across models: N-grams to Transformers on average. Moreover, we propose a lightweight BERT-based LID model (za_BERT_lid) trained with NHCLT + Vukzenzele corpus, which performs on par with our best-performing Afri-centric models.


Metalic: Meta-Learning In-Context with Protein Language Models

Abstract: Predicting the biophysical and functional properties of proteins is essential for in silico protein design. Machine learning has emerged as a promising technique for such prediction tasks. However, the relative scarcity of in vitro annotations means that these models often have little, or no, specific data on the desired fitness prediction task. As a result of limited data, protein language models (PLMs) are typically trained on general protein sequence modeling tasks, and then fine-tuned, or applied zero-shot, to protein fitness prediction. When no task data is available, the models make strong assumptions about the correlation between the protein sequence likelihood and fitness scores. In contrast, we propose meta-learning over a distribution of standard fitness prediction tasks, and demonstrate positive transfer to unseen fitness prediction tasks. Our method, called Metalic (Meta-Learning In-Context), uses in-context learning and fine-tuning, when data is available, to adapt to new tasks. Crucially, fine-tuning enables considerable generalization, even though it is not accounted for during meta-training. Our fine-tuned models achieve strong results with 18 times fewer parameters than state-of-the-art models. Moreover, our method sets a new state-of-the-art in low-data settings on ProteinGym, an established fitness-prediction benchmark. Due to data scarcity, we believe meta-learning will play a pivotal role in advancing protein engineering.

Jacob Beck
Shikha Surana
Manus McAuliffe
Oliver Bent
Thomas D. Barrett
Juan Jose Garau Luis
Paul Duckworth


Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs

Abstract: Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent development of protein language models (pLMs) with supervised fine tuning provides a promising solution to this problem. However, the fine-tuned model is tailored for particular downstream prediction task, and achieving general-purpose protein understanding remains a challenge. In this paper, we introduce Structure-Enhanced Protein Instruction Tuning (SEPIT) framework to bridge this gap. Our approach incorporates a novel structure-aware module into pLMs to enrich their structural knowledge, and subsequently integrates these enhanced pLMs with large language models (LLMs) to advance protein understanding. In this framework, we propose a novel instruction tuning pipeline. First, we warm up the enhanced pLMs using contrastive learning and structure denoising. Then, caption-based instructions are used to establish a basic understanding of proteins. Finally, we refine this understanding by employing a mixture of experts (MoEs) to capture more complex properties and functional information with the same number of activated parameters. Moreover, we construct the largest and most comprehensive protein instruction dataset to date, which allows us to train and evaluate the general-purpose protein understanding model. Extensive experiments on both open-ended generation and closed-set answer tasks demonstrate the superior performance of SEPIT over both closed-source general LLMs and open-source LLMs trained with protein knowledge.

Wei Wu
Chao Wang
Liyi Chen
Mingze Yin
Yiheng Zhu
Kun Fu
Jieping Ye
Hui Xiong
Zheng Wang


Function-Guided Conditional Generation Using Protein Language Models with Adapters

Abstract: The conditional generation of proteins with desired functions is a key goal for generative models. Existing methods based on prompting of protein language models (PLMs) can generate proteins conditioned on a target functionality, such as a desired enzyme family. However, these methods are limited to simple, tokenized conditioning and have not been shown to generalize to unseen functions. In this study, we propose ProCALM (Protein Conditionally Adapted Language Model), an approach for the conditional generation of proteins using adapters to PLMs. While previous methods have used adapters for structure-conditioned generation from PLMs, our implementation of ProCALM involves finetuning ProGen2 to condition generation based on versatile representations of protein function-e.g. enzyme family, taxonomy, or natural language descriptions. ProCALM matches or exceeds the performance of existing methods at conditional sequence generation from target functions. Impressively, it can also generalize to rare and unseen functions. Overall, ProCALM is a flexible and computationally efficient approach, and we expect that it can be extended to a wide range of generative language models.

Jason Yang
Aadyot Bhatnagar
Jeffrey A. Ruffolo
Ali Madani


Morphological evaluation of subwords vocabulary used by BETO language model

Abstract: Subword tokenization algorithms used by Large Language Models are significantly more efficient and can independently build the necessary vocabulary of words and subwords without human intervention. However, those subwords do not always align with real morphemes, potentially impacting the models' performance, though it remains uncertain when this might occur. In previous research, we proposed a method to assess the morphological quality of vocabularies, focusing on the overlap between these vocabularies and the morphemes of a given language. Our evaluation method was built on three quality measures, relevance, cohesion, and morphological accuracy, and a procedure for their assessment. By applying this method to vocabularies created by three subword tokenization algorithms, BPE, Wordpiece, and Unigram, we concluded that these vocabularies generally exhibit very low morphological quality. In this article, we apply this evaluation to the tokenizer of BETO, a BERT language model trained on large Spanish corpora. This evaluation, along with our previous results, helped us conclude that its vocabulary has a low morphological quality, and we also found that training the tokenizer in a larger corpus does not improve the morphological quality of the generated vocabulary. Additionally, this evaluation helps clarify the algorithm used by the tokenizer, that is, Wordpiece, given the inconsistencies between the authors' claims and the model's configuration.

Óscar García-Sierra
Ana Fernández-Pampillón Cesteros
Miguel Ortega-Martín


Recent advances in interpretable machine learning using structure-based protein representations

Abstract: Recent advancements in machine learning (ML) are transforming the field of structural biology. For example, AlphaFold, a groundbreaking neural network for protein structure prediction, has been widely adopted by researchers. The availability of easy-to-use interfaces and interpretable outcomes from the neural network architecture, such as the confidence scores used to color the predicted structures, have made AlphaFold accessible even to non-ML experts. In this paper, we present various methods for representing protein 3D structures from low- to high-resolution, and show how interpretable ML methods can support tasks such as predicting protein structures, protein function, and protein-protein interactions. This survey also emphasizes the significance of interpreting and visualizing ML-based inference for structure-based protein representations that enhance interpretability and knowledge discovery. Developing such interpretable approaches promises to further accelerate fields including drug development and protein design.

Luiz Felipe Vecchietti
Minji Lee
Begench Hangeldiyev
Hyunkyu Jung
Hahnbeom Park
Tae-Kyun Kim
Meeyoung Cha
Ho Min Kim


Behavioral Bias of Vision-Language Models: A Behavioral Finance View

Abstract: Large Vision-Language Models (LVLMs) evolve rapidly as Large Language Models (LLMs) was equipped with vision modules to create more human-like models. However, we should carefully evaluate their applications in different domains, as they may possess undesired biases. Our work studies the potential behavioral biases of LVLMs from a behavioral finance perspective, an interdisciplinary subject that jointly considers finance and psychology. We propose an end-to-end framework, from data collection to new evaluation metrics, to assess LVLMs' reasoning capabilities and the dynamic behaviors manifested in two established human financial behavioral biases: recency bias and authority bias. Our evaluations find that recent open-source LVLMs such as LLaVA-NeXT, MobileVLM-V2, Mini-Gemini, MiniCPM-Llama3-V 2.5 and Phi-3-vision-128k suffer significantly from these two biases, while the proprietary model GPT-4o is negligibly impacted. Our observations highlight directions in which open-source models can improve. The code is available at https://github.com/mydcxiao/vlm_behavioral_fin.


Protein-Mamba: Biological Mamba Models for Protein Function Prediction

Abstract: Protein function prediction is a pivotal task in drug discovery, significantly impacting the development of effective and safe therapeutics. Traditional machine learning models often struggle with the complexity and variability inherent in predicting protein functions, necessitating more sophisticated approaches. In this work, we introduce Protein-Mamba, a novel two-stage model that leverages both self-supervised learning and fine-tuning to improve protein function prediction. The pre-training stage allows the model to capture general chemical structures and relationships from large, unlabeled datasets, while the fine-tuning stage refines these insights using specific labeled datasets, resulting in superior prediction performance. Our extensive experiments demonstrate that Protein-Mamba achieves competitive performance, compared with a couple of state-of-the-art methods across a range of protein function datasets. This model's ability to effectively utilize both unlabeled and labeled data highlights the potential of self-supervised learning in advancing protein function prediction and offers a promising direction for future research in drug discovery.

Bohao Xu
Yingzhou Lu
Yoshitaka Inoue
Namkyeong Lee
Tianfan Fu
Jintai Chen


Natural Language Processing Methods for the Study of Protein-Ligand Interactions

Abstract: Recent advances in Natural Language Processing (NLP) have ignited interest in developing effective methods for predicting protein-ligand interactions (PLIs) given their relevance to drug discovery and protein engineering efforts and the ever-growing volume of biochemical sequence and structural data available. The parallels between human languages and the "languages" used to represent proteins and ligands have enabled the use of NLP machine learning approaches to advance PLI studies. In this review, we explain where and how such approaches have been applied in the recent literature and discuss useful mechanisms such as long short-term memory, transformers, and attention. We conclude with a discussion of the current limitations of NLP methods for the study of PLIs as well as key challenges that need to be addressed in future work.

James Michels
Ramya Bandarupalli
Amin Ahangar Akbari
Thai Le
Hong Xiao
Jing Li
Erik F. Y. Hom


THaMES: An End-to-End Tool for Hallucination Mitigation and Evaluation in Large Language Models

Abstract: Hallucination, the generation of factually incorrect content, is a growing challenge in Large Language Models (LLMs). Existing detection and mitigation methods are often isolated and insufficient for domain-specific needs, lacking a standardized pipeline. This paper introduces THaMES (Tool for Hallucination Mitigations and EvaluationS), an integrated framework and library addressing this gap. THaMES offers an end-to-end solution for evaluating and mitigating hallucinations in LLMs, featuring automated test set generation, multifaceted benchmarking, and adaptable mitigation strategies. It automates test set creation from any corpus, ensuring high data quality, diversity, and cost-efficiency through techniques like batch processing, weighted sampling, and counterfactual validation. THaMES assesses a model's ability to detect and reduce hallucinations across various tasks, including text generation and binary classification, applying optimal mitigation strategies like In-Context Learning (ICL), Retrieval Augmented Generation (RAG), and Parameter-Efficient Fine-tuning (PEFT). Evaluations of state-of-the-art LLMs using a knowledge base of academic papers, political news, and Wikipedia reveal that commercial models like GPT-4o benefit more from RAG than ICL, while open-weight models like Llama-3.1-8B-Instruct and Mistral-Nemo gain more from ICL. Additionally, PEFT significantly enhances the performance of Llama-3.1-8B-Instruct in both evaluation tasks.

Mengfei Liang
Archish Arun
Zekun Wu
Cristian Munoz
Jonathan Lutch
Emre Kazim
Adriano Koshiyama
Philip Treleaven


Unforgettable Generalization in Language Models

Abstract: When language models (LMs) are trained to forget (or "unlearn'') a skill, how precisely does their behavior change? We study the behavior of transformer LMs in which tasks have been forgotten via fine-tuning on randomized labels. Such LMs learn to generate near-random predictions for individual examples in the "training'' set used for forgetting. Across tasks, however, LMs exhibit extreme variability in whether LM predictions change on examples outside the training set. In some tasks (like entailment classification), forgetting generalizes robustly, and causes models to produce uninformative predictions on new task instances; in other tasks (like physical commonsense reasoning and scientific question answering) forgetting affects only the training examples, and models continue to perform the "forgotten'' task accurately even for examples very similar to those that appeared in the training set. Dataset difficulty is not predictive of whether a behavior can be forgotten; instead, generalization in forgetting is (weakly) predicted by the confidence of LMs' initial task predictions and the variability of LM representations of training data, with low confidence and low variability both associated with greater generalization. Perhaps most surprisingly, random-label forgetting appears to be somewhat insensitive to the contents of the training set: for example, models trained on science questions with random labels continue to answer other science questions accurately, but begin to produce random labels on entailment classification tasks. Finally, we show that even generalizable forgetting is shallow: linear probes trained on LMs' representations can still perform tasks reliably after forgetting. Our results highlight the difficulty and unpredictability of performing targeted skill removal from models via fine-tuning.


SpeechPrompt: Prompting Speech Language Models for Speech Processing Tasks

Abstract: Prompting has become a practical method for utilizing pre-trained language models (LMs). This approach offers several advantages. It allows an LM to adapt to new tasks with minimal training and parameter updates, thus achieving efficiency in both storage and computation. Additionally, prompting modifies only the LM's inputs and harnesses the generative capabilities of language models to address various downstream tasks in a unified manner. This significantly reduces the need for human labor in designing task-specific models. These advantages become even more evident as the number of tasks served by the LM scales up. Motivated by the strengths of prompting, we are the first to explore the potential of prompting speech LMs in the domain of speech processing. Recently, there has been a growing interest in converting speech into discrete units for language modeling. Our pioneer research demonstrates that these quantized speech units are highly versatile within our unified prompting framework. Not only can they serve as class labels, but they also contain rich phonetic information that can be re-synthesized back into speech signals for speech generation tasks. Specifically, we reformulate speech processing tasks into speech-to-unit generation tasks. As a result, we can seamlessly integrate tasks such as speech classification, sequence generation, and speech generation within a single, unified prompting framework. The experiment results show that the prompting method can achieve competitive performance compared to the strong fine-tuning method based on self-supervised learning models with a similar number of trainable parameters. The prompting method also shows promising results in the few-shot setting. Moreover, with the advanced speech LMs coming into the stage, the proposed prompting framework attains great potential.

Kai-Wei Chang
Haibin Wu
Yu-Kai Wang
Yuan-Kuei Wu
Hua Shen
Wei-Cheng Tseng
Iu-thing Kang
Shang-Wen Li
Hung-yi Lee

IEEE/ACM Transactions on Audio Speech and Language Processing


AlphaFolding: 4D Diffusion for Dynamic Protein Structure Prediction with Reference and Motion Guidance

Abstract: Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes. URL: https://fudan-generative-vision.github.io/AlphaFolding/#/

Kaihui Cheng
Ce Liu
Qingkun Su
Jun Wang
Liwei Zhang
Yining Tang
Yao Yao
Siyu Zhu
Yuan Qi


CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction

Abstract: Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to capture the binding mechanisms comprehensively. The recent emerging pre-trained language models trained on massive unsupervised sequences of protein and RNA have shown strong representation ability for various in-domain downstream tasks, including binding site prediction. However, applying different-domain language models collaboratively for complex-level tasks remains unexplored. In this paper, we propose CoPRA to bridge pre-trained language models from different biological domains via Complex structure for Protein-RNA binding Affinity prediction. We demonstrate for the first time that cross-biological modal language models can collaborate to improve binding affinity prediction. We propose a Co-Former to combine the cross-modal sequence and structure information and a bi-scope pre-training strategy for improving Co-Former's interaction understanding. Meanwhile, we build the largest protein-RNA binding affinity dataset PRA310 for performance evaluation. We also test our model on a public dataset for mutation effect prediction. CoPRA reaches state-of-the-art performance on all the datasets. We provide extensive analyses and verify that CoPRA can (1) accurately predict the protein-RNA binding affinity; (2) understand the binding affinity change caused by mutations; and (3) benefit from scaling data and model size.

Rong Han
Xiaohong Liu
Tong Pan
Jing Xu
Xiaoyu Wang
Wuyang Lan
Zhenyu Li
Zixuan Wang
Jiangning Song
Guangyu Wang
Ting Chen

AAAI Conference on Artificial Intelligence


ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding

Abstract: Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research. To streamline this process, we introduce ProteinGPT, a state-of-the-art multimodal large language model for proteins that enables users to upload protein sequences and/or structures for comprehensive analysis and responsive inquiries. ProteinGPT integrates protein sequence and structure encoders with linear projection layers to ensure precise representation adaptation and leverages a large language model (LLM) to generate accurate, contextually relevant responses. To train ProteinGPT, we constructed a large-scale dataset of 132,092 proteins, each annotated with 20-30 property tags and 5-10 QA pairs per protein, and optimized the instruction-tuning process using GPT-4o. Experiments demonstrate that ProteinGPT effectively generates informative responses to protein-related questions, achieving high performance on both semantic and lexical metrics and significantly outperforming baseline models and general-purpose LLMs in understanding and responding to protein-related queries. Our code and data are available at https://github.com/ProteinGPT/ProteinGPT.

Yijia Xiao
Edward Sun
Yiqiao Jin
Qifan Wang
Wei Wang


Design Proteins Using Large Language Models: Enhancements and Comparative Analyses

Abstract: Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

Kamyar Zeinalipour
Neda Jamshidi
Monica Bianchini
Marco Maggini
Marco Gori


Peptide Sequencing Via Protein Language Models

Abstract: We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Thuong Le Hoai Pham
Jillur Rahman Saurav
Aisosa A. Omere
Calvin J. Heyl
Mohammad Sadegh Nasr
Cody Tyler Reynolds
Jai Prakash Yadav Veerla
Helen H Shang
Justyn Jaworski
Alison Ravenscraft
Joseph Anthony Buonomo
Jacob M. Luber

ACM International Conference on Bioinformatics, Computational Biology and Biomedicine


Improving Text Embeddings for Smaller Language Models Using Contrastive Fine-tuning

Abstract: While Large Language Models show remarkable performance in natural language understanding, their resource-intensive nature makes them less accessible. In contrast, smaller language models such as MiniCPM offer more sustainable scalability, but often underperform without specialized optimization. In this paper, we explore the enhancement of smaller language models through the improvement of their text embeddings. We select three language models, MiniCPM, Phi-2, and Gemma, to conduct contrastive fine-tuning on the NLI dataset. Our results demonstrate that this fine-tuning method enhances the quality of text embeddings for all three models across various benchmarks, with MiniCPM showing the most significant improvements of an average 56.33% performance gain. The contrastive fine-tuning code is publicly available at https://github.com/trapoom555/Language-Model-STS-CFT.


Ranking protein-protein models with large language models and graph neural networks

Abstract: Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere with those or to guide drug design. Various strategies can be followed to model those complexes, all typically resulting in a large number of models. A challenging step in this process is the identification of good models (near-native PPI conformations) from the large pool of generated models. To address this challenge, we previously developed DeepRank-GNN-esm, a graph-based deep learning algorithm for ranking modelled PPI structures harnessing the power of protein language models. Here, we detail the use of our software with examples. DeepRank-GNN-esm is freely available at https://github.com/haddocking/DeepRank-GNN-esm


GraphPrint: Extracting Features from 3D Protein Structure for Drug Target Affinity Prediction

Abstract: Accurate drug target affinity prediction can improve drug candidate selection, accelerate the drug discovery process, and reduce drug production costs. Previous work focused on traditional fingerprints or used features extracted based on the amino acid sequence in the protein, ignoring its 3D structure which affects its binding affinity. In this work, we propose GraphPrint: a framework for incorporating 3D protein structure features for drug target affinity prediction. We generate graph representations for protein 3D structures using amino acid residue location coordinates and combine them with drug graph representation and traditional features to jointly learn drug target affinity. Our model achieves a mean square error of 0.1378 and a concordance index of 0.8929 on the KIBA dataset and improves over using traditional protein features alone. Our ablation study shows that the 3D protein structure-based features provide information complementary to traditional features.


Daisy: An integrated repeat protein curation service

Abstract: Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for protein structure prediction and repeat classification that are useful for this process. However, no service contemplates required databases and software to supplement researching on repeat proteins. In this publication we present Daisy, an integrated repeat protein curation web service. This service can process Protein Data Bank (PDB) and the AlphaFold Database entries for tandem repeats identification. In addition, it uses an algorithm to search a sequence against a library of Pfam hidden Markov model (HMM). Repeat classifications are associated with the identified families through RepeatsDB. This prediction is considered for enhancing the ReUPred algorithm execution and hastening the repeat units identification process. The service can also operate every associated PDB and AlphaFold structure with a UniProt proteome registry. Availability: The Daisy web service is freely accessible at daisy.bioinformatica.org.

Manuel Bezerra-Brandao
Ronaldo Romario Tunque Cahui
Layla Hirsh


Dihedral Angle Adherence: Evaluating Protein Structure Predictions in the Absence of Experimental Data

Abstract: Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge. The traditional method, RMSD, relies on experimentally determined structures and lacks insight into improvement areas of predictions. We propose an alternative: analyzing dihedral angles, bypassing the need for the reference structure of an evaluated protein. Our method segments proteins into amino acid subsequences and searches for matches, comparing dihedral angles across numerous proteins to compute a metric using Mahalanobis distance. Evaluated on many predictions, our approach correlates with RMSD and identifies areas for prediction enhancement. This method offers a promising route for accurate protein structure prediction assessment and improvement.


Improving AlphaFlow for Efficient Protein Ensembles Generation

Abstract: Investigating conformational landscapes of proteins is a crucial way to understand their biological functions and properties. AlphaFlow stands out as a sequence-conditioned generative model that introduces flexibility into structure prediction models by fine-tuning AlphaFold under the flow-matching framework. Despite the advantages of efficient sampling afforded by flow-matching, AlphaFlow still requires multiple runs of AlphaFold to finally generate one single conformation. Due to the heavy consumption of AlphaFold, its applicability is limited in sampling larger set of protein ensembles or the longer chains within a constrained timeframe. In this work, we propose a feature-conditioned generative model called AlphaFlow-Lit to realize efficient protein ensembles generation. In contrast to the full fine-tuning on the entire structure, we focus solely on the light-weight structure module to reconstruct the conformation. AlphaFlow-Lit performs on-par with AlphaFlow and surpasses its distilled version without pretraining, all while achieving a significant sampling acceleration of around 47 times. The advancement in efficiency showcases the potential of AlphaFlow-Lit in enabling faster and more scalable generation of protein ensembles.

Shaoning Li
Mingyu Li
Yusong Wang
Xinheng He
Nanning Zheng
Jian Zhang
Pheng-Ann Heng


Manipulating language models' training data to study syntactic constraint learning: the case of English passivization

Abstract: Grammatical rules in natural languages are often characterized by exceptions. How do language learners learn these exceptions to otherwise general patterns? Here, we study this question through the case study of English passivization. While passivization is in general quite productive, there are cases where it cannot apply (cf. the following sentence is ungrammatical: *One hour was lasted by the meeting). Using neural network language models as theories of language acquisition, we explore the sources of indirect evidence that a learner can leverage to learn whether a verb can be passivized. We first characterize English speakers' judgments of exceptions to the passive, and confirm that speakers find some verbs more passivizable than others. We then show that a neural network language model's verb passivizability judgments are largely similar to those displayed by humans, suggesting that evidence for these exceptions is available in the linguistic input. Finally, we test two hypotheses as to the source of evidence that language models use to learn these restrictions: frequency (entrenchment) and semantics (affectedness). We do so by training models on versions of the corpus that have had sentences of the types implicated by each hypothesis removed, altered, or introduced. We find support for both hypotheses: entrenchment and affectedness make independent contributions to a verb's passivizability. From a methodological point of view, this study highlights the utility of altering a language model's training data for answering questions where complete control over a learner's input is vital.


Open foundation models for Azerbaijani language

Abstract: The emergence of multilingual large language models has enabled the development of language understanding and generation systems in Azerbaijani. However, most of the production-grade systems rely on cloud solutions, such as GPT-4. While there have been several attempts to develop open foundation models for Azerbaijani, these works have not found their way into common use due to a lack of systemic benchmarking. This paper encompasses several lines of work that promote open-source foundation models for Azerbaijani. We introduce (1) a large text corpus for Azerbaijani, (2) a family of encoder-only language models trained on this dataset, (3) labeled datasets for evaluating these models, and (4) extensive evaluation that covers all major open-source models with Azerbaijani support.

Jafar Isbarov
Kavsar Huseynova
Elvin Mammadov
Mammad Hajili
Duygu Ataman


Exploring Advanced Large Language Models with LLMsuite

Abstract: This tutorial explores the advancements and challenges in the development of Large Language Models (LLMs) such as ChatGPT and Gemini. It addresses inherent limitations like temporal knowledge cutoffs, mathematical inaccuracies, and the generation of incorrect information, proposing solutions like Retrieval Augmented Generation (RAG), Program-Aided Language Models (PAL), and frameworks such as ReAct and LangChain. The integration of these techniques enhances LLM performance and reliability, especially in multi-step reasoning and complex task execution. The paper also covers fine-tuning strategies, including instruction fine-tuning, parameter-efficient methods like LoRA, and Reinforcement Learning from Human Feedback (RLHF) as well as Reinforced Self-Training (ReST). Additionally, it provides a comprehensive survey of transformer architectures and training techniques for LLMs. The source code can be accessed by contacting the author via email for a request.


DCI: An Accurate Quality Assessment Criteria for Protein Complex Structure Models

Abstract: The structure of proteins is the basis for studying protein function and drug design. The emergence of AlphaFold 2 has greatly promoted the prediction of protein 3D structures, and it is of great significance to give an overall and accurate evaluation of the predicted models, especially the complex models. Among the existing methods for evaluating multimer structures, DockQ is the most commonly used. However, as a more suitable metric for complex docking, DockQ cannot provide a unique and accurate evaluation in the non-docking situation. Therefore, it is necessary to propose an evaluation strategy that can directly evaluate the whole complex without limitation and achieve good results. In this work, we proposed DCI score, a new evaluation strategy for protein complex structure models, which only bases on distance map and CI (contact-interface) map, DCI focuses on the prediction accuracy of the contact interface based on the overall evaluation of complex structure, is not inferior to DockQ in the evaluation accuracy according to CAPRI classification, and is able to handle the non-docking situation better than DockQ. Besides, we calculated DCI score on CASP datasets and compared it with CASP official assessment, which obtained good results. In addition, we found that DCI can better evaluate the overall structure deviation caused by interface prediction errors in the case of multi-chains. Our DCI is available at \url{https://gitee.com/WendaWang/DCI-score.git}, and the online-server is available at \url{http://mialab.ruc.edu.cn/DCIServer/}.

Wenda Wang
Jiaqi Zhai
He Huang
Xinqi Gong


ProtSolM: Protein Solubility Prediction with Multi-modal Features

Abstract: Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein engineering. Existing methods either construct a supervised learning scheme on small-scale datasets with manually processed physicochemical properties, or blindly apply pre-trained protein language models to extract amino acid interaction information. The scale and quality of available training datasets leave significant room for improvement in terms of accuracy and generalization. To address these research gaps, we propose \sol, a novel deep learning method that combines pre-training and fine-tuning schemes for protein solubility prediction. ProtSolM integrates information from multiple dimensions, including physicochemical properties, amino acid sequences, and protein backbone structures. Our model is trained using \data, the largest solubility dataset that we have constructed. PDBSol includes over $60,000$ protein sequences and structures. We provide a comprehensive leaderboard of existing statistical learning and deep learning methods on independent datasets with computational and experimental labels. ProtSolM achieved state-of-the-art performance across various evaluation metrics, demonstrating its potential to significantly advance the accuracy of protein solubility prediction.

Yang Tan
Jia Zheng
Liang Hong
Bingxin Zhou


Accurate Prediction of Ligand-Protein Interaction Affinities with Fine-Tuned Small Language Models

Abstract: We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate predictions for a range of affinity values associated with ligand-protein interactions on out-of-sample data in a zero-shot setting. Only the SMILES string of the ligand and the amino acid sequence of the protein were used as the model inputs. Our results demonstrate a clear improvement over machine learning (ML) and free-energy perturbation (FEP+) based methods in accurately predicting a range of ligand-protein interaction affinities, which can be leveraged to further accelerate drug discovery campaigns against challenging therapeutic targets.


Evaluating representation learning on the protein structure universe

Abstract: We introduce ProteinWorkshop, a comprehensive benchmark suite for representation learning on protein structures with Geometric Graph Neural Networks. We consider large-scale pre-training and downstream tasks on both experimental and predicted structures to enable the systematic evaluation of the quality of the learned structural representation and their usefulness in capturing functional relationships for downstream tasks. We find that: (1) large-scale pretraining on AlphaFold structures and auxiliary tasks consistently improve the performance of both rotation-invariant and equivariant GNNs, and (2) more expressive equivariant GNNs benefit from pretraining to a greater extent compared to invariant models. We aim to establish a common ground for the machine learning and computational biology communities to rigorously compare and advance protein structure representation learning. Our open-source codebase reduces the barrier to entry for working with large protein structure datasets by providing: (1) storage-efficient dataloaders for large-scale structural databases including AlphaFoldDB and ESM Atlas, as well as (2) utilities for constructing new tasks from the entire PDB. ProteinWorkshop is available at: github.com/a-r-j/ProteinWorkshop.

Arian R. Jamasb
Alex Morehead
Chaitanya K. Joshi
Zuobai Zhang
Kieran Didi
Simon V. Mathis
Charles Harris
Jian Tang
Jianlin Cheng
Pietro Lio
Tom L. Blundell


Evaluating Large Language Models along Dimensions of Language Variation: A Systematik Invesdigatiom uv Cross-lingual Generalization

Abstract: While large language models exhibit certain cross-lingual generalization capabilities, they suffer from performance degradation (PD) on unseen closely-related languages (CRLs) and dialects relative to their high-resource language neighbour (HRLN). However, we currently lack a fundamental understanding of what kinds of linguistic distances contribute to PD, and to what extent. Furthermore, studies of cross-lingual generalization are confounded by unknown quantities of CRL language traces in the training data, and by the frequent lack of availability of evaluation data in lower-resource related languages and dialects. To address these issues, we model phonological, morphological, and lexical distance as Bayesian noise processes to synthesize artificial languages that are controllably distant from the HRLN. We analyse PD as a function of underlying noise parameters, offering insights on model robustness to isolated and composed linguistic phenomena, and the impact of task and HRL characteristics on PD. We calculate parameter posteriors on real CRL-HRLN pair data and show that they follow computed trends of artificial languages, demonstrating the viability of our noisers. Our framework offers a cheap solution for estimating task performance on an unseen CRL given HRLN performance using its posteriors, as well as for diagnosing observed PD on a CRL in terms of its linguistic distances from its HRLN, and opens doors to principled methods of mitigating performance degradation.

Niyati Bafna
Kenton Murray
David Yarowsky


FoldToken2: Learning compact, invariant and generative protein structure language

Abstract: The equivalent nature of 3D coordinates has posed long term challenges in protein structure representation learning, alignment, and generation. Can we create a compact and invariant language that equivalently represents protein structures? Towards this goal, we propose FoldToken2 to transfer equivariant structures into discrete tokens, while maintaining the recoverability of the original structures. From FoldToken1 to FoldToken2, we improve three key components: (1) invariant structure encoder, (2) vector-quantized compressor, and (3) equivalent structure decoder. We evaluate FoldToken2 on the protein structure reconstruction task and show that it outperforms previous FoldToken1 by 20\% in TMScore and 81\% in RMSD. FoldToken2 probably be the first method that works well on both single-chain and multi-chain protein structures quantization. We believe that FoldToken2 will inspire further improvement in protein structure representation learning, structure alignment, and structure generation tasks.


A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

Abstract: The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score.

Yiqing Shen
Zan Chen
Michail Mamalakis
Luhan He
Haiyang Xia
Tianbin Li
Yanzhou Su
Junjun He
Yu Guang Wang


MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training

Abstract: Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Bo Chen
Zhilei Bei
Xingyi Cheng
Pan Li
Jie Tang
Le Song


Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation

Abstract: AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step towards comprehensive, automated protein structure prediction. However, independent validation of AF3's predictions is necessary. Evaluated using the SKEMPI 2.0 database which involves 317 protein-protein complexes and 8338 mutations, AF3 complex structures give rise to a very good Pearson correlation coefficient of 0.86 for predicting protein-protein binding free energy changes upon mutation, slightly less than the 0.88 achieved earlier with the Protein Data Bank (PDB) structures. Nonetheless, AF3 complex structures led to a 8.6% increase in the prediction RMSE compared to original PDB complex structures. Additionally, some of AF3's complex structures have large errors, which were not captured in its ipTM performance metric. Finally, it is found that AF3's complex structures are not reliable for intrinsically flexible regions or domains.


PediatricsGPT: Large Language Models as Chinese Medical Assistants for Pediatric Applications

Abstract: Developing intelligent pediatric consultation systems offers promising prospects for improving diagnostic efficiency, especially in China, where healthcare resources are scarce. Despite recent advances in Large Language Models (LLMs) for Chinese medicine, their performance is sub-optimal in pediatric applications due to inadequate instruction data and vulnerable training procedures. To address the above issues, this paper builds PedCorpus, a high-quality dataset of over 300,000 multi-task instructions from pediatric textbooks, guidelines, and knowledge graph resources to fulfil diverse diagnostic demands. Upon well-designed PedCorpus, we propose PediatricsGPT, the first Chinese pediatric LLM assistant built on a systematic and robust training pipeline. In the continuous pre-training phase, we introduce a hybrid instruction pre-training mechanism to mitigate the internal-injected knowledge inconsistency of LLMs for medical domain adaptation. Immediately, the full-parameter Supervised Fine-Tuning (SFT) is utilized to incorporate the general medical knowledge schema into the models. After that, we devise a direct following preference optimization to enhance the generation of pediatrician-like humanistic responses. In the parameter-efficient secondary SFT phase, a mixture of universal-specific experts strategy is presented to resolve the competency conflict between medical generalist and pediatric expertise mastery. Extensive results based on the metrics, GPT-4, and doctor evaluations on distinct doctor downstream tasks show that PediatricsGPT consistently outperforms previous Chinese medical LLMs. Our model and dataset will be open-source for community development.

Dingkang Yang
Jinjie Wei
Dongling Xiao
Shunli Wang
Tong Wu
Gang Li
Mingcheng Li
Shuaibing Wang
Jiawei Chen
Yue Jiang
Qingyao Xu
Ke Li
Peng Zhai
Lihua Zhang


Boosting Protein Language Models with Negative Sample Mining

Abstract: We introduce a pioneering methodology for boosting large language models in the domain of protein representation learning. Our primary contribution lies in the refinement process for correlating the over-reliance on co-evolution knowledge, in a way that networks are trained to distill invaluable insights from negative samples, constituted by protein pairs sourced from disparate categories. By capitalizing on this novel approach, our technique steers the training of transformer-based models within the attention score space. This advanced strategy not only amplifies performance but also reflects the nuanced biological behaviors exhibited by proteins, offering aligned evidence with traditional biological mechanisms such as protein-protein interaction. We experimentally observed improved performance on various tasks over datasets, on top of several well-established large protein models. This innovative paradigm opens up promising horizons for further progress in the realms of protein research and computational biology.

Yaoyao Xu
Xinjian Zhao
Xiaozhuang Song
Benyou Wang
Tianshu Yu


PatchProt: Hydrophobic patch prediction using protein foundation models

Abstract: Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed hydrophobic patches from a protein sequence has been shown to be a difficult task. Fine-tuning foundation models allows for adapting a model to the specific nuances of a new task using a much smaller dataset. Additionally, multi-task deep learning offers a promising solution for addressing data gaps, simultaneously outperforming single-task methods. In this study, we harnessed a recently released leading large language model ESM-2. Efficient fine-tuning of ESM-2 was achieved by leveraging a recently developed parameter-efficient fine-tuning method. This approach enabled comprehensive training of model layers without excessive parameters and without the need to include a computationally expensive multiple sequence analysis. We explored several related tasks, at local (residue) and global (protein) levels, to improve the representation of the model. As a result, our fine-tuned ESM-2 model, PatchProt, cannot only predict hydrophobic patch areas but also outperforms existing methods at predicting primary tasks, including secondary structure and surface accessibility predictions. Importantly, our analysis shows that including related local tasks can improve predictions on more difficult global tasks. This research sets a new standard for sequence-based protein property prediction and highlights the remarkable potential of fine-tuning foundation models enriching the model representation by training over related tasks.

Dea Gogishvili
Emmanuel Minois-Genin
Jan van Eck
Sanne Abeln