Daily Papers

Recent advancements in language models have started a new era of superior information retrieval and content generation, with embedding models playing an important role in optimizing data representation efficiency and performance. While benchmarks like the Massive Text Embedding Benchmark (MTEB) have standardized the evaluation of general domain embedding models, a gap remains in specialized fields such as chemistry, which require tailored approaches due to domain-specific challenges. This paper introduces a novel benchmark, the Chemical Text Embedding Benchmark (ChemTEB), designed specifically for the chemical sciences. ChemTEB addresses the unique linguistic and semantic complexities of chemical literature and data, offering a comprehensive suite of tasks on chemical domain data. Through the evaluation of 34 open-source and proprietary models using this benchmark, we illuminate the strengths and weaknesses of current methodologies in processing and understanding chemical information. Our work aims to equip the research community with a standardized, domain-specific evaluation framework, promoting the development of more precise and efficient NLP models for chemistry-related applications. Furthermore, it provides insights into the performance of generic models in a domain-specific context. ChemTEB comes with open-source code and data, contributing further to its accessibility and utility.

Text embeddings are commonly evaluated on a small set of datasets from a single task not covering their possible applications to other tasks. It is unclear whether state-of-the-art embeddings on semantic textual similarity (STS) can be equally well applied to other tasks like clustering or reranking. This makes progress in the field difficult to track, as various models are constantly being proposed without proper evaluation. To solve this problem, we introduce the Massive Text Embedding Benchmark (MTEB). MTEB spans 8 embedding tasks covering a total of 58 datasets and 112 languages. Through the benchmarking of 33 models on MTEB, we establish the most comprehensive benchmark of text embeddings to date. We find that no particular text embedding method dominates across all tasks. This suggests that the field has yet to converge on a universal text embedding method and scale it up sufficiently to provide state-of-the-art results on all embedding tasks. MTEB comes with open-source code and a public leaderboard at https://github.com/embeddings-benchmark/mteb.

Retrieval-augmented generation (RAG) has emerged as a powerful framework for enhancing large language models (LLMs) with external knowledge, particularly in scientific domains that demand specialized and dynamic information. Despite its promise, the application of RAG in the chemistry domain remains underexplored, primarily due to the lack of high-quality, domain-specific corpora and well-curated evaluation benchmarks. In this work, we introduce ChemRAG-Bench, a comprehensive benchmark designed to systematically assess the effectiveness of RAG across a diverse set of chemistry-related tasks. The accompanying chemistry corpus integrates heterogeneous knowledge sources, including scientific literature, the PubChem database, PubMed abstracts, textbooks, and Wikipedia entries. In addition, we present ChemRAG-Toolkit, a modular and extensible RAG toolkit that supports five retrieval algorithms and eight LLMs. Using ChemRAG-Toolkit, we demonstrate that RAG yields a substantial performance gain -- achieving an average relative improvement of 17.4% over direct inference methods. We further conduct in-depth analyses on retriever architectures, corpus selection, and the number of retrieved passages, culminating in practical recommendations to guide future research and deployment of RAG systems in the chemistry domain. The code and data is available at https://chemrag.github.io.

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning, which involves pre-training Transformers on SMILES sequences -- textual descriptors of molecules. Despite its success in molecular property prediction, current practices often lead to overfitting and limited scalability due to early convergence. In this paper, we introduce a novel chemical language representation learning framework, called MolTRES, to address these issues. MolTRES incorporates generator-discriminator training, allowing the model to learn from more challenging examples that require structural understanding. In addition, we enrich molecular representations by transferring knowledge from scientific literature by integrating external materials embedding. Experimental results show that our model outperforms existing state-of-the-art models on popular molecular property prediction tasks.

Large Language Models (LLMs) have shown growing potential in molecular sciences, but they often produce chemically inaccurate descriptions and struggle to recognize or justify potential errors. This raises important concerns about their robustness and reliability in scientific applications. To support more rigorous evaluation of LLMs in chemical reasoning, we present the MolErr2Fix benchmark, designed to assess LLMs on error detection and correction in molecular descriptions. Unlike existing benchmarks focused on molecule-to-text generation or property prediction, MolErr2Fix emphasizes fine-grained chemical understanding. It tasks LLMs with identifying, localizing, explaining, and revising potential structural and semantic errors in molecular descriptions. Specifically, MolErr2Fix consists of 1,193 fine-grained annotated error instances. Each instance contains quadruple annotations, i.e,. (error type, span location, the explanation, and the correction). These tasks are intended to reflect the types of reasoning and verification required in real-world chemical communication. Evaluations of current state-of-the-art LLMs reveal notable performance gaps, underscoring the need for more robust chemical reasoning capabilities. MolErr2Fix provides a focused benchmark for evaluating such capabilities and aims to support progress toward more reliable and chemically informed language models. All annotations and an accompanying evaluation API will be publicly released to facilitate future research.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

The Massive Text Embedding Benchmark (MTEB) has become a standard evaluation platform for text embedding models. While previous work has established the core benchmark methodology, this paper focuses on the engineering aspects that ensure MTEB's continued reproducibility and extensibility. We present our approach to maintaining robust continuous integration pipelines that validate dataset integrity, automate test execution, and assess benchmark results' generalizability. We detail the design choices that collectively enhance reproducibility and usability. Furthermore, we discuss our strategies for handling community contributions and extending the benchmark with new tasks and datasets. These engineering practices have been instrumental in scaling MTEB to become more comprehensive while maintaining quality and, ultimately, relevance to the field. Our experiences offer valuable insights for benchmark maintainers facing similar challenges in ensuring reproducibility and usability in machine learning evaluation frameworks. The MTEB repository is available at: https://github.com/embeddings-benchmark/mteb

Retrieval-Augmented Generation (RAG) systems are increasingly vital for navigating the ever-expanding body of scientific literature, particularly in high-stakes domains such as chemistry. Despite the promise of RAG, foundational design choices -- such as how documents are segmented and represented -- remain underexplored in domain-specific contexts. This study presents the first large-scale, systematic evaluation of chunking strategies and embedding models tailored to chemistry-focused RAG systems. We investigate 25 chunking configurations across five method families and evaluate 48 embedding models on three chemistry-specific benchmarks, including the newly introduced QuestChemRetrieval dataset. Our results reveal that recursive token-based chunking (specifically R100-0) consistently outperforms other approaches, offering strong performance with minimal resource overhead. We also find that retrieval-optimized embeddings -- such as Nomic and Intfloat E5 variants -- substantially outperform domain-specialized models like SciBERT. By releasing our datasets, evaluation framework, and empirical benchmarks, we provide actionable guidelines for building effective and efficient chemistry-aware RAG systems.

A crucial component of many deep learning applications (such as FAQ and RAG) is dense retrieval, in which embedding models are used to convert raw text to numerical vectors and then get the most similar text by MIPS (Maximum Inner Product Search). Some text embedding benchmarks (e.g. MTEB, BEIR, and AIR-Bench) have been established to evaluate embedding models accurately. Thanks to these benchmarks, we can use SOTA models; however, the deployment and application of these models in industry were hampered by their large vector dimensions and numerous parameters. To alleviate this problem, 1) we present a distillation technique that can enable a smaller student model to achieve good performance. 2) Inspired by MRL we present a training approach of reducing the vector dimensions based on its own vectors or its teacher vectors. 3) We do simple yet effective alignment training between images and text to make our model a multimodal encoder. We trained Stella and Jasper models using the technologies above and achieved high scores on the MTEB leaderboard. We release the model and data at Hugging Face Hub (https://huggingface.co/infgrad/jasper_en_vision_language_v1) and the training logs are at https://api.wandb.ai/links/dunnzhang0/z8jqoqpb.

In this paper, we introduce a novel and simple method for obtaining high-quality text embeddings using only synthetic data and less than 1k training steps. Unlike existing methods that often depend on multi-stage intermediate pre-training with billions of weakly-supervised text pairs, followed by fine-tuning with a few labeled datasets, our method does not require building complex training pipelines or relying on manually collected datasets that are often constrained by task diversity and language coverage. We leverage proprietary LLMs to generate diverse synthetic data for hundreds of thousands of text embedding tasks across nearly 100 languages. We then fine-tune open-source decoder-only LLMs on the synthetic data using standard contrastive loss. Experiments demonstrate that our method achieves strong performance on highly competitive text embedding benchmarks without using any labeled data. Furthermore, when fine-tuned with a mixture of synthetic and labeled data, our model sets new state-of-the-art results on the BEIR and MTEB benchmarks.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

While semantic embeddings are rigorously evaluated on the Massive Text Embedding Benchmark, the evaluation of style embeddings remains fragmented, with each work relying on their own set of tasks and datasets. To bridge this gap, we introduce the Style Text Embedding Benchmark, a comprehensive open-source benchmark intended to standardize the evaluation of style embeddings. STEB encompasses 96 datasets across 7 languages, spanning applications such as authorship verification, authorship retrieval, AI-text detection, probing of linguistic features, and others. We find that semantic embeddings consistently fail in stylistic tasks, and that there is no style embedding that is universally superior across all tasks evaluated. We open-source the STEB code base at: https://github.com/rrivera1849/STEB.

Question Answering (QA) effectively evaluates language models' reasoning and knowledge depth. While QA datasets are plentiful in areas like general domain and biomedicine, academic chemistry is less explored. Chemical QA plays a crucial role in both education and research by effectively translating complex chemical information into readily understandable format. Addressing this gap, we introduce ScholarChemQA, a large-scale QA dataset constructed from chemical papers. This dataset reflects typical real-world challenges, including an imbalanced data distribution and a substantial amount of unlabeled data that can be potentially useful. Correspondingly, we introduce a QAMatch model, specifically designed to effectively answer chemical questions by fully leveraging our collected data. We first address the issue of imbalanced label distribution by re-weighting the instance-wise loss based on the inverse frequency of each class, ensuring minority classes are not dominated by majority ones during optimization. Next, we utilize the unlabeled data to enrich the learning process, generating a variety of augmentations based on a SoftMix operation and ensuring their predictions align with the same target, i.e., pseudo-labels. To ensure the quality of the pseudo-labels, we propose a calibration procedure aimed at closely aligning the pseudo-label estimates of individual samples with a desired ground truth distribution. Experiments show that our QAMatch significantly outperforms the recent similar-scale baselines and Large Language Models (LLMs) not only on our ScholarChemQA dataset but also on four benchmark datasets. We hope our benchmark and model can facilitate and promote more research on chemical QA.

Molecule and text representation learning has gained increasing interest due to its potential for enhancing the understanding of chemical information. However, existing models often struggle to capture subtle differences between molecules and their descriptions, as they lack the ability to learn fine-grained alignments between molecular substructures and chemical phrases. To address this limitation, we introduce MolBridge, a novel molecule-text learning framework based on substructure-aware alignments. Specifically, we augment the original molecule-description pairs with additional alignment signals derived from molecular substructures and chemical phrases. To effectively learn from these enriched alignments, MolBridge employs substructure-aware contrastive learning, coupled with a self-refinement mechanism that filters out noisy alignment signals. Experimental results show that MolBridge effectively captures fine-grained correspondences and outperforms state-of-the-art baselines on a wide range of molecular benchmarks, highlighting the significance of substructure-aware alignment in molecule-text learning.

Text embeddings are typically evaluated on a limited set of tasks, which are constrained by language, domain, and task diversity. To address these limitations and provide a more comprehensive evaluation, we introduce the Massive Multilingual Text Embedding Benchmark (MMTEB) - a large-scale, community-driven expansion of MTEB, covering over 500 quality-controlled evaluation tasks across 250+ languages. MMTEB includes a diverse set of challenging, novel tasks such as instruction following, long-document retrieval, and code retrieval, representing the largest multilingual collection of evaluation tasks for embedding models to date. Using this collection, we develop several highly multilingual benchmarks, which we use to evaluate a representative set of models. We find that while large language models (LLMs) with billions of parameters can achieve state-of-the-art performance on certain language subsets and task categories, the best-performing publicly available model is multilingual-e5-large-instruct with only 560 million parameters. To facilitate accessibility and reduce computational cost, we introduce a novel downsampling method based on inter-task correlation, ensuring a diverse selection while preserving relative model rankings. Furthermore, we optimize tasks such as retrieval by sampling hard negatives, creating smaller but effective splits. These optimizations allow us to introduce benchmarks that drastically reduce computational demands. For instance, our newly introduced zero-shot English benchmark maintains a ranking order similar to the full-scale version but at a fraction of the computational cost.

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Patent text embeddings enable prior art search, technology landscaping, and patent analysis, yet existing benchmarks inadequately capture patent-specific challenges. We introduce PatenTEB, a comprehensive benchmark comprising 15 tasks across retrieval, classification, paraphrase, and clustering, with 2.06 million examples. PatenTEB employs domain-stratified splits, domain specific hard negative mining, and systematic coverage of asymmetric fragment-to-document matching scenarios absent from general embedding benchmarks. We develop the patembed model family through multi-task training, spanning 67M to 344M parameters with context lengths up to 4096 tokens. External validation shows strong generalization: patembed-base achieves state-of-the-art on MTEB BigPatentClustering.v2 (0.494 V-measure vs. 0.445 previous best), while patembed-large achieves 0.377 NDCG@100 on DAPFAM. Systematic ablations reveal that multi-task training improves external generalization despite minor benchmark costs, and that domain-pretrained initialization provides consistent advantages across task families. All resources will be made available at https://github.com/iliass-y/patenteb. Keywords: patent retrieval, sentence embeddings, multi-task learning, asymmetric retrieval, benchmark evaluation, contrastive learning.

In this technical report, we propose ChemVLM, the first open-source multimodal large language model dedicated to the fields of chemistry, designed to address the incompatibility between chemical image understanding and text analysis. Built upon the VIT-MLP-LLM architecture, we leverage ChemLLM-20B as the foundational large model, endowing our model with robust capabilities in understanding and utilizing chemical text knowledge. Additionally, we employ InternVIT-6B as a powerful image encoder. We have curated high-quality data from the chemical domain, including molecules, reaction formulas, and chemistry examination data, and compiled these into a bilingual multimodal question-answering dataset. We test the performance of our model on multiple open-source benchmarks and three custom evaluation sets. Experimental results demonstrate that our model achieves excellent performance, securing state-of-the-art results in five out of six involved tasks. Our model can be found at https://huggingface.co/AI4Chem/ChemVLM-26B.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

We introduce SemCSE, an unsupervised method for learning semantic embeddings of scientific texts. Building on recent advances in contrastive learning for text embeddings, our approach leverages LLM-generated summaries of scientific abstracts to train a model that positions semantically related summaries closer together in the embedding space. This resulting objective ensures that the model captures the true semantic content of a text, in contrast to traditional citation-based approaches that do not necessarily reflect semantic similarity. To validate this, we propose a novel benchmark designed to assess a model's ability to understand and encode the semantic content of scientific texts, demonstrating that our method enforces a stronger semantic separation within the embedding space. Additionally, we evaluate SemCSE on the comprehensive SciRepEval benchmark for scientific text embeddings, where it achieves state-of-the-art performance among models of its size, thus highlighting the benefits of a semantically focused training approach.

Current evaluations of sentence embedding models typically rely on static test beds such as the Massive Text Embedding Benchmark (MTEB). While invaluable, repeated tuning on a fixed suite can inflate reported performance and obscure real-world robustness. We introduce the Paraphrasing Text Embedding Benchmark (PTEB), a dynamic protocol that stochastically generates meaning-preserving paraphrases at evaluation time and aggregates results across multiple runs. Using a cost-efficient LLM-based method grounded in semantic textual similarity gold ratings, we show that LLMs generate token-diverse but semantically preserving, paraphrases. Across 7 MTEB tasks, we validate our hypothesis that the performance of sentence encoders is sensitive to changes in token space even when semantics remain fixed. We also observe that smaller models are not disproportionately affected relative to larger ones. Our results are statistically robust over multiple runs and we extended our experiments to 3 multilingual datasets covering 10 languages. More generally, we aim to propose a new evaluation paradigm in NLP that relies less on static, pre-defined benchmarks but shifts towards dynamic, stochastic evaluation leveraging eval-time compute.

The rapid expansion of chemistry literature poses significant challenges for researchers seeking to efficiently access domain-specific knowledge. To support advancements in chemistry-focused natural language processing (NLP), we present ChemRxivQuest, a curated dataset of 970 high-quality question-answer (QA) pairs derived from 155 ChemRxiv preprints across 17 subfields of chemistry. Each QA pair is explicitly linked to its source text segment to ensure traceability and contextual accuracy. ChemRxivQuest was constructed using an automated pipeline that combines optical character recognition (OCR), GPT-4o-based QA generation, and a fuzzy matching technique for answer verification. The dataset emphasizes conceptual, mechanistic, applied, and experimental questions, enabling applications in retrieval-based QA systems, search engine development, and fine-tuning of domain-adapted large language models. We analyze the dataset's structure, coverage, and limitations, and outline future directions for expansion and expert validation. ChemRxivQuest provides a foundational resource for chemistry NLP research, education, and tool development.

Chemical reasoning inherently integrates visual, textual, and symbolic modalities, yet existing benchmarks rarely capture this complexity, often relying on simple image-text pairs with limited chemical semantics. As a result, the actual ability of Multimodal Large Language Models (MLLMs) to process and integrate chemically meaningful information across modalities remains unclear. We introduce ChemVTS-Bench, a domain-authentic benchmark designed to systematically evaluate the Visual-Textual-Symbolic (VTS) reasoning abilities of MLLMs. ChemVTS-Bench contains diverse and challenging chemical problems spanning organic molecules, inorganic materials, and 3D crystal structures, with each task presented in three complementary input modes: (1) visual-only, (2) visual-text hybrid, and (3) SMILES-based symbolic input. This design enables fine-grained analysis of modality-dependent reasoning behaviors and cross-modal integration. To ensure rigorous and reproducible evaluation, we further develop an automated agent-based workflow that standardizes inference, verifies answers, and diagnoses failure modes. Extensive experiments on state-of-the-art MLLMs reveal that visual-only inputs remain challenging, structural chemistry is the hardest domain, and multimodal fusion mitigates but does not eliminate visual, knowledge-based, or logical errors, highlighting ChemVTS-Bench as a rigorous, domain-faithful testbed for advancing multimodal chemical reasoning. All data and code will be released to support future research.

In recent years, numerous embedding models have been made available and widely used for various NLP tasks. Choosing a model that performs well for several tasks in English has been largely simplified by the Massive Text Embedding Benchmark (MTEB), but extensions to other languages remain challenging. This is why we expand MTEB to propose the first massive benchmark of sentence embeddings for French. Not only we gather 22 existing datasets in an easy-to-use interface, but we also create three new French datasets for a global evaluation over 8 different tasks. We perform a large scale comparison with 46 carefully selected embedding models, conduct comprehensive statistical tests, and analyze the correlation between model performance and many of their characteristics. We find out that even if no model is the best on all tasks, large multilingual models pre-trained on sentence similarity perform particularly well. Our work comes with open-source code, new datasets and a public leaderboard.

Medical text embedding models are foundational to a wide array of healthcare applications, ranging from clinical decision support and biomedical information retrieval to medical question answering, yet they remain hampered by two critical shortcomings. First, most models are trained on a narrow slice of medical and biological data, beside not being up to date in terms of methodology, making them ill suited to capture the diversity of terminology and semantics encountered in practice. Second, existing evaluations are often inadequate: even widely used benchmarks fail to generalize across the full spectrum of real world medical tasks. To address these gaps, we leverage MEDTE, a GTE model extensively fine-tuned on diverse medical corpora through self-supervised contrastive learning across multiple data sources, to deliver robust medical text embeddings. Alongside this model, we propose a comprehensive benchmark suite of 51 tasks spanning classification, clustering, pair classification, and retrieval modeled on the Massive Text Embedding Benchmark (MTEB) but tailored to the nuances of medical text. Our results demonstrate that this combined approach not only establishes a robust evaluation framework but also yields embeddings that consistently outperform state of the art alternatives in different tasks.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

Text embeddings are essential for many tasks, such as document retrieval, clustering, and semantic similarity assessment. In this paper, we study how to contrastively train text embedding models in a compute-optimal fashion, given a suite of pre-trained decoder-only language models. Our innovation is an algorithm that produces optimal configurations of model sizes, data quantities, and fine-tuning methods for text-embedding models at different computational budget levels. The resulting recipe, which we obtain through extensive experiments, can be used by practitioners to make informed design choices for their embedding models. Specifically, our findings suggest that full fine-tuning and low-rank adaptation fine-tuning produce optimal models at lower and higher computational budgets respectively.

Decoder-only large language model (LLM)-based embedding models are beginning to outperform BERT or T5-based embedding models in general-purpose text embedding tasks, including dense vector-based retrieval. In this work, we introduce the NV-Embed model with a variety of architectural designs and training procedures to significantly enhance the performance of LLM as a versatile embedding model, while maintaining its simplicity and reproducibility. For model architecture, we propose a latent attention layer to obtain pooled embeddings, which consistently improves retrieval and downstream task accuracy compared to mean pooling or using the last <EOS> token embedding from LLMs. To enhance representation learning, we remove the causal attention mask of LLMs during contrastive training. For model training, we introduce a two-stage contrastive instruction-tuning method. It first applies contrastive training with instructions on retrieval datasets, utilizing in-batch negatives and curated hard negative examples. At stage-2, it blends various non-retrieval datasets into instruction tuning, which not only enhances non-retrieval task accuracy but also improves retrieval performance. Combining these techniques, our NV-Embed model, using only publicly available data, has achieved a record-high score of 69.32, ranking No. 1 on the Massive Text Embedding Benchmark (MTEB) (as of May 24, 2024), with 56 tasks, encompassing retrieval, reranking, classification, clustering, and semantic textual similarity tasks. Notably, our model also attains the highest score of 59.36 on 15 retrieval tasks in the MTEB benchmark (also known as BEIR). We will open-source the model at: https://huggingface.co/nvidia/NV-Embed-v1.

The integration of Multimodal Large Language Models (MLLMs) into chemistry promises to revolutionize scientific discovery, yet their ability to comprehend the dense, graphical language of reactions within authentic literature remains underexplored. Here, we introduce RxnBench, a multi-tiered benchmark designed to rigorously evaluate MLLMs on chemical reaction understanding from scientific PDFs. RxnBench comprises two tasks: Single-Figure QA (SF-QA), which tests fine-grained visual perception and mechanistic reasoning using 1,525 questions derived from 305 curated reaction schemes, and Full-Document QA (FD-QA), which challenges models to synthesize information from 108 articles, requiring cross-modal integration of text, schemes, and tables. Our evaluation of MLLMs reveals a critical capability gap: while models excel at extracting explicit text, they struggle with deep chemical logic and precise structural recognition. Notably, models with inference-time reasoning significantly outperform standard architectures, yet none achieve 50\% accuracy on FD-QA. These findings underscore the urgent need for domain-specific visual encoders and stronger reasoning engines to advance autonomous AI chemists.

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, in this paper, we propose ChemMLLM, a unified chemical multimodal large language model for molecule understanding and generation. Also, we design five multimodal tasks across text, molecular SMILES strings, and image, and curate the datasets. We benchmark ChemMLLM against a range of general leading MLLMs and Chemical LLMs on these tasks. Experimental results show that ChemMLLM achieves superior performance across all evaluated tasks. For example, in molecule image optimization task, ChemMLLM outperforms the best baseline (GPT-4o) by 118.9\% (4.27 vs 1.95 property improvement). The code is publicly available at https://github.com/bbsbz/ChemMLLM.git.

Molecular representations are inherently task-dependent, yet most pre-trained molecular encoders are not. Task conditioning promises representations that reorganize based on task descriptions, but existing approaches rely on expensive labeled data. We show that weak supervision on programmatically derived molecular motifs is sufficient. Our Adaptive Chemical Embedding Model (ACE-Mol) learns from hundreds of motifs paired with natural language descriptors that are cheap to compute, trivial to scale. Conventional encoders slowly search the embedding space for task-relevant structure, whereas ACE-Mol immediately aligns its representations with the task. ACE-Mol achieves state-of-the-art performance across molecular property prediction benchmarks with interpretable, chemically meaningful representations.

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

Text embeddings are useful features in many applications such as semantic search and computing text similarity. Previous work typically trains models customized for different use cases, varying in dataset choice, training objective and model architecture. In this work, we show that contrastive pre-training on unsupervised data at scale leads to high quality vector representations of text and code. The same unsupervised text embeddings that achieve new state-of-the-art results in linear-probe classification also display impressive semantic search capabilities and sometimes even perform competitively with fine-tuned models. On linear-probe classification accuracy averaging over 7 tasks, our best unsupervised model achieves a relative improvement of 4% and 1.8% over previous best unsupervised and supervised text embedding models respectively. The same text embeddings when evaluated on large-scale semantic search attains a relative improvement of 23.4%, 14.7%, and 10.6% over previous best unsupervised methods on MSMARCO, Natural Questions and TriviaQA benchmarks, respectively. Similarly to text embeddings, we train code embedding models on (text, code) pairs, obtaining a 20.8% relative improvement over prior best work on code search.

Precise recognition, editing, and generation of molecules are essential prerequisites for both chemists and AI systems tackling various chemical tasks. We present MolLangBench, a comprehensive benchmark designed to evaluate fundamental molecule-language interface tasks: language-prompted molecular structure recognition, editing, and generation. To ensure high-quality, unambiguous, and deterministic outputs, we construct the recognition tasks using automated cheminformatics tools, and curate editing and generation tasks through rigorous expert annotation and validation. MolLangBench supports the evaluation of models that interface language with different molecular representations, including linear strings, molecular images, and molecular graphs. Evaluations of state-of-the-art models reveal significant limitations: the strongest model (o3) achieves 79.2% and 78.5% accuracy on recognition and editing tasks, which are intuitively simple for humans, and performs even worse on the generation task, reaching only 29.0% accuracy. These results highlight the shortcomings of current AI systems in handling even preliminary molecular recognition and manipulation tasks. We hope MolLangBench will catalyze further research toward more effective and reliable AI systems for chemical applications.

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

The evaluation of English text embeddings has transitioned from evaluating a handful of datasets to broad coverage across many tasks through benchmarks such as MTEB. However, this is not the case for multilingual text embeddings due to a lack of available benchmarks. To address this problem, we introduce the Scandinavian Embedding Benchmark (SEB). SEB is a comprehensive framework that enables text embedding evaluation for Scandinavian languages across 24 tasks, 10 subtasks, and 4 task categories. Building on SEB, we evaluate more than 26 models, uncovering significant performance disparities between public and commercial solutions not previously captured by MTEB. We open-source SEB and integrate it with MTEB, thus bridging the text embedding evaluation gap for Scandinavian languages.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

This work introduces a benchmark assessing the performance of clustering German text embeddings in different domains. This benchmark is driven by the increasing use of clustering neural text embeddings in tasks that require the grouping of texts (such as topic modeling) and the need for German resources in existing benchmarks. We provide an initial analysis for a range of pre-trained mono- and multilingual models evaluated on the outcome of different clustering algorithms. Results include strong performing mono- and multilingual models. Reducing the dimensions of embeddings can further improve clustering. Additionally, we conduct experiments with continued pre-training for German BERT models to estimate the benefits of this additional training. Our experiments suggest that significant performance improvements are possible for short text. All code and datasets are publicly available.

This paper presents E5, a family of state-of-the-art text embeddings that transfer well to a wide range of tasks. The model is trained in a contrastive manner with weak supervision signals from our curated large-scale text pair dataset (called CCPairs). E5 can be readily used as a general-purpose embedding model for any tasks requiring a single-vector representation of texts such as retrieval, clustering, and classification, achieving strong performance in both zero-shot and fine-tuned settings. We conduct extensive evaluations on 56 datasets from the BEIR and MTEB benchmarks. For zero-shot settings, E5 is the first model that outperforms the strong BM25 baseline on the BEIR retrieval benchmark without using any labeled data. When fine-tuned, E5 obtains the best results on the MTEB benchmark, beating existing embedding models with 40x more parameters.

The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep learning framework that unifies molecule detection, reaction diagram parsing, and optical chemical structure recognition (OCSR) into a single pipeline for automating the extraction of chemical data directly from page-level documents. Recognizing the lack of a standard page-level benchmark and evaluation metric, we also present a testset of 550 pages annotated with molecule bounding boxes, reaction labels, and MOLfiles, along with a novel evaluation metric. Experimental results demonstrate that MolMole outperforms existing toolkits on both our benchmark and public datasets. The benchmark testset will be publicly available, and the MolMole toolkit will be accessible soon through an interactive demo on the LG AI Research website. For commercial inquiries, please contact us at mailto:contact_ddu@lgresearch.ai{contact\_ddu@lgresearch.ai}.

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

Chemical patent documents describe a broad range of applications holding key reaction and compound information, such as chemical structure, reaction formulas, and molecular properties. These informational entities should be first identified in text passages to be utilized in downstream tasks. Text mining provides means to extract relevant information from chemical patents through information extraction techniques. As part of the Information Extraction task of the Cheminformatics Elsevier Melbourne University challenge, in this work we study the effectiveness of contextualized language models to extract reaction information in chemical patents. We assess transformer architectures trained on a generic and specialised corpora to propose a new ensemble model. Our best model, based on a majority ensemble approach, achieves an exact F1-score of 92.30% and a relaxed F1-score of 96.24%. The results show that ensemble of contextualized language models can provide an effective method to extract information from chemical patents.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

We present MatSci-NLP, a natural language benchmark for evaluating the performance of natural language processing (NLP) models on materials science text. We construct the benchmark from publicly available materials science text data to encompass seven different NLP tasks, including conventional NLP tasks like named entity recognition and relation classification, as well as NLP tasks specific to materials science, such as synthesis action retrieval which relates to creating synthesis procedures for materials. We study various BERT-based models pretrained on different scientific text corpora on MatSci-NLP to understand the impact of pretraining strategies on understanding materials science text. Given the scarcity of high-quality annotated data in the materials science domain, we perform our fine-tuning experiments with limited training data to encourage the generalize across MatSci-NLP tasks. Our experiments in this low-resource training setting show that language models pretrained on scientific text outperform BERT trained on general text. MatBERT, a model pretrained specifically on materials science journals, generally performs best for most tasks. Moreover, we propose a unified text-to-schema for multitask learning on \benchmark and compare its performance with traditional fine-tuning methods. In our analysis of different training methods, we find that our proposed text-to-schema methods inspired by question-answering consistently outperform single and multitask NLP fine-tuning methods. The code and datasets are publicly available at https://github.com/BangLab-UdeM-Mila/NLP4MatSci-ACL23.

We introduce a novel suite of state-of-the-art bilingual text embedding models that are designed to support English and another target language. These models are capable of processing lengthy text inputs with up to 8192 tokens, making them highly versatile for a range of natural language processing tasks such as text retrieval, clustering, and semantic textual similarity (STS) calculations. By focusing on bilingual models and introducing a unique multi-task learning objective, we have significantly improved the model performance on STS tasks, which outperforms the capabilities of existing multilingual models in both target language understanding and cross-lingual evaluation tasks. Moreover, our bilingual models are more efficient, requiring fewer parameters and less memory due to their smaller vocabulary needs. Furthermore, we have expanded the Massive Text Embedding Benchmark (MTEB) to include benchmarks for German and Spanish embedding models. This integration aims to stimulate further research and advancement in text embedding technologies for these languages.

Image representations are often evaluated through disjointed, task-specific protocols, leading to a fragmented understanding of model capabilities. For instance, it is unclear whether an image embedding model adept at clustering images is equally good at retrieving relevant images given a piece of text. We introduce the Massive Image Embedding Benchmark (MIEB) to evaluate the performance of image and image-text embedding models across the broadest spectrum to date. MIEB spans 38 languages across 130 individual tasks, which we group into 8 high-level categories. We benchmark 50 models across our benchmark, finding that no single method dominates across all task categories. We reveal hidden capabilities in advanced vision models such as their accurate visual representation of texts, and their yet limited capabilities in interleaved encodings and matching images and texts in the presence of confounders. We also show that the performance of vision encoders on MIEB correlates highly with their performance when used in multimodal large language models. Our code, dataset, and leaderboard are publicly available at https://github.com/embeddings-benchmark/mteb.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address these issues, we introduce SUPERChem, a benchmark of 500 expert-curated reasoning-intensive chemistry problems, covering diverse subfields and provided in both multimodal and text-only formats. Original content and an iterative curation pipeline eliminate flawed items and mitigate data contamination. Each problem is paired with an expert-authored solution path, enabling Reasoning Path Fidelity (RPF) scoring to evaluate reasoning quality beyond final-answer accuracy. Evaluations against a human baseline of 40.3% accuracy show that even the best-performing model, GPT-5 (High), reaches only 38.5%, followed closely by Gemini 2.5 Pro (37.9%) and DeepSeek-V3.1-Think (37.3%). SUPERChem elicits multi-step, multimodal reasoning, reveals model-dependent effects of visual information, and distinguishes high-fidelity reasoners from heuristic ones. By providing a challenging benchmark and a reliable evaluation framework, SUPERChem aims to facilitate the advancement of LLMs toward expert-level chemical intelligence. The dataset of the benchmark is available at https://huggingface.co/datasets/ZehuaZhao/SUPERChem.

Recent information retrieval (IR) models are pre-trained and instruction-tuned on massive datasets and tasks, enabling them to perform well on a wide range of tasks and potentially generalize to unseen tasks with instructions. However, existing IR benchmarks focus on a limited scope of tasks, making them insufficient for evaluating the latest IR models. In this paper, we propose MAIR (Massive Instructed Retrieval Benchmark), a heterogeneous IR benchmark that includes 126 distinct IR tasks across 6 domains, collected from existing datasets. We benchmark state-of-the-art instruction-tuned text embedding models and re-ranking models. Our experiments reveal that instruction-tuned models generally achieve superior performance compared to non-instruction-tuned models on MAIR. Additionally, our results suggest that current instruction-tuned text embedding models and re-ranking models still lack effectiveness in specific long-tail tasks. MAIR is publicly available at https://github.com/sunnweiwei/Mair.

The contributions of model complexity, data volume, and feature modalities to knowledge graph-based drug repurposing remain poorly quantified under rigorous temporal validation. We constructed a pharmacology knowledge graph from ChEMBL 36 comprising 5,348 entities including 3,127 drugs, 1,156 proteins, and 1,065 indications. A strict temporal split was enforced with training data up to 2022 and testing data from 2023 to 2025, together with biologically verified hard negatives mined from failed assays and clinical trials. We benchmarked five knowledge graph embedding models and a standard graph neural network with 3.44 million parameters that incorporates drug chemical structure using a graph attention encoder and ESM-2 protein embeddings. Scaling experiments ranging from 0.78 to 9.75 million parameters and from 25 to 100 percent of the data, together with feature ablation studies, were used to isolate the contributions of model capacity, graph density, and node feature modalities. Removing the graph attention based drug structure encoder and retaining only topological embeddings combined with ESM-2 protein features improved drug protein PR-AUC from 0.5631 to 0.5785 while reducing VRAM usage from 5.30 GB to 353 MB. Replacing the drug encoder with Morgan fingerprints further degraded performance, indicating that explicit chemical structure representations can be detrimental for predicting pharmacological network interactions. Increasing model size beyond 2.44 million parameters yielded diminishing returns, whereas increasing training data consistently improved performance. External validation confirmed 6 of the top 14 novel predictions as established therapeutic indications. These results show that drug pharmacological behavior can be accurately predicted using target-centric information and drug network topology alone, without requiring explicit chemical structure representations.

Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds. However, the computational burden to develop and deploy state-of-the-art models continuously increases, limiting their scalability. Most large-scale models are unimodal in nature and overlook the potential to leverage complementary molecular data modalities. To address these shortcomings, this paper introduces the Graph-Language Alignment for Chemical Inference and Exploration using Representations (GLACIER) model, a student-teacher framework that integrates molecular graphs, SMILES strings, and physicochemical descriptors to learn rich molecular embeddings. Our framework consists of three stages: (1) we pretrain three student encoders on 100,000 drug-like molecules: a message-passing neural network for molecular graphs, a transformer-based encoder for SMILES strings, and a multilayer perceptron for physicochemical descriptors, (2) we fuse these student modalities using a novel Finsler geometry-aware module, and (3) distill complementary knowledge from large teacher models, including MiniMol and MolFormer, into a single lightweight model via contrastive learning. We demonstrate that GLACIER is a robust framework that delivers high predictive performance and computational efficiency in complex molecular property prediction tasks. Our code is publicly available at https://github.com/eemokey/glacier.

Portuguese remains underrepresented in text embedding evaluation, despite being one of the most widely spoken languages in the world. As a result, embedding models are often selected based on English or multilingual metrics, while their effectiveness in Portuguese remains unclear. We present MTEB-PT, a Portuguese benchmark constructed from a subset of MMTEB, comprising 14 existing datasets across Semantic Textual Similarity (STS), classification, retrieval, and reranking. We use this benchmark to evaluate 17 open- and closed-source embedding models under a unified protocol. Our results show that Portuguese performance is strongly task-dependent: multilingual rankings do not reliably predict Portuguese-specific performance across task families, no single model dominates all settings, and models with stronger long-context capacity are particularly advantageous on longer-input tasks such as retrieval and reranking. The benchmark also shows that language-specific fine-tuning still improves model performance in Portuguese, especially on task types that match the adaptation data most closely. To examine this effect, we fine-tune three representative backbone models with Portuguese contrastive supervision and Matryoshka Representation Learning (MRL). These benchmark-informed baselines yield their strongest gains on STS, consistent with the predominantly symmetric supervision used during training, while also improving retrieval and remaining competitive under dimensional truncation. We release the MTEB-PT benchmark, the fine-tuned models, and the training and evaluation code.

In this paper, we propose Text-based Open Molecule Generation Benchmark (TOMG-Bench), the first benchmark to evaluate the open-domain molecule generation capability of LLMs. TOMG-Bench encompasses a dataset of three major tasks: molecule editing (MolEdit), molecule optimization (MolOpt), and customized molecule generation (MolCustom). Each task further contains three subtasks, with each subtask comprising 5,000 test samples. Given the inherent complexity of open molecule generation, we have also developed an automated evaluation system that helps measure both the quality and the accuracy of the generated molecules. Our comprehensive benchmarking of 25 LLMs reveals the current limitations and potential areas for improvement in text-guided molecule discovery. Furthermore, with the assistance of OpenMolIns, a specialized instruction tuning dataset proposed for solving challenges raised by TOMG-Bench, Llama3.1-8B could outperform all the open-source general LLMs, even surpassing GPT-3.5-turbo by 46.5\% on TOMG-Bench. Our codes and datasets are available through https://github.com/phenixace/TOMG-Bench.

We introduce SkMTEB, the first comprehensive MTEB-style text embedding benchmark for Slovak, a low-resource West Slavic language, comprising 31 datasets across 7 task types -- nearly 4times the depth of existing multilingual benchmark coverage for Slovak. Our evaluation of 31 embedding models reveals that large instruction-tuned multilingual models achieve the strongest performance, while existing Slovak-specific models trained for NLU tasks transfer poorly to embedding tasks. To address the need for efficient, locally-deployable Slovak embeddings, we develop e5-sk-small (45M parameters) and e5-sk-large (365M) by applying vocabulary trimming and fine-tuning to Multilingual E5 models. Despite size reductions of up to 62\%, our open-source models achieve competitive performance with proprietary APIs while remaining locally deployable for semantic search and retrieval-augmented generation (RAG). We release the benchmark, models, datasets, and code openly, hoping our approach offers a replicable path for other under-resourced languages.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

Developing improved predictive models for multi-molecular systems is crucial, as nearly every chemical product used results from a mixture of chemicals. While being a vital part of the industry pipeline, the chemical mixture space remains relatively unexplored by the Machine Learning community. In this paper, we introduce CheMixHub, a holistic benchmark for molecular mixtures, covering a corpus of 11 chemical mixtures property prediction tasks, from drug delivery formulations to battery electrolytes, totalling approximately 500k data points gathered and curated from 7 publicly available datasets. CheMixHub introduces various data splitting techniques to assess context-specific generalization and model robustness, providing a foundation for the development of predictive models for chemical mixture properties. Furthermore, we map out the modelling space of deep learning models for chemical mixtures, establishing initial benchmarks for the community. This dataset has the potential to accelerate chemical mixture development, encompassing reformulation, optimization, and discovery. The dataset and code for the benchmarks can be found at: https://github.com/chemcognition-lab/chemixhub

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Foundation models have established unified representations for natural language processing, yet this paradigm remains largely unexplored for tabular data. Existing methods face fundamental limitations: LLM-based approaches lack retrieval-compatible vector outputs, whereas text embedding models often fail to capture tabular structure and numerical semantics. To bridge this gap, we first introduce the Tabular Embedding Benchmark (TabBench), a comprehensive suite designed to evaluate the tabular understanding capability of embedding models. We then propose TabEmbed, the first generalist embedding model that unifies tabular classification and retrieval within a shared embedding space. By reformulating diverse tabular tasks as semantic matching problems, TabEmbed leverages large-scale contrastive learning with positive-aware hard negative mining to discern fine-grained structural and numerical nuances. Experimental results on TabBench demonstrate that TabEmbed significantly outperforms state-of-the-art text embedding models, establishing a new baseline for universal tabular representation learning. Code and datasets are publicly available at https://github.com/qiangminjie27/TabEmbed and https://huggingface.co/datasets/qiangminjie27/TabBench.

We introduce EmbeddingGemma, a new lightweight, open text embedding model based on the Gemma 3 language model family. Our innovative training recipe strategically captures knowledge from larger models via encoder-decoder initialization and geometric embedding distillation. We improve model robustness and expressiveness with a spread-out regularizer, and ensure generalizability by merging checkpoints from varied, optimized mixtures. Evaluated on the Massive Text Embedding Benchmark (MTEB) across multilingual, English, and code domains, EmbeddingGemma (300M) achieves state-of-the-art results. Notably, it outperforms prior top models, both proprietary and open, with fewer than 500M parameters, and provides performance comparable to models double its size, offering an exceptional performance-to-cost ratio. Remarkably, this lead persists when quantizing model weights or truncating embedding outputs. This makes EmbeddingGemma particularly well-suited for low-latency and high-throughput use cases such as on-device applications. We provide ablation studies exploring our key design choices. We release EmbeddingGemma to the community to promote further research.

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

Text embeddings are vital for tasks such as text retrieval and semantic textual similarity (STS). Recently, the advent of pretrained language models, along with unified benchmarks like the Massive Text Embedding Benchmark (MTEB), has facilitated the development of versatile general-purpose text embedding models. Advanced embedding models are typically developed using large-scale multi-task data and joint training across multiple tasks. However, our experimental analysis reveals two significant drawbacks of joint training: 1) Task Conflict: Gradients from different tasks interfere with each other, leading to negative transfer. 2) Data Imbalance: Disproportionate data distribution introduces biases that negatively impact performance across tasks. To overcome these challenges, we explore model merging-a technique that combines independently trained models to mitigate gradient conflicts and balance data distribution. We introduce a novel method, Self Positioning, which efficiently searches for optimal model combinations within the interpolation space of task vectors using stochastic gradient descent. Our experiments demonstrate that Self Positioning significantly enhances multi-task performance on the MTEB dataset, achieving an absolute improvement of 0.7 points. It outperforms traditional resampling methods while reducing computational costs. This work offers a robust approach to building generalized text embedding models with superior performance across diverse embedding-related tasks.

Recently, embedding resources, including models, benchmarks, and datasets, have been widely released to support a variety of languages. However, the Dutch language remains underrepresented, typically comprising only a small fraction of the published multilingual resources. To address this gap and encourage the further development of Dutch embeddings, we introduce new resources for their evaluation and generation. First, we introduce the Massive Text Embedding Benchmark for Dutch (MTEB-NL), which includes both existing Dutch datasets and newly created ones, covering a wide range of tasks. Second, we provide a training dataset compiled from available Dutch retrieval datasets, complemented with synthetic data generated by large language models to expand task coverage beyond retrieval. Finally, we release a series of E5-NL models compact yet efficient embedding models that demonstrate strong performance across multiple tasks. We make our resources publicly available through the Hugging Face Hub and the MTEB package.

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.

Text embedding models serve as a fundamental component in real-world search applications. By mapping queries and documents into a shared embedding space, they deliver competitive retrieval performance with high efficiency. However, their ranking fidelity remains limited compared to dedicated rerankers, especially recent LLM-based listwise rerankers, which capture fine-grained query-document and document-document interactions. In this paper, we propose a simple yet effective unified framework E^2Rank, means Efficient Embedding-based Ranking (also means Embedding-to-Rank), which extends a single text embedding model to perform both high-quality retrieval and listwise reranking through continued training under a listwise ranking objective, thereby achieving strong effectiveness with remarkable efficiency. By applying cosine similarity between the query and document embeddings as a unified ranking function, the listwise ranking prompt, which is constructed from the original query and its candidate documents, serves as an enhanced query enriched with signals from the top-K documents, akin to pseudo-relevance feedback (PRF) in traditional retrieval models. This design preserves the efficiency and representational quality of the base embedding model while significantly improving its reranking performance. Empirically, E^2Rank achieves state-of-the-art results on the BEIR reranking benchmark and demonstrates competitive performance on the reasoning-intensive BRIGHT benchmark, with very low reranking latency. We also show that the ranking training process improves embedding performance on the MTEB benchmark. Our findings indicate that a single embedding model can effectively unify retrieval and reranking, offering both computational efficiency and competitive ranking accuracy.

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

Text embedding models are widely used for semantic similarity tasks, including information retrieval, clustering, and classification. General-purpose models are typically trained with single- or multi-stage processes using contrastive loss functions. We introduce a novel training regimen that combines model distillation techniques with task-specific contrastive loss to produce compact, high-performance embedding models. Our findings suggest that this approach is more effective for training small models than purely contrastive or distillation-based training paradigms alone. Benchmark scores for the resulting models, jina-embeddings-v5-text-small and jina-embeddings-v5-text-nano, exceed or match the state-of-the-art for models of similar size. jina-embeddings-v5-text models additionally support long texts (up to 32k tokens) in many languages, and generate embeddings that remain robust under truncation and binary quantization. Model weights are publicly available, hopefully inspiring further advances in embedding model development.

We present Gecko, a compact and versatile text embedding model. Gecko achieves strong retrieval performance by leveraging a key idea: distilling knowledge from large language models (LLMs) into a retriever. Our two-step distillation process begins with generating diverse, synthetic paired data using an LLM. Next, we further refine the data quality by retrieving a set of candidate passages for each query, and relabeling the positive and hard negative passages using the same LLM. The effectiveness of our approach is demonstrated by the compactness of the Gecko. On the Massive Text Embedding Benchmark (MTEB), Gecko with 256 embedding dimensions outperforms all existing entries with 768 embedding size. Gecko with 768 embedding dimensions achieves an average score of 66.31, competing with 7x larger models and 5x higher dimensional embeddings.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

A limitation of modern document retrieval embedding methods is that they typically encode passages (chunks) from the same documents independently, often overlooking crucial contextual information from the rest of the document that could greatly improve individual chunk representations. In this work, we introduce ConTEB (Context-aware Text Embedding Benchmark), a benchmark designed to evaluate retrieval models on their ability to leverage document-wide context. Our results show that state-of-the-art embedding models struggle in retrieval scenarios where context is required. To address this limitation, we propose InSeNT (In-sequence Negative Training), a novel contrastive post-training approach which combined with late chunking pooling enhances contextual representation learning while preserving computational efficiency. Our method significantly improves retrieval quality on ConTEB without sacrificing base model performance. We further find chunks embedded with our method are more robust to suboptimal chunking strategies and larger retrieval corpus sizes. We open-source all artifacts at https://github.com/illuin-tech/contextual-embeddings.

Dense document embeddings are central to neural retrieval. The dominant paradigm is to train and construct embeddings by running encoders directly on individual documents. In this work, we argue that these embeddings, while effective, are implicitly out-of-context for targeted use cases of retrieval, and that a contextualized document embedding should take into account both the document and neighboring documents in context - analogous to contextualized word embeddings. We propose two complementary methods for contextualized document embeddings: first, an alternative contrastive learning objective that explicitly incorporates the document neighbors into the intra-batch contextual loss; second, a new contextual architecture that explicitly encodes neighbor document information into the encoded representation. Results show that both methods achieve better performance than biencoders in several settings, with differences especially pronounced out-of-domain. We achieve state-of-the-art results on the MTEB benchmark with no hard negative mining, score distillation, dataset-specific instructions, intra-GPU example-sharing, or extremely large batch sizes. Our method can be applied to improve performance on any contrastive learning dataset and any biencoder.

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in molecular chemistry. This study presents the most extensive comparison of such models to date, evaluating 25 models across 25 datasets. Under a fair comparison framework, we assess models spanning various modalities, architectures, and pretraining strategies. Using a dedicated hierarchical Bayesian statistical testing model, we arrive at a surprising result: nearly all neural models show negligible or no improvement over the baseline ECFP molecular fingerprint. Only the CLAMP model, which is also based on molecular fingerprints, performs statistically significantly better than the alternatives. These findings raise concerns about the evaluation rigor in existing studies. We discuss potential causes, propose solutions, and offer practical recommendations.

Text-based foundation models have become an important part of scientific discovery, with molecular foundation models accelerating advancements in material science and molecular design.However, existing models are constrained by closed-vocabulary tokenizers that capture only a fraction of molecular space. In this work, we systematically evaluate 34 tokenizers, including 19 chemistry-specific ones, and reveal significant gaps in their coverage of the SMILES molecular representation. To assess the impact of tokenizer choice, we introduce n-gram language models as a low-cost proxy and validate their effectiveness by pretraining and finetuning 18 RoBERTa-style encoders for molecular property prediction. To overcome the limitations of existing tokenizers, we propose two new tokenizers -- Smirk and Smirk-GPE -- with full coverage of the OpenSMILES specification. The proposed tokenizers systematically integrate nuclear, electronic, and geometric degrees of freedom; facilitating applications in pharmacology, agriculture, biology, and energy storage. Our results highlight the need for open-vocabulary modeling and chemically diverse benchmarks in cheminformatics.

Large-scale chemical reaction datasets are crucial for AI research in chemistry. However, existing chemical reaction data often exist as images within papers, making them not machine-readable and unusable for training machine learning models. In response to this challenge, we propose the RxnCaption framework for the task of chemical Reaction Diagram Parsing (RxnDP). Our framework reformulates the traditional coordinate prediction driven parsing process into an image captioning problem, which Large Vision Language Models (LVLMs) handle naturally. We introduce a strategy termed BBox and Index as Visual Prompt (BIVP), which uses our state-of-the-art molecular detector, MolYOLO, to pre-draw molecular bounding boxes and indices directly onto the input image. This turns the downstream parsing into a natural-language description problem. Extensive experiments show that the BIVP strategy significantly improves structural extraction quality while simplifying model design. We further construct the RxnCaption-15k dataset, an order of magnitude larger than prior real-world literature benchmarks, with a balanced test subset across four layout archetypes. Experiments demonstrate that RxnCaption-VL achieves state-of-the-art performance on multiple metrics. We believe our method, dataset, and models will advance structured information extraction from chemical literature and catalyze broader AI applications in chemistry. We will release data, models, and code on GitHub.

Multimodal retrieval is becoming a crucial component of modern AI applications, yet its evaluation lags behind the demands of more realistic and challenging scenarios. Existing benchmarks primarily probe surface-level semantic correspondence (e.g., object-text matching) while failing to assess the deeper reasoning required to capture complex relationships between visual and textual information. To address this gap, we introduce MR^2-Bench, a reasoning-intensive benchmark for multimodal retrieval. MR^2-Bench presents the following critical values: 1) all tasks are reasoning-driven, going beyond shallow matching to effectively assess models' capacity for logical, spatial, and causal inference; 2) it features diverse multimodal data, such as natural images, diagrams, and visual puzzles, enabling comprehensive evaluation across content types; 3) it supports complex queries and documents containing multiple images and covers diverse retrieval scenarios, more accurately reflecting real-world applications. Our benchmark contains 1,309 curated queries, derived either from manual collection and annotation or from selective consolidation of public datasets. Despite achieving strong results on existing benchmarks, current state-of-the-art models still struggle on MR^2-Bench: for example, the leading Seed1.6-Embedding model attains a Recall@1 of 77.78 on MMEB, but only 9.91 on MR^2-Bench. This substantial performance gap highlights both the increased challenge posed by our benchmark and the pressing need for further advances in reasoning-intensive multimodal retrieval. The dataset and evaluation code will be made publicly available at https://github.com/VectorSpaceLab/MR2-Bench.

GNNs and chemical fingerprints are the predominant approaches to representing molecules for property prediction. However, in NLP, transformers have become the de-facto standard for representation learning thanks to their strong downstream task transfer. In parallel, the software ecosystem around transformers is maturing rapidly, with libraries like HuggingFace and BertViz enabling streamlined training and introspection. In this work, we make one of the first attempts to systematically evaluate transformers on molecular property prediction tasks via our ChemBERTa model. ChemBERTa scales well with pretraining dataset size, offering competitive downstream performance on MoleculeNet and useful attention-based visualization modalities. Our results suggest that transformers offer a promising avenue of future work for molecular representation learning and property prediction. To facilitate these efforts, we release a curated dataset of 77M SMILES from PubChem suitable for large-scale self-supervised pretraining.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

We introduce llama-embed-nemotron-8b, an open-weights text embedding model that achieves state-of-the-art performance on the Multilingual Massive Text Embedding Benchmark (MMTEB) leaderboard as of October 21, 2025. While recent models show strong performance, their training data or methodologies are often not fully disclosed. We aim to address this by developing a fully open-source model, publicly releasing its weights and detailed ablation studies, and planning to share the curated training datasets. Our model demonstrates superior performance across all major embedding tasks -- including retrieval, classification and semantic textual similarity (STS) -- and excels in challenging multilingual scenarios, such as low-resource languages and cross-lingual setups. This state-of-the-art performance is driven by a novel data mix of 16.1 million query-document pairs, split between 7.7 million samples from public datasets and 8.4 million synthetically generated examples from various open-weight LLMs. One of our key contributions is a detailed ablation study analyzing core design choices, including a comparison of contrastive loss implementations, an evaluation of synthetic data generation (SDG) strategies, and the impact of model merging. The llama-embed-nemotron-8b is an instruction-aware model, supporting user-defined instructions to enhance performance for specific use-cases. This combination of top-tier performance, broad applicability, and user-driven flexibility enables it to serve as a universal text embedding solution.

Vector embeddings have been tasked with an ever-increasing set of retrieval tasks over the years, with a nascent rise in using them for reasoning, instruction-following, coding, and more. These new benchmarks push embeddings to work for any query and any notion of relevance that could be given. While prior works have pointed out theoretical limitations of vector embeddings, there is a common assumption that these difficulties are exclusively due to unrealistic queries, and those that are not can be overcome with better training data and larger models. In this work, we demonstrate that we may encounter these theoretical limitations in realistic settings with extremely simple queries. We connect known results in learning theory, showing that the number of top-k subsets of documents capable of being returned as the result of some query is limited by the dimension of the embedding. We empirically show that this holds true even if we restrict to k=2, and directly optimize on the test set with free parameterized embeddings. We then create a realistic dataset called LIMIT that stress tests models based on these theoretical results, and observe that even state-of-the-art models fail on this dataset despite the simple nature of the task. Our work shows the limits of embedding models under the existing single vector paradigm and calls for future research to develop methods that can resolve this fundamental limitation.

Learnable embedding vector is one of the most important applications in machine learning, and is widely used in various database-related domains. However, the high dimensionality of sparse data in recommendation tasks and the huge volume of corpus in retrieval-related tasks lead to a large memory consumption of the embedding table, which poses a great challenge to the training and deployment of models. Recent research has proposed various methods to compress the embeddings at the cost of a slight decrease in model quality or the introduction of other overheads. Nevertheless, the relative performance of these methods remains unclear. Existing experimental comparisons only cover a subset of these methods and focus on limited metrics. In this paper, we perform a comprehensive comparative analysis and experimental evaluation of embedding compression. We introduce a new taxonomy that categorizes these techniques based on their characteristics and methodologies, and further develop a modular benchmarking framework that integrates 14 representative methods. Under a uniform test environment, our benchmark fairly evaluates each approach, presents their strengths and weaknesses under different memory budgets, and recommends the best method based on the use case. In addition to providing useful guidelines, our study also uncovers the limitations of current methods and suggests potential directions for future research.

Optical chemical structure recognition (OCSR) translates molecular images into machine-readable representations like SMILES strings or molecular graphs, but remains challenging in real-world documents due to inexhaustible variations in chemical structures, shorthand conventions, and visual noise. Most existing deep-learning-based approaches rely on teacher forcing with token-level Maximum Likelihood Estimation (MLE). This training paradigm suffers from exposure bias, as models are trained under ground-truth prefixes but must condition on their own previous predictions during inference. Moreover, token-level MLE objectives hinder the optimization towards molecular-level evaluation criteria such as chemical validity and structural similarity. Here we introduce Minimum Risk Training (MRT) to OCSR and propose COMO (Closed-loop Optical Molecule recOgnition), a closed-loop framework that mitigates exposure bias by directly optimizing over molecule-level, non-differentiable objectives, by iteratively sampling and evaluating the model's own predictions. Experiments on ten benchmarks including synthetic and real-world chemical diagrams from patent and scientific literature demonstrate that COMO substantially outperforms existing rule-based and learning-based methods with less training data. Ablation studies further show that MRT is architecture-agnostic, demonstrating its potential for broad application to end-to-end OCSR systems.

Prompt-based text embedding models, which generate task-specific embeddings upon receiving tailored prompts, have recently demonstrated remarkable performance. However, their resulting embeddings often have thousands of dimensions, leading to high storage costs and increased computational costs of embedding-based operations. In this paper, we investigate how post-hoc dimensionality reduction applied to the embeddings affects the performance of various tasks that leverage these embeddings, specifically classification, clustering, retrieval, and semantic textual similarity (STS) tasks. Our experiments show that even a naive dimensionality reduction, which keeps only the first 25% of the dimensions of the embeddings, results in a very slight performance degradation, indicating that these embeddings are highly redundant. Notably, for classification and clustering, even when embeddings are reduced to less than 0.5% of the original dimensionality the performance degradation is very small. To quantitatively analyze this redundancy, we perform an analysis based on the intrinsic dimensionality and isotropy of the embeddings. Our analysis reveals that embeddings for classification and clustering, which are considered to have very high dimensional redundancy, exhibit lower intrinsic dimensionality and less isotropy compared with those for retrieval and STS.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

AI systems have achieved remarkable success in processing text and relational data, yet visual document processing remains relatively underexplored. Whereas traditional systems require OCR transcriptions to convert these visual documents into text and metadata, recent advances in multimodal foundation models offer retrieval and generation directly from document images. This raises a key question: How do image-based systems compare to established text-based methods? We introduce IRPAPERS, a benchmark of 3,230 pages from 166 scientific papers, with both an image and an OCR transcription for each page. Using 180 needle-in-the-haystack questions, we compare image- and text-based retrieval and question answering systems. Text retrieval using Arctic 2.0 embeddings, BM25, and hybrid text search achieved 46% Recall@1, 78% Recall@5, and 91% Recall@20, while image-based retrieval reaches 43%, 78%, and 93%, respectively. The two modalities exhibit complementary failures, enabling multimodal hybrid search to outperform either alone, achieving 49% Recall@1, 81% Recall@5, and 95% Recall@20. We further evaluate efficiency-performance tradeoffs with MUVERA and assess multiple multi-vector image embedding models. Among closed-source models, Cohere Embed v4 page image embeddings outperform Voyage 3 Large text embeddings and all tested open-source models, achieving 58% Recall@1, 87% Recall@5, and 97% Recall@20. For question answering, text-based RAG systems achieved higher ground-truth alignment than image-based systems (0.82 vs. 0.71), and both benefit substantially from increased retrieval depth, with multi-document retrieval outperforming oracle single-document retrieval. We analyze the complementary limitations of unimodal text and image representations and identify question types that require one modality over the other. The IRPAPERS dataset and all experimental code are publicly available.

In this work, we aim to connect two research areas: instruction models and retrieval-based models. While instruction-tuned Large Language Models (LLMs) excel at extracting information from text, they are not suitable for semantic retrieval. Similarity search over embedding vectors allows to index and query vectors, but the similarity reflected in the embedding is sub-optimal for many use cases. We identify the task of retrieving sentences based on abstract descriptions of their content. We demonstrate the inadequacy of current text embeddings and propose an alternative model that significantly improves when used in standard nearest neighbor search. The model is trained using positive and negative pairs sourced through prompting an a large language model (LLM). While it is easy to source the training material from an LLM, the retrieval task cannot be performed by the LLM directly. This demonstrates that data from LLMs can be used not only for distilling more efficient specialized models than the original LLM, but also for creating new capabilities not immediately possible using the original model.

Chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) in natural language to perform complex reasoning. However, chemical reasoning is inherently continuous and structural, and forcing it into discrete linguistic tokens introduces a fundamental representation mismatch that constrains both efficiency and performance. We introduce LatentChem, a latent reasoning interface that decouples chemical computation from textual generation, enabling models to perform multi-step reasoning directly in continuous latent space while emitting language only for final outputs. Remarkably, we observe a consistent emergent behavior: when optimized solely for task success, models spontaneously internalize reasoning, progressively abandoning verbose textual derivations in favor of implicit latent computation. This shift is not merely stylistic but computationally advantageous. Across diverse chemical reasoning benchmarks, LatentChem achieves a 59.88\% non-tie win rate over strong CoT-based baselines on ChemCoTBench, while delivering a 10.84times average inference speedup. Our results provide empirical evidence that chemical reasoning is more naturally and effectively realized as continuous latent dynamics rather than discretized linguistic trajectories.

We consider the problem of producing compact architectures for text classification, such that the full model fits in a limited amount of memory. After considering different solutions inspired by the hashing literature, we propose a method built upon product quantization to store word embeddings. While the original technique leads to a loss in accuracy, we adapt this method to circumvent quantization artefacts. Our experiments carried out on several benchmarks show that our approach typically requires two orders of magnitude less memory than fastText while being only slightly inferior with respect to accuracy. As a result, it outperforms the state of the art by a good margin in terms of the compromise between memory usage and accuracy.

We present MolT5 - a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. MolT5 allows for new, useful, and challenging analogs of traditional vision-language tasks, such as molecule captioning and text-based de novo molecule generation (altogether: translation between molecules and language), which we explore for the first time. Since MolT5 pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Furthermore, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. Our results show that MolT5-based models are able to generate outputs, both molecules and captions, which in many cases are high quality.

We present QZhou-Embedding, a general-purpose contextual text embedding model with exceptional text representation capabilities. Built upon the Qwen2.5-7B-Instruct foundation model, we designed a unified multi-task framework comprising specialized data transformation and training strategies. The data transformation scheme enables the incorporation of more diverse textual training datasets, while the task-specific training strategies enhance model learning efficiency. We developed a data synthesis pipeline leveraging LLM API, incorporating techniques such as paraphrasing, augmentation, and hard negative example generation to improve the semantic richness and sample difficulty of the training set. Additionally, we employ a two-stage training strategy, comprising initial retrieval-focused pretraining followed by full-task fine-tuning, enabling the embedding model to extend its capabilities based on robust retrieval performance. Our model achieves state-of-the-art results on the MTEB and CMTEB benchmarks, ranking first on both leaderboards (August 27 2025), and simultaneously achieves state-of-the-art performance on tasks including reranking, clustering, etc. Our findings demonstrate that higher-quality, more diverse data is crucial for advancing retrieval model performance, and that leveraging LLMs generative capabilities can further optimize data quality for embedding model breakthroughs. Our model weights are released on HuggingFace under Apache 2.0 license. For reproducibility, we provide evaluation code and instructions on GitHub.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

The peer review process is crucial for ensuring the quality and reliability of scholarly work, yet assigning suitable reviewers remains a significant challenge. Traditional manual methods are labor-intensive and often ineffective, leading to nonconstructive or biased reviews. This paper introduces the exHarmony (eHarmony but for connecting experts to manuscripts) benchmark, designed to address these challenges by re-imagining the Reviewer Assignment Problem (RAP) as a retrieval task. Utilizing the extensive data from OpenAlex, we propose a novel approach that considers a host of signals from the authors, most similar experts, and the citation relations as potential indicators for a suitable reviewer for a manuscript. This approach allows us to develop a standard benchmark dataset for evaluating the reviewer assignment problem without needing explicit labels. We benchmark various methods, including traditional lexical matching, static neural embeddings, and contextualized neural embeddings, and introduce evaluation metrics that assess both relevance and diversity in the context of RAP. Our results indicate that while traditional methods perform reasonably well, contextualized embeddings trained on scholarly literature show the best performance. The findings underscore the importance of further research to enhance the diversity and effectiveness of reviewer assignments.

There has been rapid growth in biomedical literature, yet capturing the heterogeneity of the bibliographic information of these articles remains relatively understudied. Although graph mining research via heterogeneous graph neural networks has taken center stage, it remains unclear whether these approaches capture the heterogeneity of the PubMed database, a vast digital repository containing over 33 million articles. We introduce PubMed Graph Benchmark (PGB), a new benchmark dataset for evaluating heterogeneous graph embeddings for biomedical literature. The benchmark contains rich metadata including abstract, authors, citations, MeSH terms, MeSH hierarchy, and some other information. The benchmark contains three different evaluation tasks encompassing systematic reviews, node classification, and node clustering. In PGB, we aggregate the metadata associated with the biomedical articles from PubMed into a unified source and make the benchmark publicly available for any future works.

In this paper, we propose KaLM-Embedding-V2, a versatile and compact embedding model, which achieves impressive performance in general-purpose text embedding tasks by leveraging superior training techniques and data. Our key innovations include: (1) To better align the architecture with representation learning, we remove the causal attention mask and adopt a fully bidirectional transformer with simple yet effective mean-pooling to produce fixed-length embeddings; (2) We employ a multi-stage training pipeline: (i) pre-training on large-scale weakly supervised open-source corpora; (ii) fine-tuning on high-quality retrieval and non-retrieval datasets; and (iii) model-soup parameter averaging for robust generalization. Besides, we introduce a focal-style reweighting mechanism that concentrates learning on difficult samples and an online hard-negative mixing strategy to continuously enrich hard negatives without expensive offline mining; (3) We collect over 20 categories of data for pre-training and 100 categories of data for fine-tuning, to boost both the performance and generalization of the embedding model. Extensive evaluations on the Massive Text Embedding Benchmark (MTEB) Chinese and English show that our model significantly outperforms others of comparable size, and competes with 3x, 14x, 18x, and 26x larger embedding models, setting a new standard for a versatile and compact embedding model with less than 1B parameters.

Low-resource languages (LRLs) often lack high-quality, large-scale datasets for training effective text embedding models, hindering their application in tasks like retrieval-augmented generation (RAG) and semantic search. In this work, we challenge the prevailing assumption that effective semantic alignment requires massive datasets or pristine, human-verified translations. Focusing on Armenian (an LRL with a unique script), we introduce a cost-effective adaptation strategy using small scale noisy synthetic data generated by translating English Reddit title-body pairs with open-weights models. We establish a comprehensive evaluation benchmark comprising existing datasets, translated data, and a manually curated dataset. Our experiments reveal a surprising "Less is More" phenomenon: fine-tuning a multilingual encoder (mE5) on just 10,000 noisy synthetic pairs yields 11-12\% average improvements across the benchmark with a 20\%+ relative improvement in retrieval performance, matching the performance of models trained on ~1 million examples. Furthermore, we demonstrate that neither increasing data scale, improving translation quality via state-of-the-art LLMs, nor diversifying data domains yields significant gains over this minimal baseline. We validate the generalizability of these findings on another LRL with a unique script. Our results suggest that semantic alignment for LRLs saturates early and is highly robust to noise, democratizing high-performance embedding creation for resource-constrained communities. We release the model, data, and the benchmark at https://metric-ai-lab.github.io/less-is-more-embeddings/ to facilitate further research.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

In this report, we introduce pplx-embed, a family of multilingual embedding models that employ multi-stage contrastive learning on a diffusion-pretrained language model backbone for web-scale retrieval. By leveraging bidirectional attention through diffusion-based pretraining, our models capture comprehensive bidirectional context within passages, enabling the use of mean pooling and a late chunking strategy to better preserve global context across long documents. We release two model types: pplx-embed-v1 for standard retrieval, and pplx-embed-context-v1 for contextualized embeddings that incorporate global document context into passage representations. pplx-embed-v1 achieves competitive performance on the MTEB(Multilingual, v2), MTEB(Code), MIRACL, BERGEN, and ToolRet retrieval benchmarks, while pplx-embed-context-v1 sets new records on the ConTEB benchmark. Beyond public benchmarks, pplx-embed-v1 demonstrates strong performance on our internal evaluation suite, which focuses on real-world, large-scale search scenarios over tens of millions of documents. These results validate the models' effectiveness in production environments where retrieval quality and efficiency are critical at scale.

High-throughput reaction condition (RC) screening is fundamental to chemical synthesis. However, current RC screening suffers from laborious and costly trial-and-error workflows. Traditional computer-aided synthesis planning (CASP) tools fail to find suitable RCs due to data sparsity and inadequate reaction representations. Nowadays, large language models (LLMs) are capable of tackling chemistry-related problems, such as molecule design, and chemical logic Q\&A tasks. However, LLMs have not yet achieved accurate predictions of chemical reaction conditions. Here, we present MM-RCR, a text-augmented multimodal LLM that learns a unified reaction representation from SMILES, reaction graphs, and textual corpus for chemical reaction recommendation (RCR). To train MM-RCR, we construct 1.2 million pair-wised Q\&A instruction datasets. Our experimental results demonstrate that MM-RCR achieves state-of-the-art performance on two open benchmark datasets and exhibits strong generalization capabilities on out-of-domain (OOD) and High-Throughput Experimentation (HTE) datasets. MM-RCR has the potential to accelerate high-throughput condition screening in chemical synthesis.

Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may output the correct molecule, product, or option while its reasoning violates chemical logic. Existing process-level evaluators are hard to scale because LLM judges and human step-level process annotation are costly, inconsistent, and vulnerable to hallucination. We introduce ChemCoTBench-V2, a rule-verifiable diagnostic benchmark for low-cost, auditable evaluation of structured, verifier-addressable chemical reasoning traces. It spans molecular understanding, molecule editing, molecular optimization, and reaction prediction, with 5,620 evaluation samples across 18 reporting tasks. Models must expose key intermediate steps in expert-designed templates, and those steps are checked with deterministic chemistry rules and, for closed-answer tasks, reference traces rather than another LLM judge. Open-ended molecular optimization is evaluated with oracle-verifiable state constraints rather than strict trace matching. The benchmark reports three separate signals: final-answer correctness, template adherence, and step-wise verifier correctness over expert-refined intermediate commitments. Experiments on frontier models reveal a persistent gap between final-answer success and structured-reasoning-state consistency: models often follow the requested format while failing chemical-step checks, or answer correctly with weak supporting reasoning. ChemCoTBench-V2 enables fine-grained model comparison and identifies the concrete step at which the trace first violates the verifier.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

Vietnam ranks among the top countries in terms of both internet traffic and online toxicity. As a result, implementing embedding models for recommendation and content control duties in applications is crucial. However, a lack of large-scale test datasets, both in volume and task diversity, makes it tricky for scientists to effectively evaluate AI models before deploying them in real-world, large-scale projects. To solve this important problem, we introduce a Vietnamese benchmark, VN-MTEB for embedding models, which we created by translating a large number of English samples from the Massive Text Embedding Benchmark using our new automated framework. We leverage the strengths of large language models (LLMs) and cutting-edge embedding models to conduct translation and filtering processes to retain high-quality samples, guaranteeing a natural flow of language and semantic fidelity while preserving named entity recognition (NER) and code snippets. Our comprehensive benchmark consists of 41 datasets from six tasks specifically designed for Vietnamese text embeddings. In our analysis, we find that bigger and more complex models using Rotary Positional Embedding outperform those using Absolute Positional Embedding in embedding tasks. Datasets are available at HuggingFace: https://huggingface.co/collections/GreenNode/vn-mteb-68871433f0f7573b8e1a6686

We introduce JFinTEB, the first comprehensive benchmark specifically designed for evaluating Japanese financial text embeddings. Existing embedding benchmarks provide limited coverage of language-specific and domain-specific aspects found in Japanese financial texts. Our benchmark encompasses diverse task categories including retrieval and classification tasks that reflect realistic and well-defined financial text processing scenarios. The retrieval tasks leverage instruction-following datasets and financial text generation queries, while classification tasks cover sentiment analysis, document categorization, and domain-specific classification challenges derived from economic survey data. We conduct extensive evaluations across a wide range of embedding models, including Japanese-specific models of various sizes, multilingual models, and commercial embedding services. We publicly release JFinTEB datasets and evaluation framework at https://github.com/retarfi/JFinTEB to facilitate future research and provide a standardized evaluation protocol for the Japanese financial text mining community. This work addresses a critical gap in Japanese financial text processing resources and establishes a foundation for advancing domain-specific embedding research.

Answering real-world user queries, such as product search, often requires accurate retrieval of information from semi-structured knowledge bases or databases that involve blend of unstructured (e.g., textual descriptions of products) and structured (e.g., entity relations of products) information. However, previous works have mostly studied textual and relational retrieval tasks as separate topics. To address the gap, we develop STARK, a large-scale Semi-structure retrieval benchmark on Textual and Relational Knowledge Bases. We design a novel pipeline to synthesize natural and realistic user queries that integrate diverse relational information and complex textual properties, as well as their ground-truth answers. Moreover, we rigorously conduct human evaluation to validate the quality of our benchmark, which covers a variety of practical applications, including product recommendations, academic paper searches, and precision medicine inquiries. Our benchmark serves as a comprehensive testbed for evaluating the performance of retrieval systems, with an emphasis on retrieval approaches driven by large language models (LLMs). Our experiments suggest that the STARK datasets present significant challenges to the current retrieval and LLM systems, indicating the demand for building more capable retrieval systems that can handle both textual and relational aspects.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

Text embeddings for Portuguese have no dedicated benchmark: evaluation rests on translated corpora such as English MS MARCO or on thin multilingual coverage, with native tasks scattered and unconsolidated. We introduce MTEB-PT, a benchmark of 22 native Brazilian-Portuguese tasks across seven categories (classification, multilabel classification, pair classification, semantic textual similarity, clustering, retrieval, and reranking), admitting only data created or found in Portuguese and excluding translations by construction. We evaluate 93 models spanning 23M to 27B parameters: 73 open-weight and 20 closed commercial APIs. Alongside the leaderboard we report a statistical layer for every headline comparison: per-task bootstrap confidence intervals, paired-bootstrap significance, a task- and instance-level discrimination analysis (how sharply each task separates models) adapted from Item Response Theory, and a cross-leaderboard correlation. Three findings stand out. The benchmark cleanly separates about a dozen tiers of models, though the top six are statistically too close to order. An openly licensed, self-hostable model reaches that leading tier, so strong Portuguese embedding quality does not require a commercial API. And a model's rank on the global multilingual leaderboard predicts its Portuguese rank only moderately (Spearman rho = 0.75 over 55 shared models; one model ranks 3rd there and 49th here), so a native benchmark measures something the multilingual boards do not. We release every task, our code, and a public leaderboard, so practitioners can choose Portuguese embedding models on native evidence.

In this paper, we introduce a comprehensive benchmark for Persian (Farsi) text embeddings, built upon the Massive Text Embedding Benchmark (MTEB). Our benchmark includes 63 datasets spanning seven different tasks: classification, clustering, pair classification, reranking, retrieval, summary retrieval, and semantic textual similarity. The datasets are formed as a combination of existing, translated, and newly generated data, offering a diverse evaluation framework for Persian language models. Given the increasing use of text embedding models in chatbots, evaluation datasets are becoming inseparable ingredients in chatbot challenges and Retrieval-Augmented Generation systems. As a contribution, we include chatbot evaluation datasets in the MTEB benchmark for the first time. In addition, in this paper, we introduce the new task of summary retrieval which is not part of the tasks included in standard MTEB. Another contribution of this paper is the introduction of a substantial number of new Persian language NLP datasets suitable for training and evaluation, some of which have no previous counterparts in Persian. We evaluate the performance of several Persian and multilingual embedding models in a range of tasks. This work introduces an open-source benchmark with datasets, code and a public leaderboard.

Multimodal documents contain diverse elements, such as tables, figures, and layouts, which can complicate retrieval tasks. While current approaches typically combine dense visual embedding models with supervised rerankers to achieve high-precision retrieval, they face inherent limitations. First, the coarse-grained nature of dense embeddings tends to obfuscate explicit semantics, failing to leverage structurally salient information. Second, supervised reranking models suffer from generalization bottlenecks, as their performance heavily relies on domain-specific training data. Furthermore, existing benchmarks often lack diverse assessment dimensions and comprehensive relevance annotations, limiting reliable evaluation. To address these challenges, we propose DocRetriever, a plug-and-play framework. It enhances visual retrieval via a layout-aware sparse embedding technique, enabling effective hybrid encoding without the overhead of optical character recognition (OCR). We also introduce a generalizable reranker that leverages reasoning-augmented demonstrations and optimized sampling to improve accuracy in few-shot settings. Finally, we construct a new benchmark, MultiDocR, to enable more rigorous evaluation. Experiments across diverse benchmarks validate DocRetriever's superiority over state-of-the-art methods.

Large language models (LLMs) have increasingly been explored as powerful text embedders. Existing LLM-based text embedding approaches often leverage the embedding of the final token, typically a reserved special token such as [EOS]. However, these tokens have not been intentionally trained to capture the semantics of the whole context, limiting their capacity as text embeddings, especially for retrieval and re-ranking tasks. We propose to add a new training stage before contrastive learning to enrich the semantics of the final token embedding. This stage employs bidirectional generative reconstruction tasks, namely EBQ2D (Embedding-Based Query-to-Document) and EBD2Q (Embedding-Based Document-to-Query), which interleave to anchor the [EOS] embedding and reconstruct either side of Query-Document pairs. Experimental results demonstrate that our additional training stage significantly improves LLM performance on the Massive Text Embedding Benchmark (MTEB), achieving new state-of-the-art results across different LLM base models and scales.

Sentence embeddings are essential for NLP tasks such as semantic search, re-ranking, and textual similarity. Although multilingual benchmarks like MMTEB broaden coverage, Southeast Asia (SEA) datasets are scarce and often machine-translated, missing native linguistic properties. With nearly 700 million speakers, the SEA region lacks a region-specific embedding benchmark. We introduce SEA-BED, the first large-scale SEA embedding benchmark with 169 datasets across 9 tasks and 10 languages, where 71% are formulated by humans, not machine generation or translation. We address three research questions: (1) which SEA languages and tasks are challenging, (2) whether SEA languages show unique performance gaps globally, and (3) how human vs. machine translations affect evaluation. We evaluate 17 embedding models across six studies, analyzing task and language challenges, cross-benchmark comparisons, and translation trade-offs. Results show sharp ranking shifts, inconsistent model performance among SEA languages, and the importance of human-curated datasets for low-resource languages like Burmese.

Embedding models play a pivot role in modern NLP applications such as IR and RAG. While the context limit of LLMs has been pushed beyond 1 million tokens, embedding models are still confined to a narrow context window not exceeding 8k tokens, refrained from application scenarios requiring long inputs such as legal contracts. This paper explores context window extension of existing embedding models, pushing the limit to 32k without requiring additional training. First, we examine the performance of current embedding models for long context retrieval on our newly constructed LongEmbed benchmark. LongEmbed comprises two synthetic tasks and four carefully chosen real-world tasks, featuring documents of varying length and dispersed target information. Benchmarking results underscore huge room for improvement in these models. Based on this, comprehensive experiments show that training-free context window extension strategies like position interpolation can effectively extend the context window of existing embedding models by several folds, regardless of their original context being 512 or beyond 4k. Furthermore, for models employing absolute position encoding (APE), we show the possibility of further fine-tuning to harvest notable performance gains while strictly preserving original behavior for short inputs. For models using rotary position embedding (RoPE), significant enhancements are observed when employing RoPE-specific methods, such as NTK and SelfExtend, indicating RoPE's superiority over APE for context window extension. To facilitate future research, we release E5-Base-4k and E5-RoPE-Base, along with the LongEmbed benchmark.

Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance remains limited. Existing benchmarks and metrics typically rely on published synthetic procedures and Top-K accuracy based on single ground-truth, which does not capture the open-ended nature of real-world synthesis planning. We propose a new benchmarking framework for single-step retrosynthesis that evaluates both general-purpose and chemistry-specialized LLMs using ChemCensor, a novel metric for chemical plausibility. By emphasizing plausibility over exact match, this approach better aligns with human synthesis planning practices. We also introduce CREED, a novel dataset comprising millions of ChemCensor-validated reaction records for LLM training, and use it to train a model that improves over the LLM baselines under this benchmark.

Word and sentence embeddings are useful feature representations in natural language processing. However, intrinsic evaluation for embeddings lags far behind, and there has been no significant update since the past decade. Word and sentence similarity tasks have become the de facto evaluation method. It leads models to overfit to such evaluations, negatively impacting embedding models' development. This paper first points out the problems using semantic similarity as the gold standard for word and sentence embedding evaluations. Further, we propose a new intrinsic evaluation method called EvalRank, which shows a much stronger correlation with downstream tasks. Extensive experiments are conducted based on 60+ models and popular datasets to certify our judgments. Finally, the practical evaluation toolkit is released for future benchmarking purposes.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Effective medical text retrieval requires both high accuracy and low latency. While LLM-based embedding models possess powerful retrieval capabilities, their prohibitive latency and high computational cost limit their application in real-time scenarios. Furthermore, the lack of comprehensive and high-fidelity benchmarks hinders progress in Chinese medical text retrieval. In this work, we introduce the Chinese Medical Text Embedding Benchmark (CMedTEB), a benchmark spanning three kinds of practical embedding tasks: retrieval, reranking, and semantic textual similarity (STS). Distinct from purely automated datasets, CMedTEB is curated via a rigorous multi-LLM voting pipeline validated by clinical experts, ensuring gold-standard label quality while effectively mitigating annotation noise. On this foundation, we propose the Chinese Medical Asymmetric REtriever (CARE), an asymmetric architecture that pairs a lightweight BERT-style encoder for online query encoding with a powerful LLM-based encoder for offline document encoding. However, optimizing such an asymmetric retriever with two structurally different encoders presents distinctive challenges. To address this, we introduce a novel two-stage training strategy that progressively bridges the query and document representations. Extensive experiments demonstrate that CARE surpasses state-of-the-art symmetric models on CMedTEB, achieving superior retrieval performance without increasing inference latency.

We explore the effectiveness of an LLM-guided query refinement paradigm for extending the usability of embedding models to challenging zero-shot search and classification tasks. Our approach refines the embedding representation of a user query using feedback from a generative LLM on a small set of documents, enabling embeddings to adapt in real time to the target task. We conduct extensive experiments with state-of-the-art text embedding models across a diverse set of challenging search and classification benchmarks. Empirical results indicate that LLM-guided query refinement yields consistent gains across all models and datasets, with relative improvements of up to +25% in literature search, intent detection, key-point matching, and nuanced query-instruction following. The refined queries improve ranking quality and induce clearer binary separation across the corpus, enabling the embedding space to better reflect the nuanced, task-specific constraints of each ad-hoc user query. Importantly, this expands the range of practical settings in which embedding models can be effectively deployed, making them a compelling alternative when costly LLM pipelines are not viable at corpus-scale. We release our experimental code for reproducibility, at https://github.com/IBM/task-aware-embedding-refinement.

In this paper, we introduce the Polish Massive Text Embedding Benchmark (PL-MTEB), a comprehensive benchmark for text embeddings in the Polish language. PL-MTEB comprises 30 diverse NLP tasks across five categories: classification, clustering, pair classification, information retrieval, and semantic text similarity. Within the scope of this work, we added 12 new Polish-language tasks to MTEB based on existing datasets and prepared two new datasets used to create four clustering tasks. We evaluated 30 publicly available text embedding models, including Polish and multilingual models. We analyzed the results in detail for specific task types and model sizes. We made the prepared datasets, the source code for evaluation, and the obtained results available to the public at https://github.com/rafalposwiata/pl-mteb.

Scientific illustrations are essential tools for communicating research findings, especially in natural science, where they visualize complex concepts and processes. As Text-to-Image (T2I) models become increasingly capable, researchers have started to use them for scientific illustration generation. However, existing benchmarks often assess outputs at a holistic level, overlooking fine-grained elements, while scientific reasoning ability and output conciseness remain under-quantified. We introduce FEPBench, a benchmark built from carefully selected high-quality scientific illustrations across multiple disciplines and layout types. With the assistance of multimodal large language models (MLLMs) and human experts, we provide fine-grained atom set annotations and systematically evaluate T2I models along three dimensions: instruction faithfulness, reasoning enrichment, and semantic precision. Our evaluation further decomposes model performance across visual, textual, relation, and layout elements. Results show that even state-of-the-art (SOTA) closed-source models, such as GPT Image 2 and Nano Banana Pro, still suffer from text-rendering bottlenecks, limited reasoning enrichment, and difficulty balancing generation richness with precision. These findings provide practical guidance for improving and deploying T2I models in scientific illustration generation. Benchmark data, atom set annotations, and evaluation code will be released by us.