Daily Papers

Large language models (LLMs) often fail to learn effective long chain-of-thought (Long CoT) reasoning from human or non-Long-CoT LLMs imitation. To understand this, we propose that effective and learnable Long CoT trajectories feature stable molecular-like structures in unified view, which are formed by three interaction types: Deep-Reasoning (covalent-like), Self-Reflection (hydrogen-bond-like), and Self-Exploration (van der Waals-like). Analysis of distilled trajectories reveals these structures emerge from Long CoT fine-tuning, not keyword imitation. We introduce Effective Semantic Isomers and show that only bonds promoting fast entropy convergence support stable Long CoT learning, while structural competition impairs training. Drawing on these findings, we present Mole-Syn, a distribution-transfer-graph method that guides synthesis of effective Long CoT structures, boosting performance and RL stability across benchmarks.

The recent success of distributed word representations has led to an increased interest in analyzing the properties of their spatial distribution. Several studies have suggested that contextualized word embedding models do not isotropically project tokens into vector space. However, current methods designed to measure isotropy, such as average random cosine similarity and the partition score, have not been thoroughly analyzed and are not appropriate for measuring isotropy. We propose IsoScore: a novel tool that quantifies the degree to which a point cloud uniformly utilizes the ambient vector space. Using rigorously designed tests, we demonstrate that IsoScore is the only tool available in the literature that accurately measures how uniformly distributed variance is across dimensions in vector space. Additionally, we use IsoScore to challenge a number of recent conclusions in the NLP literature that have been derived using brittle metrics of isotropy. We caution future studies from using existing tools to measure isotropy in contextualized embedding space as resulting conclusions will be misleading or altogether inaccurate.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Semantic code search is the task of retrieving a code snippet given a textual description of its functionality. Recent work has been focused on using similarity metrics between neural embeddings of text and code. However, current language models are known to struggle with longer, compositional text, and multi-step reasoning. To overcome this limitation, we propose supplementing the query sentence with a layout of its semantic structure. The semantic layout is used to break down the final reasoning decision into a series of lower-level decisions. We use a Neural Module Network architecture to implement this idea. We compare our model - NS3 (Neuro-Symbolic Semantic Search) - to a number of baselines, including state-of-the-art semantic code retrieval methods, and evaluate on two datasets - CodeSearchNet and Code Search and Question Answering. We demonstrate that our approach results in more precise code retrieval, and we study the effectiveness of our modular design when handling compositional queries.

We define deriving semantic class targets as a novel multi-modal task. By doing so, we aim to improve classification schemes in the physical sciences which can be severely abstracted and obfuscating. We address this task for upcoming radio astronomy surveys and present the derived semantic radio galaxy morphology class targets.

Large Language Models(LLMs) have demonstrated remarkable performance across various domains, yet their capabilities in molecular reasoning remain insufficiently explored. Current approaches tend to rely heavily on general-purpose prompting, which lacks domain-specific molecular semantics, while those that use fine-tuning strategies often face challenges with interpretability and reasoning depth. To address these issues, we introduce MolReasoner, a two-stage framework designed to transition LLMs from memorization towards chemical reasoning. First, we propose Mol-SFT, which initializes the model's reasoning abilities via synthetic Chain-of-Thought(CoT) samples generated by GPT-4o and verified for chemical accuracy. Subsequently, Mol-RL applies reinforcement learning with specialized reward functions designed explicitly to align chemical structures with linguistic descriptions, thereby enhancing molecular reasoning capabilities. Our approach notably enhances interpretability, improving the model 's molecular understanding and enabling better generalization. Extensive experiments demonstrate that MolReasoner outperforms existing methods, and marking a significant shift from memorization-based outputs to robust chemical reasoning.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

Despite their remarkable successes, state-of-the-art large language models (LLMs), including vision-and-language models (VLMs) and unimodal language models (ULMs), fail to understand precise semantics. For example, semantically equivalent sentences expressed using different lexical compositions elicit diverging representations. The degree of this divergence and its impact on encoded semantics is not very well understood. In this paper, we introduce the SUGARCREPE++ dataset to analyze the sensitivity of VLMs and ULMs to lexical and semantic alterations. Each sample in SUGARCREPE++ dataset consists of an image and a corresponding triplet of captions: a pair of semantically equivalent but lexically different positive captions and one hard negative caption. This poses a 3-way semantic (in)equivalence problem to the language models. We comprehensively evaluate VLMs and ULMs that differ in architecture, pre-training objectives and datasets to benchmark the performance of SUGARCREPE++ dataset. Experimental results highlight the difficulties of VLMs in distinguishing between lexical and semantic variations, particularly in object attributes and spatial relations. Although VLMs with larger pre-training datasets, model sizes, and multiple pre-training objectives achieve better performance on SUGARCREPE++, there is a significant opportunity for improvement. We show that all the models which achieve better performance on compositionality datasets need not perform equally well on SUGARCREPE++, signifying that compositionality alone may not be sufficient for understanding semantic and lexical alterations. Given the importance of the property that the SUGARCREPE++ dataset targets, it serves as a new challenge to the vision-and-language community.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

This document offers a detailed linguistic description of SNACS (Semantic Network of Adposition and Case Supersenses; Schneider et al., 2018), an inventory of 52 semantic labels ("supersenses") that characterize the use of adpositions and case markers at a somewhat coarse level of granularity, as demonstrated in the STREUSLE corpus (https://github.com/nert-nlp/streusle/ ; version 4.5 tracks guidelines version 2.6). Though the SNACS inventory aspires to be universal, this document is specific to English; documentation for other languages will be published separately. Version 2 is a revision of the supersense inventory proposed for English by Schneider et al. (2015, 2016) (henceforth "v1"), which in turn was based on previous schemes. The present inventory was developed after extensive review of the v1 corpus annotations for English, plus previously unanalyzed genitive case possessives (Blodgett and Schneider, 2018), as well as consideration of adposition and case phenomena in Hebrew, Hindi, Korean, and German. Hwang et al. (2017) present the theoretical underpinnings of the v2 scheme. Schneider et al. (2018) summarize the scheme, its application to English corpus data, and an automatic disambiguation task. Liu et al. (2021) offer an English Lexical Semantic Recognition tagger that includes SNACS labels in its output. This documentation can also be browsed alongside corpus data on the Xposition website (Gessler et al., 2022): http://www.xposition.org/

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.

PaECTER is a publicly available, open-source document-level encoder specific for patents. We fine-tune BERT for Patents with examiner-added citation information to generate numerical representations for patent documents. PaECTER performs better in similarity tasks than current state-of-the-art models used in the patent domain. More specifically, our model outperforms the next-best patent specific pre-trained language model (BERT for Patents) on our patent citation prediction test dataset on two different rank evaluation metrics. PaECTER predicts at least one most similar patent at a rank of 1.32 on average when compared against 25 irrelevant patents. Numerical representations generated by PaECTER from patent text can be used for downstream tasks such as classification, tracing knowledge flows, or semantic similarity search. Semantic similarity search is especially relevant in the context of prior art search for both inventors and patent examiners. PaECTER is available on Hugging Face.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Natural Language Understanding has seen an increasing number of publications in the last few years, especially after robust word embeddings models became prominent, when they proved themselves able to capture and represent semantic relationships from massive amounts of data. Nevertheless, traditional models often fall short in intrinsic issues of linguistics, such as polysemy and homonymy. Any expert system that makes use of natural language in its core, can be affected by a weak semantic representation of text, resulting in inaccurate outcomes based on poor decisions. To mitigate such issues, we propose a novel approach called Most Suitable Sense Annotation (MSSA), that disambiguates and annotates each word by its specific sense, considering the semantic effects of its context. Our approach brings three main contributions to the semantic representation scenario: (i) an unsupervised technique that disambiguates and annotates words by their senses, (ii) a multi-sense embeddings model that can be extended to any traditional word embeddings algorithm, and (iii) a recurrent methodology that allows our models to be re-used and their representations refined. We test our approach on six different benchmarks for the word similarity task, showing that our approach can produce state-of-the-art results and outperforms several more complex state-of-the-art systems.

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.

We introduce a method to measure uncertainty in large language models. For tasks like question answering, it is essential to know when we can trust the natural language outputs of foundation models. We show that measuring uncertainty in natural language is challenging because of "semantic equivalence" -- different sentences can mean the same thing. To overcome these challenges we introduce semantic entropy -- an entropy which incorporates linguistic invariances created by shared meanings. Our method is unsupervised, uses only a single model, and requires no modifications to off-the-shelf language models. In comprehensive ablation studies we show that the semantic entropy is more predictive of model accuracy on question answering data sets than comparable baselines.

To deploy large language models (LLMs) in high-stakes application domains that require substantively accurate responses to open-ended prompts, we need reliable, computationally inexpensive methods that assess the trustworthiness of long-form responses generated by LLMs. However, existing approaches often rely on claim-by-claim fact-checking, which is computationally expensive and brittle in long-form responses to open-ended prompts. In this work, we introduce semantic isotropy -- the degree of uniformity across normalized text embeddings on the unit sphere -- and use it to assess the trustworthiness of long-form responses generated by LLMs. To do so, we generate several long-form responses, embed them, and estimate the level of semantic isotropy of these responses as the angular dispersion of the embeddings on the unit sphere. We find that higher semantic isotropy -- that is, greater embedding dispersion -- reliably signals lower factual consistency across samples. Our approach requires no labeled data, no fine-tuning, and no hyperparameter selection, and can be used with open- or closed-weight embedding models. Across multiple domains, our method consistently outperforms existing approaches in predicting nonfactuality in long-form responses using only a handful of samples -- offering a practical, low-cost approach for integrating trust assessment into real-world LLM workflows.

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.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

The existing search tools for exploring the NASA Astrophysics Data System (ADS) can be quite rich and empowering (e.g., similar and trending operators), but researchers are not yet allowed to fully leverage semantic search. For example, a query for "results from the Planck mission" should be able to distinguish between all the various meanings of Planck (person, mission, constant, institutions and more) without further clarification from the user. At ADS, we are applying modern machine learning and natural language processing techniques to our dataset of recent astronomy publications to train astroBERT, a deeply contextual language model based on research at Google. Using astroBERT, we aim to enrich the ADS dataset and improve its discoverability, and in particular we are developing our own named entity recognition tool. We present here our preliminary results and lessons learned.

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.

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation. However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings. To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension. These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties. We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks. Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

Semantic parsing (SP) allows humans to leverage vast knowledge resources through natural interaction. However, parsers are mostly designed for and evaluated on English resources, such as CFQ (Keysers et al., 2020), the current standard benchmark based on English data generated from grammar rules and oriented towards Freebase, an outdated knowledge base. We propose a method for creating a multilingual, parallel dataset of question-query pairs, grounded in Wikidata. We introduce such a dataset, which we call Multilingual Compositional Wikidata Questions (MCWQ), and use it to analyze the compositional generalization of semantic parsers in Hebrew, Kannada, Chinese and English. While within-language generalization is comparable across languages, experiments on zero-shot cross-lingual transfer demonstrate that cross-lingual compositional generalization fails, even with state-of-the-art pretrained multilingual encoders. Furthermore, our methodology, dataset and results will facilitate future research on SP in more realistic and diverse settings than has been possible with existing resources.

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. mCLM, with only 3B parameters, achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

State-of-the-art visual grounding models can achieve high detection accuracy, but they are not designed to distinguish between all objects versus only certain objects of interest. In natural language, in order to specify a particular object or set of objects of interest, humans use determiners such as "my", "either" and "those". Determiners, as an important word class, are a type of schema in natural language about the reference or quantity of the noun. Existing grounded referencing datasets place much less emphasis on determiners, compared to other word classes such as nouns, verbs and adjectives. This makes it difficult to develop models that understand the full variety and complexity of object referencing. Thus, we have developed and released the DetermiNet dataset , which comprises 250,000 synthetically generated images and captions based on 25 determiners. The task is to predict bounding boxes to identify objects of interest, constrained by the semantics of the given determiner. We find that current state-of-the-art visual grounding models do not perform well on the dataset, highlighting the limitations of existing models on reference and quantification tasks.

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing the Geo2Seq, which converts molecular geometries into SE(3)-invariant 1D discrete sequences. Geo2Seq consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with Geo2Seq, various LMs excel in molecular geometry generation, especially in controlled generation tasks.

The semantic capabilities of large language models (LLMs) have the potential to enable rich analytics and reasoning over vast knowledge corpora. Unfortunately, existing systems either empirically optimize expensive LLM-powered operations with no performance guarantees, or serve a limited set of row-wise LLM operations, providing limited robustness, expressiveness and usability. We introduce semantic operators, the first formalism for declarative and general-purpose AI-based transformations based on natural language specifications (e.g., filtering, sorting, joining or aggregating records using natural language criteria). Each operator opens a rich space for execution plans, similar to relational operators. Our model specifies the expected behavior of each operator with a high-quality gold algorithm, and we develop an optimization framework that reduces cost, while providing accuracy guarantees with respect to a gold algorithm. Using this approach, we propose several novel optimizations to accelerate semantic filtering, joining, group-by and top-k operations by up to 1,000times. We implement semantic operators in the LOTUS system and demonstrate LOTUS' effectiveness on real, bulk-semantic processing applications, including fact-checking, biomedical multi-label classification, search, and topic analysis. We show that the semantic operator model is expressive, capturing state-of-the-art AI pipelines in a few operator calls, and making it easy to express new pipelines that match or exceed quality of recent LLM-based analytic systems by up to 170%, while offering accuracy guarantees. Overall, LOTUS programs match or exceed the accuracy of state-of-the-art AI pipelines for each task while running up to 3.6times faster than the highest-quality baselines. LOTUS is publicly available at https://github.com/lotus-data/lotus.

We explore the use of large pretrained language models as few-shot semantic parsers. The goal in semantic parsing is to generate a structured meaning representation given a natural language input. However, language models are trained to generate natural language. To bridge the gap, we use language models to paraphrase inputs into a controlled sublanguage resembling English that can be automatically mapped to a target meaning representation. Our results demonstrate that with only a small amount of data and very little code to convert into English-like representations, our blueprint for rapidly bootstrapping semantic parsers leads to surprisingly effective performance on multiple community tasks, greatly exceeding baseline methods also trained on the same limited data.

Formal and distributional semantic models offer complementary benefits in modeling meaning. The categorical compositional distributional (DisCoCat) model of meaning of Coecke et al. (arXiv:1003.4394v1 [cs.CL]) combines aspected of both to provide a general framework in which meanings of words, obtained distributionally, are composed using methods from the logical setting to form sentence meaning. Concrete consequences of this general abstract setting and applications to empirical data are under active study (Grefenstette et al., arxiv:1101.0309; Grefenstette and Sadrzadeh, arXiv:1106.4058v1 [cs.CL]). . In this paper, we extend this study by examining transitive verbs, represented as matrices in a DisCoCat. We discuss three ways of constructing such matrices, and evaluate each method in a disambiguation task developed by Grefenstette and Sadrzadeh (arXiv:1106.4058v1 [cs.CL]).

How can a robot efficiently extract a desired object from a shelf when it is fully occluded by other objects? Prior works propose geometric approaches for this problem but do not consider object semantics. Shelves in pharmacies, restaurant kitchens, and grocery stores are often organized such that semantically similar objects are placed close to one another. Can large language models (LLMs) serve as semantic knowledge sources to accelerate robotic mechanical search in semantically arranged environments? With Semantic Spatial Search on Shelves (S^4), we use LLMs to generate affinity matrices, where entries correspond to semantic likelihood of physical proximity between objects. We derive semantic spatial distributions by synthesizing semantics with learned geometric constraints. S^4 incorporates Optical Character Recognition (OCR) and semantic refinement with predictions from ViLD, an open-vocabulary object detection model. Simulation experiments suggest that semantic spatial search reduces the search time relative to pure spatial search by an average of 24% across three domains: pharmacy, kitchen, and office shelves. A manually collected dataset of 100 semantic scenes suggests that OCR and semantic refinement improve object detection accuracy by 35%. Lastly, physical experiments in a pharmacy shelf suggest 47.1% improvement over pure spatial search. Supplementary material can be found at https://sites.google.com/view/s4-rss/home.

Understanding how semantic meaning is encoded in the representation spaces of large language models is a fundamental problem in interpretability. In this paper, we study the two foundational questions in this area. First, how are categorical concepts, such as {'mammal', 'bird', 'reptile', 'fish'}, represented? Second, how are hierarchical relations between concepts encoded? For example, how is the fact that 'dog' is a kind of 'mammal' encoded? We show how to extend the linear representation hypothesis to answer these questions. We find a remarkably simple structure: simple categorical concepts are represented as simplices, hierarchically related concepts are orthogonal in a sense we make precise, and (in consequence) complex concepts are represented as polytopes constructed from direct sums of simplices, reflecting the hierarchical structure. We validate these theoretical results on the Gemma large language model, estimating representations for 957 hierarchically related concepts using data from WordNet.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

Given the success of Large Language Models (LLMs), there has been considerable interest in studying the properties of model activations. The literature overwhelmingly agrees that LLM representations are dominated by a few ``outlier dimensions'' with exceedingly high variance and magnitude. Several studies in Natural Language Processing (NLP) have sought to mitigate the impact of such outlier dimensions and force LLMs to be isotropic (i.e., have uniform variance across all dimensions in embedding space). Isotropy is thought to be a desirable property for LLMs that improves model performance and more closely aligns textual representations with human intuition. However, many of the claims regarding isotropy in NLP have been based on the average cosine similarity of embeddings, which has recently been shown to be a flawed measure of isotropy. In this paper, we propose I-STAR: IsoScore*-based STable Anisotropic Regularization, a novel regularization method that can be used to increase or decrease levels of isotropy in embedding space during training. I-STAR uses IsoScore*, the first accurate measure of isotropy that is both differentiable and stable on mini-batch computations. In contrast to several previous works, we find that decreasing isotropy in contextualized embeddings improves performance on the majority of tasks and models considered in this paper.

We present PhiloBERTA, a cross-lingual transformer model that measures semantic relationships between ancient Greek and Latin lexicons. Through analysis of selected term pairs from classical texts, we use contextual embeddings and angular similarity metrics to identify precise semantic alignments. Our results show that etymologically related pairs demonstrate significantly higher similarity scores, particularly for abstract philosophical concepts such as epist\=em\=e (scientia) and dikaiosyn\=e (iustitia). Statistical analysis reveals consistent patterns in these relationships (p = 0.012), with etymologically related pairs showing remarkably stable semantic preservation compared to control pairs. These findings establish a quantitative framework for examining how philosophical concepts moved between Greek and Latin traditions, offering new methods for classical philological research.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

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.

We propose using automatically generated natural language definitions of contextualised word usages as interpretable word and word sense representations. Given a collection of usage examples for a target word, and the corresponding data-driven usage clusters (i.e., word senses), a definition is generated for each usage with a specialised Flan-T5 language model, and the most prototypical definition in a usage cluster is chosen as the sense label. We demonstrate how the resulting sense labels can make existing approaches to semantic change analysis more interpretable, and how they can allow users -- historical linguists, lexicographers, or social scientists -- to explore and intuitively explain diachronic trajectories of word meaning. Semantic change analysis is only one of many possible applications of the `definitions as representations' paradigm. Beyond being human-readable, contextualised definitions also outperform token or usage sentence embeddings in word-in-context semantic similarity judgements, making them a new promising type of lexical representation for NLP.

A diversity of tasks use language models trained on semantic similarity data. While there are a variety of datasets that capture semantic similarity, they are either constructed from modern web data or are relatively small datasets created in the past decade by human annotators. This study utilizes a novel source, newly digitized articles from off-copyright, local U.S. newspapers, to assemble a massive-scale semantic similarity dataset spanning 70 years from 1920 to 1989 and containing nearly 400M positive semantic similarity pairs. Historically, around half of articles in U.S. local newspapers came from newswires like the Associated Press. While local papers reproduced articles from the newswire, they wrote their own headlines, which form abstractive summaries of the associated articles. We associate articles and their headlines by exploiting document layouts and language understanding. We then use deep neural methods to detect which articles are from the same underlying source, in the presence of substantial noise and abridgement. The headlines of reproduced articles form positive semantic similarity pairs. The resulting publicly available HEADLINES dataset is significantly larger than most existing semantic similarity datasets and covers a much longer span of time. It will facilitate the application of contrastively trained semantic similarity models to a variety of tasks, including the study of semantic change across space and time.

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.

Psychological research consistently finds that human ratings of words across diverse semantic scales can be reduced to a low-dimensional form with relatively little information loss. We find that the semantic associations encoded in the embedding matrices of large language models (LLMs) exhibit a similar structure. We show that the projections of words on semantic directions defined by antonym pairs (e.g. kind - cruel) correlate highly with human ratings, and further find that these projections effectively reduce to a 3-dimensional subspace within LLM embeddings, closely resembling the patterns derived from human survey responses. Moreover, we find that shifting tokens along one semantic direction causes off-target effects on geometrically aligned features proportional to their cosine similarity. These findings suggest that semantic features are entangled within LLMs similarly to how they are interconnected in human language, and a great deal of semantic information, despite its apparent complexity, is surprisingly low-dimensional. Furthermore, accounting for this semantic structure may prove essential for avoiding unintended consequences when steering features.

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.

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

This paper describes the organization and findings of AXOLOTL'24, the first multilingual explainable semantic change modeling shared task. We present new sense-annotated diachronic semantic change datasets for Finnish and Russian which were employed in the shared task, along with a surprise test-only German dataset borrowed from an existing source. The setup of AXOLOTL'24 is new to the semantic change modeling field, and involves subtasks of identifying unknown (novel) senses and providing dictionary-like definitions to these senses. The methods of the winning teams are described and compared, thus paving a path towards explainability in computational approaches to historical change of meaning.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

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/.

Effective scientific communication depends on accurate citations that validate sources and guide readers to supporting evidence. Yet academic literature faces mounting challenges: semantic citation errors that misrepresent sources, AI-generated hallucinated references, and traditional citation formats that point to entire papers without indicating which sections substantiate specific claims. We introduce SemanticCite, an AI-powered system that verifies citation accuracy through full-text source analysis while providing rich contextual information via detailed reasoning and relevant text snippets. Our approach combines multiple retrieval methods with a four-class classification system (Supported, Partially Supported, Unsupported, Uncertain) that captures nuanced claim-source relationships and enables appropriate remedial actions for different error types. Our experiments show that fine-tuned lightweight language models achieve performance comparable to large commercial systems with significantly lower computational requirements, making large-scale citation verification practically feasible. The system provides transparent, evidence-based explanations that support user understanding and trust. We contribute a comprehensive dataset of over 1,000 citations with detailed alignments, functional classifications, semantic annotations, and bibliometric metadata across eight disciplines, alongside fine-tuned models and the complete verification framework as open-source software. SemanticCite addresses critical challenges in research integrity through scalable citation verification, streamlined peer review, and quality control for AI-generated content, providing an open-source foundation for maintaining citation accuracy at scale.

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.

The ability of Large Language Models (LLMs) to encode syntactic and semantic structures of language is well examined in NLP. Additionally, analogy identification, in the form of word analogies are extensively studied in the last decade of language modeling literature. In this work we specifically look at how LLMs' abilities to capture sentence analogies (sentences that convey analogous meaning to each other) vary with LLMs' abilities to encode syntactic and semantic structures of sentences. Through our analysis, we find that LLMs' ability to identify sentence analogies is positively correlated with their ability to encode syntactic and semantic structures of sentences. Specifically, we find that the LLMs which capture syntactic structures better, also have higher abilities in identifying sentence analogies.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

We present a new resource for the NLP community, namely a large (3.5M+ sentence) knowledge base of *generic statements*, e.g., "Trees remove carbon dioxide from the atmosphere", collected from multiple corpora. This is the first large resource to contain *naturally occurring* generic sentences, as opposed to extracted or crowdsourced triples, and thus is rich in high-quality, general, semantically complete statements. All GenericsKB sentences are annotated with their topical term, surrounding context (sentences), and a (learned) confidence. We also release GenericsKB-Best (1M+ sentences), containing the best-quality generics in GenericsKB augmented with selected, synthesized generics from WordNet and ConceptNet. In tests on two existing datasets requiring multihop reasoning (OBQA and QASC), we find using GenericsKB can result in higher scores and better explanations than using a much larger corpus. This demonstrates that GenericsKB can be a useful resource for NLP applications, as well as providing data for linguistic studies of generics and their semantics. GenericsKB is available at https://allenai.org/data/genericskb.

Does semantic communication require a semantic information theory parallel to Shannon's information theory, or can Shannon's work be generalized for semantic communication? This paper advocates for the latter and introduces a semantic generalization of Shannon's information theory (G theory for short). The core idea is to replace the distortion constraint with the semantic constraint, achieved by utilizing a set of truth functions as a semantic channel. These truth functions enable the expressions of semantic distortion, semantic information measures, and semantic information loss. Notably, the maximum semantic information criterion is equivalent to the maximum likelihood criterion and similar to the Regularized Least Squares criterion. This paper shows G theory's applications to daily and electronic semantic communication, machine learning, constraint control, Bayesian confirmation, portfolio theory, and information value. The improvements in machine learning methods involve multilabel learning and classification, maximum mutual information classification, mixture models, and solving latent variables. Furthermore, insights from statistical physics are discussed: Shannon information is similar to free energy; semantic information to free energy in local equilibrium systems; and information efficiency to the efficiency of free energy in performing work. The paper also proposes refining Friston's minimum free energy principle into the maximum information efficiency principle. Lastly, it compares G theory with other semantic information theories and discusses its limitation in representing the semantics of complex data.

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.

Many current NLP systems are built from language models trained to optimize unsupervised objectives on large amounts of raw text. Under what conditions might such a procedure acquire meaning? Our systematic experiments with synthetic data reveal that, with languages where all expressions have context-independent denotations (i.e., languages with strong transparency), both autoregressive and masked language models successfully learn to emulate semantic relations between expressions. However, when denotations are changed to be context-dependent with the language otherwise unmodified, this ability degrades. Turning to natural language, our experiments with a specific phenomenon -- referential opacity -- add to the growing body of evidence that current language models do not represent natural language semantics well. We show this failure relates to the context-dependent nature of natural language form-meaning mappings.

Bilingual lexical processing is shaped by the complex interplay of phonological, orthographic, and semantic features of two languages within an integrated mental lexicon. In humans, this is evident in the ease with which cognate words - words similar in both orthographic form and meaning (e.g., blind, meaning "sightless" in both English and German) - are processed, compared to the challenges posed by interlingual homographs, which share orthographic form but differ in meaning (e.g., gift, meaning "present" in English but "poison" in German). We investigate how multilingual Large Language Models (LLMs) handle such phenomena, focusing on English-Spanish, English-French, and English-German cognates, non-cognate, and interlingual homographs. Specifically, we evaluate their ability to disambiguate meanings and make semantic judgments, both when these word types are presented in isolation or within sentence contexts. Our findings reveal that while certain LLMs demonstrate strong performance in recognizing cognates and non-cognates in isolation, they exhibit significant difficulty in disambiguating interlingual homographs, often performing below random baselines. This suggests LLMs tend to rely heavily on orthographic similarities rather than semantic understanding when interpreting interlingual homographs. Further, we find LLMs exhibit difficulty in retrieving word meanings, with performance in isolative disambiguation tasks having no correlation with semantic understanding. Finally, we study how the LLM processes interlingual homographs in incongruent sentences. We find models to opt for different strategies in understanding English and non-English homographs, highlighting a lack of a unified approach to handling cross-lingual ambiguities.

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

Dense retrieval has become a prominent method to obtain relevant context or world knowledge in open-domain NLP tasks. When we use a learned dense retriever on a retrieval corpus at inference time, an often-overlooked design choice is the retrieval unit in which the corpus is indexed, e.g. document, passage, or sentence. We discover that the retrieval unit choice significantly impacts the performance of both retrieval and downstream tasks. Distinct from the typical approach of using passages or sentences, we introduce a novel retrieval unit, proposition, for dense retrieval. Propositions are defined as atomic expressions within text, each encapsulating a distinct factoid and presented in a concise, self-contained natural language format. We conduct an empirical comparison of different retrieval granularity. Our results reveal that proposition-based retrieval significantly outperforms traditional passage or sentence-based methods in dense retrieval. Moreover, retrieval by proposition also enhances the performance of downstream QA tasks, since the retrieved texts are more condensed with question-relevant information, reducing the need for lengthy input tokens and minimizing the inclusion of extraneous, irrelevant information.

Semantic parsing is the task of mapping natural language to logic form. In question answering, semantic parsing can be used to map the question to logic form and execute the logic form to get the answer. One key problem for semantic parsing is the hard label work. We study this problem in another way: we do not use the logic form any more. Instead we only use the schema and answer info. We think that the logic form step can be injected into the deep model. The reason why we think removing the logic form step is possible is that human can do the task without explicit logic form. We use BERT-based model and do the experiment in the WikiSQL dataset, which is a large natural language to SQL dataset. Our experimental evaluations that show that our model can achieves the baseline results in WikiSQL dataset.

We present Lean Finder, a semantic search engine for Lean and mathlib that understands and aligns with the intents of mathematicians. Progress in formal theorem proving is often hindered by the difficulty of locating relevant theorems and the steep learning curve of the Lean 4 language, making advancement slow and labor-intensive. Existing Lean search engines, though helpful, rely primarily on informalizations (natural language translation of the formal statements), while largely overlooking the mismatch with real-world user queries. In contrast, we propose a user-centered semantic search tailored to the needs of mathematicians. Our approach begins by analyzing and clustering the semantics of public Lean discussions, then fine-tuning text embeddings on synthesized queries that emulate user intents. We further align Lean Finder with mathematicians' preferences using diverse feedback signals, encoding it with a rich awareness of their goals from multiple perspectives. Evaluations on real-world queries, informalized statements, and proof states demonstrate that our Lean Finder achieves over 30% relative improvement compared to previous search engines and GPT-4o. In addition, Lean Finder is compatible with LLM-based theorem provers, bridging retrieval with formal reasoning. Lean Finder is available at: https://leanfinder.github.io

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.

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.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

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.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Semantic code search is the task of retrieving relevant code given a natural language query. While related to other information retrieval tasks, it requires bridging the gap between the language used in code (often abbreviated and highly technical) and natural language more suitable to describe vague concepts and ideas. To enable evaluation of progress on code search, we are releasing the CodeSearchNet Corpus and are presenting the CodeSearchNet Challenge, which consists of 99 natural language queries with about 4k expert relevance annotations of likely results from CodeSearchNet Corpus. The corpus contains about 6 million functions from open-source code spanning six programming languages (Go, Java, JavaScript, PHP, Python, and Ruby). The CodeSearchNet Corpus also contains automatically generated query-like natural language for 2 million functions, obtained from mechanically scraping and preprocessing associated function documentation. In this article, we describe the methodology used to obtain the corpus and expert labels, as well as a number of simple baseline solutions for the task. We hope that CodeSearchNet Challenge encourages researchers and practitioners to study this interesting task further and will host a competition and leaderboard to track the progress on the challenge. We are also keen on extending CodeSearchNet Challenge to more queries and programming languages in the future.

Vector databases typically rely on approximate nearest neighbor (ANN) search to retrieve the top-k closest vectors to a query in embedding space. While effective, this approach often yields semantically redundant results, missing the diversity and contextual richness required by applications such as retrieval-augmented generation (RAG), multi-hop QA, and memory-augmented agents. We introduce a new retrieval paradigm: semantic compression, which aims to select a compact, representative set of vectors that captures the broader semantic structure around a query. We formalize this objective using principles from submodular optimization and information geometry, and show that it generalizes traditional top-k retrieval by prioritizing coverage and diversity. To operationalize this idea, we propose graph-augmented vector retrieval, which overlays semantic graphs (e.g., kNN or knowledge-based links) atop vector spaces to enable multi-hop, context-aware search. We theoretically analyze the limitations of proximity-based retrieval under high-dimensional concentration and highlight how graph structures can improve semantic coverage. Our work outlines a foundation for meaning-centric vector search systems, emphasizing hybrid indexing, diversity-aware querying, and structured semantic retrieval. We make our implementation publicly available to foster future research in this area.

The degree of semantic relatedness of two units of language has long been considered fundamental to understanding meaning. Additionally, automatically determining relatedness has many applications such as question answering and summarization. However, prior NLP work has largely focused on semantic similarity, a subset of relatedness, because of a lack of relatedness datasets. In this paper, we introduce a dataset for Semantic Textual Relatedness, STR-2022, that has 5,500 English sentence pairs manually annotated using a comparative annotation framework, resulting in fine-grained scores. We show that human intuition regarding relatedness of sentence pairs is highly reliable, with a repeat annotation correlation of 0.84. We use the dataset to explore questions on what makes sentences semantically related. We also show the utility of STR-2022 for evaluating automatic methods of sentence representation and for various downstream NLP tasks. Our dataset, data statement, and annotation questionnaire can be found at: https://doi.org/10.5281/zenodo.7599667

Consumer research costs companies billions annually yet suffers from panel biases and limited scale. Large language models (LLMs) offer an alternative by simulating synthetic consumers, but produce unrealistic response distributions when asked directly for numerical ratings. We present semantic similarity rating (SSR), a method that elicits textual responses from LLMs and maps these to Likert distributions using embedding similarity to reference statements. Testing on an extensive dataset comprising 57 personal care product surveys conducted by a leading corporation in that market (9,300 human responses), SSR achieves 90% of human test-retest reliability while maintaining realistic response distributions (KS similarity > 0.85). Additionally, these synthetic respondents provide rich qualitative feedback explaining their ratings. This framework enables scalable consumer research simulations while preserving traditional survey metrics and interpretability.

Informally, the 'linear representation hypothesis' is the idea that high-level concepts are represented linearly as directions in some representation space. In this paper, we address two closely related questions: What does "linear representation" actually mean? And, how do we make sense of geometric notions (e.g., cosine similarity or projection) in the representation space? To answer these, we use the language of counterfactuals to give two formalizations of "linear representation", one in the output (word) representation space, and one in the input (sentence) space. We then prove these connect to linear probing and model steering, respectively. To make sense of geometric notions, we use the formalization to identify a particular (non-Euclidean) inner product that respects language structure in a sense we make precise. Using this causal inner product, we show how to unify all notions of linear representation. In particular, this allows the construction of probes and steering vectors using counterfactual pairs. Experiments with LLaMA-2 demonstrate the existence of linear representations of concepts, the connection to interpretation and control, and the fundamental role of the choice of inner product.

Word Sense Disambiguation (WSD) is the task of associating a word in a given context with its most suitable meaning among a set of possible candidates. While the task has recently witnessed renewed interest, with systems achieving performances above the estimated inter-annotator agreement, at the time of writing it still struggles to find downstream applications. We argue that one of the reasons behind this is the difficulty of applying WSD to plain text. Indeed, in the standard formulation, models work under the assumptions that a) all the spans to disambiguate have already been identified, and b) all the possible candidate senses of each span are provided, both of which are requirements that are far from trivial. In this work, we present a new task called Word Sense Linking (WSL) where, given an input text and a reference sense inventory, systems have to both identify which spans to disambiguate and then link them to their most suitable meaning.We put forward a transformer-based architecture for the task and thoroughly evaluate both its performance and those of state-of-the-art WSD systems scaled to WSL, iteratively relaxing the assumptions of WSD. We hope that our work will foster easier integration of lexical semantics into downstream applications.

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 46% on molecular tasks and 66% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery.

Semantic representations of text, i.e. representations of natural language which capture meaning by geometry, are essential for areas such as information retrieval and document grouping. High-dimensional trained dense vectors have received much attention in recent years as such representations. We investigate the structure of semantic spaces that arise from embeddings made with Sentence-BERT and find that the representations suffer from a well-known problem in high dimensions called hubness. Hubness results in asymmetric neighborhood relations, such that some texts (the hubs) are neighbours of many other texts while most texts (so-called anti-hubs), are neighbours of few or no other texts. We quantify the semantic quality of the embeddings using hubness scores and error rate of a neighbourhood based classifier. We find that when hubness is high, we can reduce error rate and hubness using hubness reduction methods. We identify a combination of two methods as resulting in the best reduction. For example, on one of the tested pretrained models, this combined method can reduce hubness by about 75% and error rate by about 9%. Thus, we argue that mitigating hubness in the embedding space provides better semantic representations of text.

State-of-the-art supervised NLP models achieve high accuracy but are also susceptible to failures on inputs from low-data regimes, such as domains that are not represented in training data. As an approximation to collecting ground-truth labels for the specific domain, we study the use of large language models (LLMs) for annotating inputs and improving the generalization of NLP models. Specifically, given a budget for LLM annotations, we present an algorithm for sampling the most informative inputs to annotate and retrain the NLP model. We find that popular active learning strategies such as uncertainty-based sampling do not work well. Instead, we propose a sampling strategy based on the difference in prediction scores between the base model and the finetuned NLP model, utilizing the fact that most NLP models are finetuned from a base model. Experiments with classification (semantic similarity) and ranking (semantic search) tasks show that our sampling strategy leads to significant gains in accuracy for both the training and target domains.

The paper focuses on deep learning semantic search algorithms applied in the HR domain. The aim of the article is developing a novel approach to training a Siamese network to link the skills mentioned in the job ad with the title. It has been shown that the title normalization process can be based either on classification or similarity comparison approaches. While classification algorithms strive to classify a sample into predefined set of categories, similarity search algorithms take a more flexible approach, since they are designed to find samples that are similar to a given query sample, without requiring pre-defined classes and labels. In this article semantic similarity search to find candidates for title normalization has been used. A pre-trained language model has been adapted while teaching it to match titles and skills based on co-occurrence information. For the purpose of this research fifty billion title-descriptions pairs had been collected for training the model and thirty three thousand title-description-normalized title triplets, where normalized job title was picked up manually by job ad creator for testing purposes. As baselines FastText, BERT, SentenceBert and JobBert have been used. As a metric of the accuracy of the designed algorithm is Recall in top one, five and ten model's suggestions. It has been shown that the novel training objective lets it achieve significant improvement in comparison to other generic and specific text encoders. Two settings with treating titles as standalone strings, and with included skills as additional features during inference have been used and the results have been compared in this article. Improvements by 10% and 21.5% have been achieved using VacancySBERT and VacancySBERT (with skills) respectively. The benchmark has been developed as open-source to foster further research in the area.

Do state-of-the-art models for language understanding already have, or can they easily learn, abilities such as boolean coordination, quantification, conditionals, comparatives, and monotonicity reasoning (i.e., reasoning about word substitutions in sentential contexts)? While such phenomena are involved in natural language inference (NLI) and go beyond basic linguistic understanding, it is unclear the extent to which they are captured in existing NLI benchmarks and effectively learned by models. To investigate this, we propose the use of semantic fragments---systematically generated datasets that each target a different semantic phenomenon---for probing, and efficiently improving, such capabilities of linguistic models. This approach to creating challenge datasets allows direct control over the semantic diversity and complexity of the targeted linguistic phenomena, and results in a more precise characterization of a model's linguistic behavior. Our experiments, using a library of 8 such semantic fragments, reveal two remarkable findings: (a) State-of-the-art models, including BERT, that are pre-trained on existing NLI benchmark datasets perform poorly on these new fragments, even though the phenomena probed here are central to the NLI task. (b) On the other hand, with only a few minutes of additional fine-tuning---with a carefully selected learning rate and a novel variation of "inoculation"---a BERT-based model can master all of these logic and monotonicity fragments while retaining its performance on established NLI benchmarks.

Most available semantic parsing datasets, comprising of pairs of natural utterances and logical forms, were collected solely for the purpose of training and evaluation of natural language understanding systems. As a result, they do not contain any of the richness and variety of natural-occurring utterances, where humans ask about data they need or are curious about. In this work, we release SEDE, a dataset with 12,023 pairs of utterances and SQL queries collected from real usage on the Stack Exchange website. We show that these pairs contain a variety of real-world challenges which were rarely reflected so far in any other semantic parsing dataset, propose an evaluation metric based on comparison of partial query clauses that is more suitable for real-world queries, and conduct experiments with strong baselines, showing a large gap between the performance on SEDE compared to other common datasets.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

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 semantic matching capabilities of neural information retrieval can ameliorate synonymy and polysemy problems of symbolic approaches. However, neural models' dense representations are more suitable for re-ranking, due to their inefficiency. Sparse representations, either in symbolic or latent form, are more efficient with an inverted index. Taking the merits of the sparse and dense representations, we propose an ultra-high dimensional (UHD) representation scheme equipped with directly controllable sparsity. UHD's large capacity and minimal noise and interference among the dimensions allow for binarized representations, which are highly efficient for storage and search. Also proposed is a bucketing method, where the embeddings from multiple layers of BERT are selected/merged to represent diverse linguistic aspects. We test our models with MS MARCO and TREC CAR, showing that our models outperforms other sparse models

Composition models of distributional semantics are used to construct phrase representations from the representations of their words. Composition models are typically situated on two ends of a spectrum. They either have a small number of parameters but compose all phrases in the same way, or they perform word-specific compositions at the cost of a far larger number of parameters. In this paper we propose transformation weighting (TransWeight), a composition model that consistently outperforms existing models on nominal compounds, adjective-noun phrases and adverb-adjective phrases in English, German and Dutch. TransWeight drastically reduces the number of parameters needed compared to the best model in the literature by composing similar words in the same way.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.

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.

Hallucination in large language models (LLMs) can be detected by assessing the uncertainty of model outputs, typically measured using entropy. Semantic entropy (SE) enhances traditional entropy estimation by quantifying uncertainty at the semantic cluster level. However, as modern LLMs generate longer one-sentence responses, SE becomes less effective because it overlooks two crucial factors: intra-cluster similarity (the spread within a cluster) and inter-cluster similarity (the distance between clusters). To address these limitations, we propose a simple black-box uncertainty quantification method inspired by nearest neighbor estimates of entropy. Our approach can also be easily extended to white-box settings by incorporating token probabilities. Additionally, we provide theoretical results showing that our method generalizes semantic entropy. Extensive empirical results demonstrate its effectiveness compared to semantic entropy across two recent LLMs (Phi3 and Llama3) and three common text generation tasks: question answering, text summarization, and machine translation. Our code is available at https://github.com/BigML-CS-UCLA/SNNE.

We present our submission to the AXOLOTL-24 shared task. The shared task comprises two subtasks: identifying new senses that words gain with time (when comparing newer and older time periods) and producing the definitions for the identified new senses. We implemented a conceptually simple and computationally inexpensive solution to both subtasks. We trained adapter-based binary classification models to match glosses with usage examples and leveraged the probability output of the models to identify novel senses. The same models were used to match examples of novel sense usages with Wiktionary definitions. Our submission attained third place on the first subtask and the first place on the second subtask.

Multi-component compounding is a prevalent phenomenon in Sanskrit, and understanding the implicit structure of a compound's components is crucial for deciphering its meaning. Earlier approaches in Sanskrit have focused on binary compounds and neglected the multi-component compound setting. This work introduces the novel task of nested compound type identification (NeCTI), which aims to identify nested spans of a multi-component compound and decode the implicit semantic relations between them. To the best of our knowledge, this is the first attempt in the field of lexical semantics to propose this task. We present 2 newly annotated datasets including an out-of-domain dataset for this task. We also benchmark these datasets by exploring the efficacy of the standard problem formulations such as nested named entity recognition, constituency parsing and seq2seq, etc. We present a novel framework named DepNeCTI: Dependency-based Nested Compound Type Identifier that surpasses the performance of the best baseline with an average absolute improvement of 13.1 points F1-score in terms of Labeled Span Score (LSS) and a 5-fold enhancement in inference efficiency. In line with the previous findings in the binary Sanskrit compound identification task, context provides benefits for the NeCTI task. The codebase and datasets are publicly available at: https://github.com/yaswanth-iitkgp/DepNeCTI

We present OpenGloss, a synthetic encyclopedic dictionary and semantic knowledge graph for English that integrates lexicographic definitions, encyclopedic context, etymological histories, and semantic relationships in a unified resource. OpenGloss contains 537K senses across 150K lexemes, on par with WordNet 3.1 and Open English WordNet, while providing more than four times as many sense definitions. These lexemes include 9.1M semantic edges, 1M usage examples, 3M collocations, and 60M words of encyclopedic content. Generated through a multi-agent procedural generation pipeline with schema-validated LLM outputs and automated quality assurance, the entire resource was produced in under one week for under $1,000. This demonstrates that structured generation can create comprehensive lexical resources at cost and time scales impractical for manual curation, enabling rapid iteration as foundation models improve. The resource addresses gaps in pedagogical applications by providing integrated content -- definitions, examples, collocations, encyclopedias, etymology -- that supports both vocabulary learning and natural language processing tasks. As a synthetically generated resource, OpenGloss reflects both the capabilities and limitations of current foundation models. The dataset is publicly available on Hugging Face under CC-BY 4.0, enabling researchers and educators to build upon and adapt this resource.

We present the first shared task on Semantic Textual Relatedness (STR). While earlier shared tasks primarily focused on semantic similarity, we instead investigate the broader phenomenon of semantic relatedness across 14 languages: Afrikaans, Algerian Arabic, Amharic, English, Hausa, Hindi, Indonesian, Kinyarwanda, Marathi, Moroccan Arabic, Modern Standard Arabic, Punjabi, Spanish, and Telugu. These languages originate from five distinct language families and are predominantly spoken in Africa and Asia -- regions characterised by the relatively limited availability of NLP resources. Each instance in the datasets is a sentence pair associated with a score that represents the degree of semantic textual relatedness between the two sentences. Participating systems were asked to rank sentence pairs by their closeness in meaning (i.e., their degree of semantic relatedness) in the 14 languages in three main tracks: (a) supervised, (b) unsupervised, and (c) crosslingual. The task attracted 163 participants. We received 70 submissions in total (across all tasks) from 51 different teams, and 38 system description papers. We report on the best-performing systems as well as the most common and the most effective approaches for the three different tracks.

Exploring and quantifying semantic relatedness is central to representing language. It holds significant implications across various NLP tasks, including offering insights into the capabilities and performance of Large Language Models (LLMs). While earlier NLP research primarily focused on semantic similarity, often within the English language context, we instead investigate the broader phenomenon of semantic relatedness. In this paper, we present SemRel, a new semantic relatedness dataset collection annotated by native speakers across 14 languages:Afrikaans, Algerian Arabic, Amharic, English, Hausa, Hindi, Indonesian, Kinyarwanda, Marathi, Moroccan Arabic, Modern Standard Arabic, Punjabi, Spanish, and Telugu. These languages originate from five distinct language families and are predominantly spoken in Africa and Asia -- regions characterised by a relatively limited availability of NLP resources. Each instance in the SemRel datasets is a sentence pair associated with a score that represents the degree of semantic textual relatedness between the two sentences. The scores are obtained using a comparative annotation framework. We describe the data collection and annotation processes, related challenges when building the datasets, and their impact and utility in NLP. We further report experiments for each language and across the different languages.

Semantics of a sentence is defined with much less ambiguity than semantics of a single word, and it should be better preserved by translation to another language. If multilingual sentence embeddings intend to represent sentence semantics, then the similarity between embeddings of any two sentences must be invariant with respect to translation. Based on this suggestion, we consider a simple linear cross-lingual mapping as a possible improvement of the multilingual embeddings. We also consider deviation from orthogonality conditions as a measure of deficiency of the embeddings.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Semantic text classification has undergone significant advances in recent years due to the rise of large language models (LLMs) and their high dimensional embeddings. While LLM-embeddings are frequently used to store and retrieve text by semantic similarity in vector databases, the global structure semantic relationships in text corpora often remains opaque. Herein we propose a nested density clustering approach, to infer hierarchical trees of semantically related texts. The method starts by identifying texts of strong semantic similarity as it searches for dense clusters in LLM embedding space. As the density criterion is gradually relaxed, these dense clusters merge into more diffuse clusters, until the whole dataset is represented by a single cluster -- the root of the tree. By embedding dense clusters into increasingly diffuse ones, we construct a tree structure that captures hierarchical semantic relationships among texts. We outline how this approach can be used to classify textual data for abstracts of scientific abstracts as a case study. This enables the data-driven discovery research areas and their subfields without predefined categories. To evaluate the general applicability of the method, we further apply it to established benchmark datasets such as the 20 Newsgroups and IMDB 50k Movie Reviews, demonstrating its robustness across domains. Finally we discuss possible applications on scientometrics, topic evolution, highlighting how nested density trees can reveal semantic structure and evolution in textual datasets.

In multi-user semantic communication, language mismatche poses a significant challenge when independently trained agents interact. We present a novel semantic equalization algorithm that enables communication between agents with different languages without additional retraining. Our algorithm is based on relative representations, a framework that enables different agents employing different neural network models to have unified representation. It proceeds by projecting the latent vectors of different models into a common space defined relative to a set of data samples called anchors, whose number equals the dimension of the resulting space. A communication between different agents translates to a communication of semantic symbols sampled from this relative space. This approach, in addition to aligning the semantic representations of different agents, allows compressing the amount of information being exchanged, by appropriately selecting the number of anchors. Eventually, we introduce a novel anchor selection strategy, which advantageously determines prototypical anchors, capturing the most relevant information for the downstream task. Our numerical results show the effectiveness of the proposed approach allowing seamless communication between agents with radically different models, including differences in terms of neural network architecture and datasets used for initial training.

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.

Language Models are the core for almost any Natural Language Processing system nowadays. One of their particularities is their contextualized representations, a game changer feature when a disambiguation between word senses is necessary. In this paper we aim to explore to what extent language models are capable of discerning among senses at inference time. We performed this analysis by prompting commonly used Languages Models such as BERT or RoBERTa to perform the task of Word Sense Disambiguation (WSD). We leverage the relation between word senses and domains, and cast WSD as a textual entailment problem, where the different hypothesis refer to the domains of the word senses. Our results show that this approach is indeed effective, close to supervised systems.

Open-domain semantic parsing remains a challenging task, as models often rely on heuristics and struggle to handle unseen concepts. In this paper, we investigate the potential of large language models (LLMs) for this task and introduce Retrieval-Augmented Semantic Parsing (RASP), a simple yet effective approach that integrates external lexical knowledge into the parsing process. Our experiments not only show that LLMs outperform previous encoder-decoder baselines for semantic parsing, but that RASP further enhances their ability to predict unseen concepts, nearly doubling the performance of previous models on out-of-distribution concepts. These findings highlight the promise of leveraging large language models and retrieval mechanisms for robust and open-domain semantic parsing.

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.

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.

Semantic search for candidate retrieval is an important yet neglected problem in retrieval-based Chatbots, which aims to select a bunch of candidate responses efficiently from a large pool. The existing bottleneck is to ensure the model architecture having two points: 1) rich interactions between a query and a response to produce query-relevant responses; 2) ability of separately projecting the query and the response into latent spaces to apply efficiently in semantic search during online inference. To tackle this problem, we propose a novel approach, called Multitask-based Semantic Search Neural Network (MSSNN) for candidate retrieval, which accomplishes query-response interactions through multi-tasks. The method employs a Seq2Seq modeling task to learn a good query encoder, and then performs a word prediction task to build response embeddings, finally conducts a simple matching model to form the dot-product scorer. Experimental studies have demonstrated the potential of the proposed approach.

We propose semantic entropy probes (SEPs), a cheap and reliable method for uncertainty quantification in Large Language Models (LLMs). Hallucinations, which are plausible-sounding but factually incorrect and arbitrary model generations, present a major challenge to the practical adoption of LLMs. Recent work by Farquhar et al. (2024) proposes semantic entropy (SE), which can detect hallucinations by estimating uncertainty in the space semantic meaning for a set of model generations. However, the 5-to-10-fold increase in computation cost associated with SE computation hinders practical adoption. To address this, we propose SEPs, which directly approximate SE from the hidden states of a single generation. SEPs are simple to train and do not require sampling multiple model generations at test time, reducing the overhead of semantic uncertainty quantification to almost zero. We show that SEPs retain high performance for hallucination detection and generalize better to out-of-distribution data than previous probing methods that directly predict model accuracy. Our results across models and tasks suggest that model hidden states capture SE, and our ablation studies give further insights into the token positions and model layers for which this is the case.

Recent studies of the emergent capabilities of transformer-based Natural Language Understanding (NLU) models have indicated that they have an understanding of lexical and compositional semantics. We provide evidence that suggests these claims should be taken with a grain of salt: we find that state-of-the-art Natural Language Inference (NLI) models are sensitive towards minor semantics preserving surface-form variations, which lead to sizable inconsistent model decisions during inference. Notably, this behaviour differs from valid and in-depth comprehension of compositional semantics, however does neither emerge when evaluating model accuracy on standard benchmarks nor when probing for syntactic, monotonic, and logically robust reasoning. We propose a novel framework to measure the extent of semantic sensitivity. To this end, we evaluate NLI models on adversarially generated examples containing minor semantics-preserving surface-form input noise. This is achieved using conditional text generation, with the explicit condition that the NLI model predicts the relationship between the original and adversarial inputs as a symmetric equivalence entailment. We systematically study the effects of the phenomenon across NLI models for in- and out-of- domain settings. Our experiments show that semantic sensitivity causes performance degradations of 12.92% and 23.71% average over in- and out-of- domain settings, respectively. We further perform ablation studies, analysing this phenomenon across models, datasets, and variations in inference and show that semantic sensitivity can lead to major inconsistency within model predictions.

The widespread adoption of large language models (LLMs) has created an urgent need for robust tools to detect LLM-generated text, especially in light of paraphrasing techniques that often evade existing detection methods. To address this challenge, we present a novel semantic-enhanced framework for detecting LLM-generated text (SEFD) that leverages a retrieval-based mechanism to fully utilize text semantics. Our framework improves upon existing detection methods by systematically integrating retrieval-based techniques with traditional detectors, employing a carefully curated retrieval mechanism that strikes a balance between comprehensive coverage and computational efficiency. We showcase the effectiveness of our approach in sequential text scenarios common in real-world applications, such as online forums and Q\&A platforms. Through comprehensive experiments across various LLM-generated texts and detection methods, we demonstrate that our framework substantially enhances detection accuracy in paraphrasing scenarios while maintaining robustness for standard LLM-generated content.

Humans organize knowledge into compact categories through semantic compression by mapping diverse instances to abstract representations while preserving meaning (e.g., robin and blue jay are both birds; most birds can fly). These concepts reflect a trade-off between expressive fidelity and representational simplicity. Large Language Models (LLMs) demonstrate remarkable linguistic abilities, yet whether their internal representations strike a human-like trade-off between compression and semantic fidelity is unclear. We introduce a novel information-theoretic framework, drawing from Rate-Distortion Theory and the Information Bottleneck principle, to quantitatively compare these strategies. Analyzing token embeddings from a diverse suite of LLMs against seminal human categorization benchmarks, we uncover key divergences. While LLMs form broad conceptual categories that align with human judgment, they struggle to capture the fine-grained semantic distinctions crucial for human understanding. More fundamentally, LLMs demonstrate a strong bias towards aggressive statistical compression, whereas human conceptual systems appear to prioritize adaptive nuance and contextual richness, even if this results in lower compressional efficiency by our measures. These findings illuminate critical differences between current AI and human cognitive architectures, guiding pathways toward LLMs with more human-aligned conceptual representations.

While large language models (LLMs) have achieved impressive progress, their application in scientific domains such as chemistry remains hindered by shallow domain understanding and limited reasoning capabilities. In this work, we focus on the specific field of chemistry and develop a Chemical Reasoner LLM, ChemDFM-R. We first construct a comprehensive dataset of atomized knowledge points to enhance the model's understanding of the fundamental principles and logical structure of chemistry. Then, we propose a mix-sourced distillation strategy that integrates expert-curated knowledge with general-domain reasoning skills, followed by domain-specific reinforcement learning to enhance chemical reasoning. Experiments on diverse chemical benchmarks demonstrate that ChemDFM-R achieves state-of-the-art performance while providing interpretable, rationale-driven outputs. Further case studies illustrate how explicit reasoning chains significantly improve the reliability, transparency, and practical utility of the model in real-world human-AI collaboration scenarios.

Superlatives are used to single out elements with a maximal/minimal property. Semantically, superlatives perform a set comparison: something (or some things) has the min/max property out of a set. As such, superlatives provide an ideal phenomenon for studying implicit phenomena and discourse restrictions. While this comparison set is often not explicitly defined, its (implicit) restrictions can be inferred from the discourse context the expression appears in. In this work we provide an extensive computational study on the semantics of superlatives. We propose a unified account of superlative semantics which allows us to derive a broad-coverage annotation schema. Using this unified schema we annotated a multi-domain dataset of superlatives and their semantic interpretations. We specifically focus on interpreting implicit or ambiguous superlative expressions, by analyzing how the discourse context restricts the set of interpretations. In a set of experiments we then analyze how well models perform at variations of predicting superlative semantics, with and without context. We show that the fine-grained semantics of superlatives in context can be challenging for contemporary models, including GPT-4.

Semantic parsers convert natural language to logical forms, which can be evaluated on knowledge bases (KBs) to produce denotations. Recent semantic parsers have been developed with sequence-to-sequence (seq2seq) pre-trained language models (PLMs) or large language models, where the models treat logical forms as sequences of tokens. For syntactic and semantic validity, the semantic parsers use grammars that enable constrained decoding. However, the grammars lack the ability to utilize large information of KBs, although logical forms contain representations of KB elements, such as entities or relations. In this work, we propose a grammar augmented with candidate expressions for semantic parsing on a large KB with a seq2seq PLM. The grammar defines actions as production rules, and our semantic parser predicts actions during inference under the constraints by types and candidate expressions. We apply the grammar to knowledge base question answering, where the constraints by candidate expressions assist a semantic parser to generate valid KB elements. We also introduce two special rules, sub-type inference and union types, and a mask caching algorithm. In particular, sub-type inference and the mask caching algorithm greatly increase the decoding speed of our semantic parser. We experimented on two benchmarks, KQA Pro and Overnight, where the constraints by candidate expressions increased the accuracy of our semantic parser, whether it was trained with strong supervision or weak supervision. In addition, our semantic parser had a fast decoding speed in the experiments. Our source code is publicly available at https://github.com/daehwannam/candexpr-sp.git.

We present the full-size Russian complexly NER-labeled corpus of Internet user reviews, along with an evaluation of accuracy levels reached on this corpus by a set of advanced deep learning neural networks to extract the pharmacologically meaningful entities from Russian texts. The corpus annotation includes mentions of the following entities: Medication (33005 mentions), Adverse Drug Reaction (1778), Disease (17403), and Note (4490). Two of them - Medication and Disease - comprise a set of attributes. A part of the corpus has the coreference annotation with 1560 coreference chains in 300 documents. Special multi-label model based on a language model and the set of features is developed, appropriate for presented corpus labeling. The influence of the choice of different modifications of the models: word vector representations, types of language models pre-trained for Russian, text normalization styles, and other preliminary processing are analyzed. The sufficient size of our corpus allows to study the effects of particularities of corpus labeling and balancing entities in the corpus. As a result, the state of the art for the pharmacological entity extraction problem for Russian is established on a full-size labeled corpus. In case of the adverse drug reaction (ADR) recognition, it is 61.1 by the F1-exact metric that, as our analysis shows, is on par with the accuracy level for other language corpora with similar characteristics and the ADR representativnes. The evaluated baseline precision of coreference relation extraction on the corpus is 71, that is higher the results reached on other Russian corpora.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

Coecke, Sadrzadeh, and Clark (arXiv:1003.4394v1 [cs.CL]) developed a compositional model of meaning for distributional semantics, in which each word in a sentence has a meaning vector and the distributional meaning of the sentence is a function of the tensor products of the word vectors. Abstractly speaking, this function is the morphism corresponding to the grammatical structure of the sentence in the category of finite dimensional vector spaces. In this paper, we provide a concrete method for implementing this linear meaning map, by constructing a corpus-based vector space for the type of sentence. Our construction method is based on structured vector spaces whereby meaning vectors of all sentences, regardless of their grammatical structure, live in the same vector space. Our proposed sentence space is the tensor product of two noun spaces, in which the basis vectors are pairs of words each augmented with a grammatical role. This enables us to compare meanings of sentences by simply taking the inner product of their vectors.

This paper presents a multilingual study of word meaning representations in context. We assess the ability of both static and contextualized models to adequately represent different lexical-semantic relations, such as homonymy and synonymy. To do so, we created a new multilingual dataset that allows us to perform a controlled evaluation of several factors such as the impact of the surrounding context or the overlap between words, conveying the same or different senses. A systematic assessment on four scenarios shows that the best monolingual models based on Transformers can adequately disambiguate homonyms in context. However, as they rely heavily on context, these models fail at representing words with different senses when occurring in similar sentences. Experiments are performed in Galician, Portuguese, English, and Spanish, and both the dataset (with more than 3,000 evaluation items) and new models are freely released with this study.

In question-answering tasks, determining when to trust the outputs is crucial to the alignment of large language models (LLMs). Kuhn et al. (2023) introduces semantic entropy as a measure of uncertainty, by incorporating linguistic invariances from the same meaning. It primarily relies on setting threshold to measure the level of semantic equivalence relation. We propose a more nuanced framework that extends beyond such thresholding by developing a Shapley-based uncertainty metric that captures the continuous nature of semantic relationships. We establish three fundamental properties that characterize valid uncertainty metrics and prove that our Shapley uncertainty satisfies these criteria. Through extensive experiments, we demonstrate that our Shapley uncertainty more accurately predicts LLM performance in question-answering and other datasets, compared to similar baseline measures.

The exploitation of syntactic graphs (SyGs) as a word's context has been shown to be beneficial for distributional semantic models (DSMs), both at the level of individual word representations and in deriving phrasal representations via composition. However, notwithstanding the potential performance benefit, the syntactically-aware DSMs proposed to date have huge numbers of parameters (compared to conventional DSMs) and suffer from data sparsity. Furthermore, the encoding of the SyG links (i.e., the syntactic relations) has been largely limited to linear maps. The knowledge graphs' literature, on the other hand, has proposed light-weight models employing different geometric transformations (GTs) to encode edges in a knowledge graph (KG). Our work explores the possibility of adopting this family of models to encode SyGs. Furthermore, we investigate which GT better encodes syntactic relations, so that these representations can be used to enhance phrase-level composition via syntactic contextualisation.

We propose a novel dependency-based hybrid tree model for semantic parsing, which converts natural language utterance into machine interpretable meaning representations. Unlike previous state-of-the-art models, the semantic information is interpreted as the latent dependency between the natural language words in our joint representation. Such dependency information can capture the interactions between the semantics and natural language words. We integrate a neural component into our model and propose an efficient dynamic-programming algorithm to perform tractable inference. Through extensive experiments on the standard multilingual GeoQuery dataset with eight languages, we demonstrate that our proposed approach is able to achieve state-of-the-art performance across several languages. Analysis also justifies the effectiveness of using our new dependency-based representation.

Multilingual language models have significantly advanced due to rapid progress in natural language processing. Models like BLOOM 1.7B, trained on diverse multilingual datasets, aim to bridge linguistic gaps. However, their effectiveness in capturing linguistic knowledge, particularly for low-resource languages, remains an open question. This study critically examines MLMs capabilities in multilingual understanding, semantic representation, and cross-lingual knowledge transfer. While these models perform well for high-resource languages, they struggle with less-represented ones. Additionally, traditional evaluation methods often overlook their internal syntactic and semantic encoding. This research addresses key limitations through three objectives. First, it assesses semantic similarity by analyzing multilingual word embeddings for consistency using cosine similarity. Second, it examines BLOOM-1.7B and Qwen2 through Named Entity Recognition and sentence similarity tasks to understand their linguistic structures. Third, it explores cross-lingual knowledge transfer by evaluating generalization from high-resource to low-resource languages in sentiment analysis and text classification. By leveraging linguistic probing, performance metrics, and visualizations, this study provides insights into the strengths and limitations of MLMs. The findings aim to enhance multilingual NLP models, ensuring better support for both high- and low-resource languages, thereby promoting inclusivity in language technologies.

We introduce LexBench, a comprehensive evaluation suite enabled to test language models (LMs) on ten semantic phrase processing tasks. Unlike prior studies, it is the first work to propose a framework from the comparative perspective to model the general semantic phrase (i.e., lexical collocation) and three fine-grained semantic phrases, including idiomatic expression, noun compound, and verbal construction. Thanks to \ourbenchmark, we assess the performance of 15 LMs across model architectures and parameter scales in classification, extraction, and interpretation tasks. Through the experiments, we first validate the scaling law and find that, as expected, large models excel better than the smaller ones in most tasks. Second, we investigate further through the scaling semantic relation categorization and find that few-shot LMs still lag behind vanilla fine-tuned models in the task. Third, through human evaluation, we find that the performance of strong models is comparable to the human level regarding semantic phrase processing. Our benchmarking findings can serve future research aiming to improve the generic capability of LMs on semantic phrase comprehension. Our source code and data are available at https://github.com/jacklanda/LexBench

Understanding and designing biomolecules, such as proteins and small molecules, is central to advancing drug discovery, synthetic biology, and enzyme engineering. Recent breakthroughs in Artificial Intelligence (AI) have revolutionized biomolecular research, achieving remarkable accuracy in biomolecular prediction and design. However, a critical gap remains between AI's computational power and researchers' intuition, using natural language to align molecular complexity with human intentions. Large Language Models (LLMs) have shown potential to interpret human intentions, yet their application to biomolecular research remains nascent due to challenges including specialized knowledge requirements, multimodal data integration, and semantic alignment between natural language and biomolecules. To address these limitations, we present InstructBioMol, a novel LLM designed to bridge natural language and biomolecules through a comprehensive any-to-any alignment of natural language, molecules, and proteins. This model can integrate multimodal biomolecules as input, and enable researchers to articulate design goals in natural language, providing biomolecular outputs that meet precise biological needs. Experimental results demonstrate InstructBioMol can understand and design biomolecules following human instructions. Notably, it can generate drug molecules with a 10% improvement in binding affinity and design enzymes that achieve an ESP Score of 70.4, making it the only method to surpass the enzyme-substrate interaction threshold of 60.0 recommended by the ESP developer. This highlights its potential to transform real-world biomolecular research.