Daily Papers

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.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

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.

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA.

Large language models (LLMs) have shown remarkable in-context learning (ICL) capabilities on textual data. We explore whether these capabilities can be extended to continuous vectors from diverse domains, obtained from black-box pretrained encoders. By aligning input data with an LLM's embedding space through lightweight projectors, we observe that LLMs can effectively process and learn from these projected vectors, which we term Vector-ICL. In particular, we find that pretraining projectors with general language modeling objectives enables Vector-ICL, while task-specific finetuning further enhances performance. In our experiments across various tasks and modalities, including text reconstruction, numerical function regression, text classification, summarization, molecule captioning, time-series classification, graph classification, and fMRI decoding, Vector-ICL often surpasses both few-shot ICL and domain-specific model or tuning. We further conduct analyses and case studies, indicating the potential of LLMs to process vector representations beyond traditional token-based paradigms.

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

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

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

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.

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

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.

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

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

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.

Image captioning is a central task in computer vision which has experienced substantial progress following the advent of vision-language pre-training techniques. In this paper, we highlight a frequently overlooked limitation of captioning models that often fail to capture semantically significant elements. This drawback can be traced back to the text-image datasets; while their captions typically offer a general depiction of image content, they frequently omit salient details. To mitigate this limitation, we propose FuseCap - a novel method for enriching captions with additional visual information, obtained from vision experts, such as object detectors, attribute recognizers, and Optical Character Recognizers (OCR). Our approach fuses the outputs of such vision experts with the original caption using a large language model (LLM), yielding enriched captions that present a comprehensive image description. We validate the effectiveness of the proposed caption enrichment method through both quantitative and qualitative analysis. Our method is then used to curate the training set of a captioning model based BLIP which surpasses current state-of-the-art approaches in generating accurate and detailed captions while using significantly fewer parameters and training data. As additional contributions, we provide a dataset comprising of 12M image-enriched caption pairs and show that the proposed method largely improves image-text retrieval.

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

Scientific figure captioning is a complex task that requires generating contextually appropriate descriptions of visual content. However, existing methods often fall short by utilizing incomplete information, treating the task solely as either an image-to-text or text summarization problem. This limitation hinders the generation of high-quality captions that fully capture the necessary details. Moreover, existing data sourced from arXiv papers contain low-quality captions, posing significant challenges for training large language models (LLMs). In this paper, we introduce a framework called Multi-LLM Collaborative Figure Caption Generation (MLBCAP) to address these challenges by leveraging specialized LLMs for distinct sub-tasks. Our approach unfolds in three key modules: (Quality Assessment) We utilize multimodal LLMs to assess the quality of training data, enabling the filtration of low-quality captions. (Diverse Caption Generation) We then employ a strategy of fine-tuning/prompting multiple LLMs on the captioning task to generate candidate captions. (Judgment) Lastly, we prompt a prominent LLM to select the highest quality caption from the candidates, followed by refining any remaining inaccuracies. Human evaluations demonstrate that informative captions produced by our approach rank better than human-written captions, highlighting its effectiveness. Our code is available at https://github.com/teamreboott/MLBCAP

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.

Image captioning is a fundamental task in vision-language understanding, where the model predicts a textual informative caption to a given input image. In this paper, we present a simple approach to address this task. We use CLIP encoding as a prefix to the caption, by employing a simple mapping network, and then fine-tunes a language model to generate the image captions. The recently proposed CLIP model contains rich semantic features which were trained with textual context, making it best for vision-language perception. Our key idea is that together with a pre-trained language model (GPT2), we obtain a wide understanding of both visual and textual data. Hence, our approach only requires rather quick training to produce a competent captioning model. Without additional annotations or pre-training, it efficiently generates meaningful captions for large-scale and diverse datasets. Surprisingly, our method works well even when only the mapping network is trained, while both CLIP and the language model remain frozen, allowing a lighter architecture with less trainable parameters. Through quantitative evaluation, we demonstrate our model achieves comparable results to state-of-the-art methods on the challenging Conceptual Captions and nocaps datasets, while it is simpler, faster, and lighter. Our code is available in https://github.com/rmokady/CLIP_prefix_caption.

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

Weakly-Supervised Scene Graph Generation (WSSGG) research has recently emerged as an alternative to the fully-supervised approach that heavily relies on costly annotations. In this regard, studies on WSSGG have utilized image captions to obtain unlocalized triplets while primarily focusing on grounding the unlocalized triplets over image regions. However, they have overlooked the two issues involved in the triplet formation process from the captions: 1) Semantic over-simplification issue arises when extracting triplets from captions, where fine-grained predicates in captions are undesirably converted into coarse-grained predicates, resulting in a long-tailed predicate distribution, and 2) Low-density scene graph issue arises when aligning the triplets in the caption with entity/predicate classes of interest, where many triplets are discarded and not used in training, leading to insufficient supervision. To tackle the two issues, we propose a new approach, i.e., Large Language Model for weakly-supervised SGG (LLM4SGG), where we mitigate the two issues by leveraging the LLM's in-depth understanding of language and reasoning ability during the extraction of triplets from captions and alignment of entity/predicate classes with target data. To further engage the LLM in these processes, we adopt the idea of Chain-of-Thought and the in-context few-shot learning strategy. To validate the effectiveness of LLM4SGG, we conduct extensive experiments on Visual Genome and GQA datasets, showing significant improvements in both Recall@K and mean Recall@K compared to the state-of-the-art WSSGG methods. A further appeal is that LLM4SGG is data-efficient, enabling effective model training with a small amount of training images.

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.

Novel object captioning (NOC) aims to describe images containing objects without observing their ground truth captions during training. Due to the absence of caption annotation, captioning models cannot be directly optimized via sequence-to-sequence training or CIDEr optimization. As a result, we present Paraphrasing-to-Captioning (P2C), a two-stage learning framework for NOC, which would heuristically optimize the output captions via paraphrasing. With P2C, the captioning model first learns paraphrasing from a language model pre-trained on text-only corpus, allowing expansion of the word bank for improving linguistic fluency. To further enforce the output caption sufficiently describing the visual content of the input image, we perform self-paraphrasing for the captioning model with fidelity and adequacy objectives introduced. Since no ground truth captions are available for novel object images during training, our P2C leverages cross-modality (image-text) association modules to ensure the above caption characteristics can be properly preserved. In the experiments, we not only show that our P2C achieves state-of-the-art performances on nocaps and COCO Caption datasets, we also verify the effectiveness and flexibility of our learning framework by replacing language and cross-modality association models for NOC. Implementation details and code are available in the supplementary materials.

Humans describe complex scenes with compositionality, using simple text descriptions enriched with links and relationships. While vision-language research has aimed to develop models with compositional understanding capabilities, this is not reflected yet in existing datasets which, for the most part, still use plain text to describe images. In this work, we propose a new annotation strategy, graph-based captioning (GBC) that describes an image using a labelled graph structure, with nodes of various types. The nodes in GBC are created using, in a first stage, object detection and dense captioning tools nested recursively to uncover and describe entity nodes, further linked together in a second stage by highlighting, using new types of nodes, compositions and relations among entities. Since all GBC nodes hold plain text descriptions, GBC retains the flexibility found in natural language, but can also encode hierarchical information in its edges. We demonstrate that GBC can be produced automatically, using off-the-shelf multimodal LLMs and open-vocabulary detection models, by building a new dataset, GBC10M, gathering GBC annotations for about 10M images of the CC12M dataset. We use GBC10M to showcase the wealth of node captions uncovered by GBC, as measured with CLIP training. We show that using GBC nodes' annotations -- notably those stored in composition and relation nodes -- results in significant performance boost on downstream models when compared to other dataset formats. To further explore the opportunities provided by GBC, we also propose a new attention mechanism that can leverage the entire GBC graph, with encouraging experimental results that show the extra benefits of incorporating the graph structure. Our datasets are released at https://huggingface.co/graph-based-captions.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

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.

Image captioning is a multimodal problem that has drawn extensive attention in both the natural language processing and computer vision community. In this paper, we present a novel image captioning architecture to better explore semantics available in captions and leverage that to enhance both image representation and caption generation. Our models first construct caption-guided visual relationship graphs that introduce beneficial inductive bias using weakly supervised multi-instance learning. The representation is then enhanced with neighbouring and contextual nodes with their textual and visual features. During generation, the model further incorporates visual relationships using multi-task learning for jointly predicting word and object/predicate tag sequences. We perform extensive experiments on the MSCOCO dataset, showing that the proposed framework significantly outperforms the baselines, resulting in the state-of-the-art performance under a wide range of evaluation metrics.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Supervised visual captioning models typically require a large scale of images or videos paired with descriptions in a specific language (i.e., the vision-caption pairs) for training. However, collecting and labeling large-scale datasets is time-consuming and expensive for many scenarios and languages. Therefore, sufficient labeled pairs are usually not available. To deal with the label shortage problem, we present a simple yet effective zero-shot approach MultiCapCLIP that can generate visual captions for different scenarios and languages without any labeled vision-caption pairs of downstream datasets. In the training stage, MultiCapCLIP only requires text data for input. Then it conducts two main steps: 1) retrieving concept prompts that preserve the corresponding domain knowledge of new scenarios; 2) auto-encoding the prompts to learn writing styles to output captions in a desired language. In the testing stage, MultiCapCLIP instead takes visual data as input directly to retrieve the concept prompts to generate the final visual descriptions. The extensive experiments on image and video captioning across four benchmarks and four languages (i.e., English, Chinese, German, and French) confirm the effectiveness of our approach. Compared with state-of-the-art zero-shot and weakly-supervised methods, our method achieves 4.8% and 21.5% absolute improvements in terms of BLEU@4 and CIDEr metrics. Our code is available at https://github.com/yangbang18/MultiCapCLIP.

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.

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.

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.

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.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

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

Image captioning is one of the straightforward tasks that can take advantage of large-scale web-crawled data which provides rich knowledge about the visual world for a captioning model. However, since web-crawled data contains image-text pairs that are aligned at different levels, the inherent noises (e.g., misaligned pairs) make it difficult to learn a precise captioning model. While the filtering strategy can effectively remove noisy data, however, it leads to a decrease in learnable knowledge and sometimes brings about a new problem of data deficiency. To take the best of both worlds, we propose a noise-aware learning framework, which learns rich knowledge from the whole web-crawled data while being less affected by the noises. This is achieved by the proposed quality controllable model, which is learned using alignment levels of the image-text pairs as an additional control signal during training. The alignment-conditioned training allows the model to generate high-quality captions of well-aligned by simply setting the control signal to desired alignment level at inference time. Through in-depth analysis, we show that our controllable captioning model is effective in handling noise. In addition, with two tasks of zero-shot captioning and text-to-image retrieval using generated captions (i.e., self-retrieval), we also demonstrate our model can produce high-quality captions in terms of descriptiveness and distinctiveness. Code is available at https://github.com/kakaobrain/noc.

Image captioning aims to describe visual content in natural language. As 'a picture is worth a thousand words', there could be various correct descriptions for an image. However, with maximum likelihood estimation as the training objective, the captioning model is penalized whenever its prediction mismatches with the label. For instance, when the model predicts a word expressing richer semantics than the label, it will be penalized and optimized to prefer more concise expressions, referred to as conciseness optimization. In contrast, predictions that are more concise than labels lead to richness optimization. Such conflicting optimization directions could eventually result in the model generating general descriptions. In this work, we introduce Semipermeable MaxImum Likelihood Estimation (SMILE), which allows richness optimization while blocking conciseness optimization, thus encouraging the model to generate longer captions with more details. Extensive experiments on two mainstream image captioning datasets MSCOCO and Flickr30K demonstrate that SMILE significantly enhances the descriptiveness of generated captions. We further provide in-depth investigations to facilitate a better understanding of how SMILE works.

We introduce a versatile flexible-captioning vision-language model (VLM) capable of generating region-specific descriptions of varying lengths. The model, FlexCap, is trained to produce length-conditioned captions for input bounding boxes, and this allows control over the information density of its output, with descriptions ranging from concise object labels to detailed captions. To achieve this we create large-scale training datasets of image region descriptions of varying length, starting from captioned images. This flexible-captioning capability has several valuable applications. First, FlexCap demonstrates superior performance in dense captioning tasks on the Visual Genome dataset. Second, a visual question answering (VQA) system can be built by employing FlexCap to generate localized descriptions as inputs to a large language model. The resulting system achieves state-of-the-art zero-shot performance on a number of VQA datasets. We also demonstrate a localize-then-describe approach with FlexCap can be better at open-ended object detection than a describe-then-localize approach with other VLMs. We highlight a novel characteristic of FlexCap, which is its ability to extract diverse visual information through prefix conditioning. Finally, we qualitatively demonstrate FlexCap's broad applicability in tasks such as image labeling, object attribute recognition, and visual dialog. Project webpage: https://flex-cap.github.io .

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

Existing visual parsers for molecule diagrams translate pixel-based raster images such as PNGs to chemical structure representations (e.g., SMILES). However, PDFs created by word processors including LaTeX and Word provide explicit locations and shapes for characters, lines, and polygons. We extract symbols from born-digital PDF molecule images and then apply simple graph transformations to capture both visual and chemical structure in editable ChemDraw files (CDXML). Our fast ( PDF rightarrow visual graph rightarrow chemical graph ) pipeline does not require GPUs, Optical Character Recognition (OCR) or vectorization. We evaluate on standard benchmarks using SMILES strings, along with a novel evaluation that provides graph-based metrics and error compilation using LgEval. The geometric information in born-digital PDFs produces a highly accurate parser, motivating generating training data for visual parsers that recognize from raster images, with extracted graphics, visual structure, and chemical structure as annotations. To do this we render SMILES strings in Indigo, parse molecule structure, and then validate recognized structure to select correct files.

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

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

The task of image captioning demands an algorithm to generate natural language descriptions of visual inputs. Recent advancements have seen a convergence between image captioning research and the development of Large Language Models (LLMs) and Multimodal LLMs -- like GPT-4V and Gemini -- which extend the capabilities of text-only LLMs to multiple modalities. This paper investigates whether Multimodal LLMs can supplant traditional image captioning networks by evaluating their performance on various image description benchmarks. We explore both the zero-shot capabilities of these models and their adaptability to different semantic domains through fine-tuning methods, including prompt learning, prefix tuning, and low-rank adaptation. Our results demonstrate that while Multimodal LLMs achieve impressive zero-shot performance, fine-tuning for specific domains while maintaining their generalization capabilities intact remains challenging. We discuss the implications of these findings for future research in image captioning and the development of more adaptable Multimodal LLMs.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a meticulously curated, comprehensive instruction dataset expressly designed for the biomolecular realm. Mol-Instructions is composed of three pivotal components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions, each curated to enhance the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on the representative LLM, we underscore the potency of Mol-Instructions to enhance the adaptability and cognitive acuity of large models within the complex sphere of biomolecular studies, thereby promoting advancements in the biomolecular research community. Mol-Instructions is made publicly accessible for future research endeavors and will be subjected to continual updates for enhanced applicability.

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.

We present the first approach to automated audio captioning. We employ an encoder-decoder scheme with an alignment model in between. The input to the encoder is a sequence of log mel-band energies calculated from an audio file, while the output is a sequence of words, i.e. a caption. The encoder is a multi-layered, bi-directional gated recurrent unit (GRU) and the decoder a multi-layered GRU with a classification layer connected to the last GRU of the decoder. The classification layer and the alignment model are fully connected layers with shared weights between timesteps. The proposed method is evaluated using data drawn from a commercial sound effects library, ProSound Effects. The resulting captions were rated through metrics utilized in machine translation and image captioning fields. Results from metrics show that the proposed method can predict words appearing in the original caption, but not always correctly ordered.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which incorporates functional group information directly into the representations. This strategic reduction in tokenization granularity in a way that is intentionally interfaced with key drivers of functional properties (i.e., functional groups) enhances the model's understanding of chemical language, expands the chemical lexicon, more effectively bridging SMILES and natural language, and ultimately advances the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. By leveraging contrastive learning, FARM aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

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.

Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery.

Modern image captioning models are usually trained with text similarity objectives. However, since reference captions in public datasets often describe the most salient common objects, models trained with text similarity objectives tend to ignore specific and detailed aspects of an image that distinguish it from others. Toward more descriptive and distinctive caption generation, we propose using CLIP, a multimodal encoder trained on huge image-text pairs from web, to calculate multimodal similarity and use it as a reward function. We also propose a simple finetuning strategy of the CLIP text encoder to improve grammar that does not require extra text annotation. This completely eliminates the need for reference captions during the reward computation. To comprehensively evaluate descriptive captions, we introduce FineCapEval, a new dataset for caption evaluation with fine-grained criteria: overall, background, object, relations. In our experiments on text-to-image retrieval and FineCapEval, the proposed CLIP-guided model generates more distinctive captions than the CIDEr-optimized model. We also show that our unsupervised grammar finetuning of the CLIP text encoder alleviates the degeneration problem of the naive CLIP reward. Lastly, we show human analysis where the annotators strongly prefer the CLIP reward to the CIDEr and MLE objectives according to various criteria. Code and Data: https://github.com/j-min/CLIP-Caption-Reward

Generating a description of an image is called image captioning. Image captioning requires to recognize the important objects, their attributes and their relationships in an image. It also needs to generate syntactically and semantically correct sentences. Deep learning-based techniques are capable of handling the complexities and challenges of image captioning. In this survey paper, we aim to present a comprehensive review of existing deep learning-based image captioning techniques. We discuss the foundation of the techniques to analyze their performances, strengths and limitations. We also discuss the datasets and the evaluation metrics popularly used in deep learning based automatic image captioning.

Image captioning is conventionally formulated as the task of generating captions for images that match the distribution of reference image-caption pairs. However, reference captions in standard captioning datasets are short and may not uniquely identify the images they describe. These problems are further exacerbated when models are trained directly on image-alt text pairs collected from the internet. In this work, we show that it is possible to generate more specific captions with minimal changes to the training process. We implement classifier-free guidance for an autoregressive captioning model by fine-tuning it to estimate both conditional and unconditional distributions over captions. The guidance scale applied at decoding controls a trade-off between maximizing p(caption|image) and p(image|caption). Compared to standard greedy decoding, decoding with a guidance scale of 2 substantially improves reference-free metrics such as CLIPScore (0.808 vs. 0.775) and captiontoimage retrieval performance in the CLIP embedding space (recall@1 44.6% vs. 26.5%), but worsens standard reference-based captioning metrics (e.g., CIDEr 78.6 vs 126.1). We further explore the use of language models to guide the decoding process, obtaining small improvements over the Pareto frontier of reference-free vs. reference-based captioning metrics that arises from classifier-free guidance, and substantially improving the quality of captions generated from a model trained only on minimally curated web data.

Researchers use figures to communicate rich, complex information in scientific papers. The captions of these figures are critical to conveying effective messages. However, low-quality figure captions commonly occur in scientific articles and may decrease understanding. In this paper, we propose an end-to-end neural framework to automatically generate informative, high-quality captions for scientific figures. To this end, we introduce SCICAP, a large-scale figure-caption dataset based on computer science arXiv papers published between 2010 and 2020. After pre-processing - including figure-type classification, sub-figure identification, text normalization, and caption text selection - SCICAP contained more than two million figures extracted from over 290,000 papers. We then established baseline models that caption graph plots, the dominant (19.2%) figure type. The experimental results showed both opportunities and steep challenges of generating captions for scientific figures.

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.

Image descriptions can help visually impaired people to quickly understand the image content. While we made significant progress in automatically describing images and optical character recognition, current approaches are unable to include written text in their descriptions, although text is omnipresent in human environments and frequently critical to understand our surroundings. To study how to comprehend text in the context of an image we collect a novel dataset, TextCaps, with 145k captions for 28k images. Our dataset challenges a model to recognize text, relate it to its visual context, and decide what part of the text to copy or paraphrase, requiring spatial, semantic, and visual reasoning between multiple text tokens and visual entities, such as objects. We study baselines and adapt existing approaches to this new task, which we refer to as image captioning with reading comprehension. Our analysis with automatic and human studies shows that our new TextCaps dataset provides many new technical challenges over previous datasets.

With the emergence of diffusion models as the frontline of generative models, many researchers have proposed molecule generation techniques using conditional diffusion models. However, due to the fundamental nature of a molecule, which carries highly entangled correlations within a small number of atoms and bonds, it becomes difficult for a model to connect raw data with the conditions when the conditions become more complex as natural language. To address this, here we present a novel latent diffusion model dubbed LDMol, which enables a natural text-conditioned molecule generation. Specifically, LDMol is composed of three building blocks: a molecule encoder that produces a chemically informative feature space, a natural language-conditioned latent diffusion model using a Diffusion Transformer (DiT), and an autoregressive decoder for molecule re. In particular, recognizing that multiple SMILES notations can represent the same molecule, we employ a contrastive learning strategy to extract the chemical informative feature space. LDMol not only beats the existing baselines on the text-to-molecule generation benchmark but is also capable of zero-shot inference with unseen scenarios. Furthermore, we show that LDMol can be applied to downstream tasks such as molecule-to-text retrieval and text-driven molecule editing, demonstrating its versatility as a diffusion model.

Image captioning, like many tasks involving vision and language, currently relies on Transformer-based architectures for extracting the semantics in an image and translating it into linguistically coherent descriptions. Although successful, the attention operator only considers a weighted summation of projections of the current input sample, therefore ignoring the relevant semantic information which can come from the joint observation of other samples. In this paper, we devise a network which can perform attention over activations obtained while processing other training samples, through a prototypical memory model. Our memory models the distribution of past keys and values through the definition of prototype vectors which are both discriminative and compact. Experimentally, we assess the performance of the proposed model on the COCO dataset, in comparison with carefully designed baselines and state-of-the-art approaches, and by investigating the role of each of the proposed components. We demonstrate that our proposal can increase the performance of an encoder-decoder Transformer by 3.7 CIDEr points both when training in cross-entropy only and when fine-tuning with self-critical sequence training. Source code and trained models are available at: https://github.com/aimagelab/PMA-Net.

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.

Neural captioners are typically trained to mimic human-generated references without optimizing for any specific communication goal, leading to problems such as the generation of vague captions. In this paper, we show that fine-tuning an out-of-the-box neural captioner with a self-supervised discriminative communication objective helps to recover a plain, visually descriptive language that is more informative about image contents. Given a target image, the system must learn to produce a description that enables an out-of-the-box text-conditioned image retriever to identify such image among a set of candidates. We experiment with the popular ClipCap captioner, also replicating the main results with BLIP. In terms of similarity to ground-truth human descriptions, the captions emerging from discriminative finetuning lag slightly behind those generated by the non-finetuned model, when the latter is trained and tested on the same caption dataset. However, when the model is used without further tuning to generate captions for out-of-domain datasets, our discriminatively-finetuned captioner generates descriptions that resemble human references more than those produced by the same captioner without finetuning. We further show that, on the Conceptual Captions dataset, discriminatively finetuned captions are more helpful than either vanilla ClipCap captions or ground-truth captions for human annotators tasked with an image discrimination task.

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

Image captioning aims at generating descriptive and meaningful textual descriptions of images, enabling a broad range of vision-language applications. Prior works have demonstrated that harnessing the power of Contrastive Image Language Pre-training (CLIP) offers a promising approach to achieving zero-shot captioning, eliminating the need for expensive caption annotations. However, the widely observed modality gap in the latent space of CLIP harms the performance of zero-shot captioning by breaking the alignment between paired image-text features. To address this issue, we conduct an analysis on the CLIP latent space which leads to two findings. Firstly, we observe that the CLIP's visual feature of image subregions can achieve closer proximity to the paired caption due to the inherent information loss in text descriptions. In addition, we show that the modality gap between a paired image-text can be empirically modeled as a zero-mean Gaussian distribution. Motivated by the findings, we propose a novel zero-shot image captioning framework with text-only training to reduce the modality gap. In particular, we introduce a subregion feature aggregation to leverage local region information, which produces a compact visual representation for matching text representation. Moreover, we incorporate a noise injection and CLIP reranking strategy to boost captioning performance. We also extend our framework to build a zero-shot VQA pipeline, demonstrating its generality. Through extensive experiments on common captioning and VQA datasets such as MSCOCO, Flickr30k and VQAV2, we show that our method achieves remarkable performance improvements. Code is available at https://github.com/Artanic30/MacCap.

Image captioning models typically follow an encoder-decoder architecture which uses abstract image feature vectors as input to the encoder. One of the most successful algorithms uses feature vectors extracted from the region proposals obtained from an object detector. In this work we introduce the Object Relation Transformer, that builds upon this approach by explicitly incorporating information about the spatial relationship between input detected objects through geometric attention. Quantitative and qualitative results demonstrate the importance of such geometric attention for image captioning, leading to improvements on all common captioning metrics on the MS-COCO dataset.

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

With the development of computer-assisted techniques, research communities including biochemistry and deep learning have been devoted into the drug discovery field for over a decade. Various applications of deep learning have drawn great attention in drug discovery, such as molecule generation, molecular property prediction, retrosynthesis prediction, and reaction prediction. While most existing surveys only focus on one of the applications, limiting the view of researchers in the community. In this paper, we present a comprehensive review on the aforementioned four aspects, and discuss the relationships among different applications. The latest literature and classical benchmarks are presented for better understanding the development of variety of approaches. We commence by summarizing the molecule representation format in these works, followed by an introduction of recent proposed approaches for each of the four tasks. Furthermore, we review a variety of commonly used datasets and evaluation metrics and compare the performance of deep learning-based models. Finally, we conclude by identifying remaining challenges and discussing the future trend for deep learning methods in drug discovery.

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.

Large datasets of paired images and text have become increasingly popular for learning generic representations for vision and vision-and-language tasks. Such datasets have been built by querying search engines or collecting HTML alt-text -- since web data is noisy, they require complex filtering pipelines to maintain quality. We explore alternate data sources to collect high quality data with minimal filtering. We introduce RedCaps -- a large-scale dataset of 12M image-text pairs collected from Reddit. Images and captions from Reddit depict and describe a wide variety of objects and scenes. We collect data from a manually curated set of subreddits, which give coarse image labels and allow us to steer the dataset composition without labeling individual instances. We show that captioning models trained on RedCaps produce rich and varied captions preferred by humans, and learn visual representations that transfer to many downstream tasks.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

The massive growth of image-text data through web crawling inherently presents the challenge of variability in data quality. This paper introduces a novel algorithm, rooted in human knowledge, to compress this vast corpus of web-crawled image-text datasets to a compact and high-quality form. Our method unfolds in three major steps. First, we collect an image-text dataset, wherein each image is associated with multiple captions sourced from diverse origins. Then, to systemically capture human preferences regarding the best caption paired with each image, we establish a comprehensive set of both subjective and objective criteria for critically guiding the alignment assessment from labelers. Lastly, we train a reward model on the annotated dataset to internalize the nuanced human understanding of image-text alignment. The resulting reward model thus can act as a human-like referee to filter misaligned/low-quality image-text pairs. Extensive experiments demonstrate that we are able to secure (or even improve) model performance by compressing the image-text datasets up to ~90%. An impressive example is that, by aggressively reducing the total training sample from 130M to 15.5M (e.g., ~9x smaller), our BLIP-B/16 models still consistently show superior performance compared with the full-size-dataset counterpart on image-text retrieval (Flickr30K, COCO) by ~2.5% in Recall@1, and on image-captioning (Nocaps, COCO) by ~10.0% in CIDEr and ~2.7% in SPICE.

Recent text-to-image matching models apply contrastive learning to large corpora of uncurated pairs of images and sentences. While such models can provide a powerful score for matching and subsequent zero-shot tasks, they are not capable of generating caption given an image. In this work, we repurpose such models to generate a descriptive text given an image at inference time, without any further training or tuning steps. This is done by combining the visual-semantic model with a large language model, benefiting from the knowledge in both web-scale models. The resulting captions are much less restrictive than those obtained by supervised captioning methods. Moreover, as a zero-shot learning method, it is extremely flexible and we demonstrate its ability to perform image arithmetic in which the inputs can be either images or text, and the output is a sentence. This enables novel high-level vision capabilities such as comparing two images or solving visual analogy tests. Our code is available at: https://github.com/YoadTew/zero-shot-image-to-text.

Video captioning aims to generate natural language descriptions according to the content, where representation learning plays a crucial role. Existing methods are mainly developed within the supervised learning framework via word-by-word comparison of the generated caption against the ground-truth text without fully exploiting linguistic semantics. In this work, we propose a hierarchical modular network to bridge video representations and linguistic semantics from three levels before generating captions. In particular, the hierarchy is composed of: (I) Entity level, which highlights objects that are most likely to be mentioned in captions. (II) Predicate level, which learns the actions conditioned on highlighted objects and is supervised by the predicate in captions. (III) Sentence level, which learns the global semantic representation and is supervised by the whole caption. Each level is implemented by one module. Extensive experimental results show that the proposed method performs favorably against the state-of-the-art models on the two widely-used benchmarks: MSVD 104.0% and MSR-VTT 51.5% in CIDEr score.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Image captioning, which generates natural language descriptions of the visual information in an image, is a crucial task in vision-language research. Previous models have typically addressed this task by aligning the generative capabilities of machines with human intelligence through statistical fitting of existing datasets. While effective for normal images, they may struggle to accurately describe those where certain parts of the image are obscured or edited, unlike humans who excel in such cases. These weaknesses they exhibit, including hallucinations and limited interpretability, often hinder performance in scenarios with shifted association patterns. In this paper, we present a generic image captioning framework that employs causal inference to make existing models more capable of interventional tasks, and counterfactually explainable. Our approach includes two variants leveraging either total effect or natural direct effect. Integrating them into the training process enables models to handle counterfactual scenarios, increasing their generalizability. Extensive experiments on various datasets show that our method effectively reduces hallucinations and improves the model's faithfulness to images, demonstrating high portability across both small-scale and large-scale image-to-text models. The code is available at https://github.com/Aman-4-Real/See-or-Guess.

Molecule generation with desired properties has grown immensely in popularity by disruptively changing the way scientists design molecular structures and providing support for chemical and materials design. However, despite the promising outcome, previous machine learning-based deep generative models suffer from a reliance on complex, task-specific fine-tuning, limited dimensional latent spaces, or the quality of expert rules. In this work, we propose MolGen, a pre-trained molecular language model that effectively learns and shares knowledge across multiple generation tasks and domains. Specifically, we pre-train MolGen with the chemical language SELFIES on more than 100 million unlabelled molecules. We further propose multi-task molecular prefix tuning across several molecular generation tasks and different molecular domains (synthetic & natural products) with a self-feedback mechanism. Extensive experiments show that MolGen can obtain superior performances on well-known molecular generation benchmark datasets. The further analysis illustrates that MolGen can accurately capture the distribution of molecules, implicitly learn their structural characteristics, and efficiently explore the chemical space with the guidance of multi-task molecular prefix tuning. Codes, datasets, and the pre-trained model will be available in https://github.com/zjunlp/MolGen.

We propose Wolf, a WOrLd summarization Framework for accurate video captioning. Wolf is an automated captioning framework that adopts a mixture-of-experts approach, leveraging complementary strengths of Vision Language Models (VLMs). By utilizing both image and video models, our framework captures different levels of information and summarizes them efficiently. Our approach can be applied to enhance video understanding, auto-labeling, and captioning. To evaluate caption quality, we introduce CapScore, an LLM-based metric to assess the similarity and quality of generated captions compared to the ground truth captions. We further build four human-annotated datasets in three domains: autonomous driving, general scenes, and robotics, to facilitate comprehensive comparisons. We show that Wolf achieves superior captioning performance compared to state-of-the-art approaches from the research community (VILA1.5, CogAgent) and commercial solutions (Gemini-Pro-1.5, GPT-4V). For instance, in comparison with GPT-4V, Wolf improves CapScore both quality-wise by 55.6% and similarity-wise by 77.4% on challenging driving videos. Finally, we establish a benchmark for video captioning and introduce a leaderboard, aiming to accelerate advancements in video understanding, captioning, and data alignment. Leaderboard: https://wolfv0.github.io/leaderboard.html.

Language-image pre-training largely relies on how precisely and thoroughly a text describes its paired image. In practice, however, the contents of an image can be so rich that well describing them requires lengthy captions (e.g., with 10 sentences), which are usually missing in existing datasets. Consequently, there are currently no clear evidences on whether and how language-image pre-training could benefit from long captions. To figure this out, we first re-caption 30M images with detailed descriptions using a pre-trained Multi-modality Large Language Model (MLLM), and then study the usage of the resulting captions under a contrastive learning framework. We observe that, each sentence within a long caption is very likely to describe the image partially (e.g., an object). Motivated by this, we propose to dynamically sample sub-captions from the text label to construct multiple positive pairs, and introduce a grouping loss to match the embeddings of each sub-caption with its corresponding local image patches in a self-supervised manner. Experimental results on a wide rage of downstream tasks demonstrate the consistent superiority of our method, termed DreamLIP, over previous alternatives, highlighting its fine-grained representational capacity. It is noteworthy that, on the tasks of image-text retrieval and semantic segmentation, our model trained with 30M image-text pairs achieves on par or even better performance than CLIP trained with 400M pairs. Project page is available at https://zyf0619sjtu.github.io/dream-lip.

We present Pix2Cap-COCO, the first panoptic pixel-level caption dataset designed to advance fine-grained visual understanding. To achieve this, we carefully design an automated annotation pipeline that prompts GPT-4V to generate pixel-aligned, instance-specific captions for individual objects within images, enabling models to learn more granular relationships between objects and their contexts. This approach results in 167,254 detailed captions, with an average of 22.94 words per caption. Building on Pix2Cap-COCO, we introduce a novel task, panoptic segmentation-captioning, which challenges models to recognize instances in an image and provide detailed descriptions for each simultaneously. To benchmark this task, we design a robust baseline based on X-Decoder. The experimental results demonstrate that Pix2Cap-COCO is a particularly challenging dataset, as it requires models to excel in both fine-grained visual understanding and detailed language generation. Furthermore, we leverage Pix2Cap-COCO for Supervised Fine-Tuning (SFT) on large multimodal models (LMMs) to enhance their performance. For example, training with Pix2Cap-COCO significantly improves the performance of GPT4RoI, yielding gains in CIDEr +1.4%, ROUGE +0.4%, and SPICE +0.5% on Visual Genome dataset, and strengthens its region understanding ability on the ViP-BENCH, with an overall improvement of +5.1%, including notable increases in recognition accuracy +11.2% and language generation quality +22.2%.

In this paper we describe the Microsoft COCO Caption dataset and evaluation server. When completed, the dataset will contain over one and a half million captions describing over 330,000 images. For the training and validation images, five independent human generated captions will be provided. To ensure consistency in evaluation of automatic caption generation algorithms, an evaluation server is used. The evaluation server receives candidate captions and scores them using several popular metrics, including BLEU, METEOR, ROUGE and CIDEr. Instructions for using the evaluation server are provided.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

Image Captioning, the task of automatic generation of image captions, has attracted attentions from researchers in many fields of computer science, being computer vision, natural language processing and machine learning in recent years. This paper contributes to research on Image Captioning task in terms of extending dataset to a different language - Vietnamese. So far, there is no existed Image Captioning dataset for Vietnamese language, so this is the foremost fundamental step for developing Vietnamese Image Captioning. In this scope, we first build a dataset which contains manually written captions for images from Microsoft COCO dataset relating to sports played with balls, we called this dataset UIT-ViIC. UIT-ViIC consists of 19,250 Vietnamese captions for 3,850 images. Following that, we evaluate our dataset on deep neural network models and do comparisons with English dataset and two Vietnamese datasets built by different methods. UIT-ViIC is published on our lab website for research purposes.

Controllable image captioning is an emerging multimodal topic that aims to describe the image with natural language following human purpose, e.g., looking at the specified regions or telling in a particular text style. State-of-the-art methods are trained on annotated pairs of input controls and output captions. However, the scarcity of such well-annotated multimodal data largely limits their usability and scalability for interactive AI systems. Leveraging unimodal instruction-following foundation models is a promising alternative that benefits from broader sources of data. In this paper, we present Caption AnyThing (CAT), a foundation model augmented image captioning framework supporting a wide range of multimodel controls: 1) visual controls, including points, boxes, and trajectories; 2) language controls, such as sentiment, length, language, and factuality. Powered by Segment Anything Model (SAM) and ChatGPT, we unify the visual and language prompts into a modularized framework, enabling the flexible combination between different controls. Extensive case studies demonstrate the user intention alignment capabilities of our framework, shedding light on effective user interaction modeling in vision-language applications. Our code is publicly available at https://github.com/ttengwang/Caption-Anything.

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.

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

Recent advancements in multimodal models highlight the value of rewritten captions for improving performance, yet key challenges remain. For example, while synthetic captions often provide superior quality and image-text alignment, it is not clear whether they can fully replace AltTexts: the role of synthetic captions and their interaction with original web-crawled AltTexts in pre-training is still not well understood. Moreover, different multimodal foundation models may have unique preferences for specific caption formats, but efforts to identify the optimal captions for each model remain limited. In this work, we propose a novel, controllable, and scalable captioning pipeline designed to generate diverse caption formats tailored to various multimodal models. By examining Short Synthetic Captions (SSC) towards Dense Synthetic Captions (DSC+) as case studies, we systematically explore their effects and interactions with AltTexts across models such as CLIP, multimodal LLMs, and diffusion models. Our findings reveal that a hybrid approach that keeps both synthetic captions and AltTexts can outperform the use of synthetic captions alone, improving both alignment and performance, with each model demonstrating preferences for particular caption formats. This comprehensive analysis provides valuable insights into optimizing captioning strategies, thereby advancing the pre-training of multimodal foundation models.

This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

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.

Massive web datasets play a key role in the success of large vision-language models like CLIP and Flamingo. However, the raw web data is noisy, and existing filtering methods to reduce noise often come at the expense of data diversity. Our work focuses on caption quality as one major source of noise, and studies how generated captions can increase the utility of web-scraped datapoints with nondescript text. Through exploring different mixing strategies for raw and generated captions, we outperform the best filtering method proposed by the DataComp benchmark by 2% on ImageNet and 4% on average across 38 tasks, given a candidate pool of 128M image-text pairs. Our best approach is also 2x better at Flickr and MS-COCO retrieval. We then analyze what makes synthetic captions an effective source of text supervision. In experimenting with different image captioning models, we also demonstrate that the performance of a model on standard image captioning benchmarks (e.g., NoCaps CIDEr) is not a reliable indicator of the utility of the captions it generates for multimodal training. Finally, our experiments with using generated captions at DataComp's large scale (1.28B image-text pairs) offer insights into the limitations of synthetic text, as well as the importance of image curation with increasing training data quantity.

Image-to-text generation aims to describe images using natural language. Recently, zero-shot image captioning based on pre-trained vision-language models (VLMs) and large language models (LLMs) has made significant progress. However, we have observed and empirically demonstrated that these methods are susceptible to modality bias induced by LLMs and tend to generate descriptions containing objects (entities) that do not actually exist in the image but frequently appear during training (i.e., object hallucination). In this paper, we propose ViECap, a transferable decoding model that leverages entity-aware decoding to generate descriptions in both seen and unseen scenarios. ViECap incorporates entity-aware hard prompts to guide LLMs' attention toward the visual entities present in the image, enabling coherent caption generation across diverse scenes. With entity-aware hard prompts, ViECap is capable of maintaining performance when transferring from in-domain to out-of-domain scenarios. Extensive experiments demonstrate that ViECap sets a new state-of-the-art cross-domain (transferable) captioning and performs competitively in-domain captioning compared to previous VLMs-based zero-shot methods. Our code is available at: https://github.com/FeiElysia/ViECap

In this work, we focus on improving the captions generated by image-caption generation systems. We propose a novel re-ranking approach that leverages visual-semantic measures to identify the ideal caption that maximally captures the visual information in the image. Our re-ranker utilizes the Belief Revision framework (Blok et al., 2003) to calibrate the original likelihood of the top-n captions by explicitly exploiting the semantic relatedness between the depicted caption and the visual context. Our experiments demonstrate the utility of our approach, where we observe that our re-ranker can enhance the performance of a typical image-captioning system without the necessity of any additional training or fine-tuning.

Image captioning models are widely used to describe recent and archived pictures with the objective of improving their accessibility and retrieval. Yet, these approaches tend to be inefficient and biased at retrieving people's names. In this work we introduce AstroCaptions, a dataset for the image captioning task. This dataset specifically contains thousands of public fig-ures that are complex to identify for a traditional model. We also propose a novel post-processing method to insert identified people's names inside the caption using explainable AI tools and the grounding capabilities of vi-sion-language models. The results obtained with this method show signifi-cant improvements of captions quality and a potential of reducing halluci-nations. Up to 93.2% of the persons detected can be inserted in the image captions leading to improvements in the BLEU, ROUGE, CIDEr and METEOR scores of each captioning model.

News Image Captioning aims to create captions from news articles and images, emphasizing the connection between textual context and visual elements. Recognizing the significance of human faces in news images and the face-name co-occurrence pattern in existing datasets, we propose a face-naming module for learning better name embeddings. Apart from names, which can be directly linked to an image area (faces), news image captions mostly contain context information that can only be found in the article. We design a retrieval strategy using CLIP to retrieve sentences that are semantically close to the image, mimicking human thought process of linking articles to images. Furthermore, to tackle the problem of the imbalanced proportion of article context and image context in captions, we introduce a simple yet effective method Contrasting with Language Model backbone (CoLaM) to the training pipeline. We conduct extensive experiments to demonstrate the efficacy of our framework. We out-perform the previous state-of-the-art (without external data) by 7.97/5.80 CIDEr scores on GoodNews/NYTimes800k. Our code is available at https://github.com/tingyu215/VACNIC.

Effectively aligning with human judgment when evaluating machine-generated image captions represents a complex yet intriguing challenge. Existing evaluation metrics like CIDEr or CLIP-Score fall short in this regard as they do not take into account the corresponding image or lack the capability of encoding fine-grained details and penalizing hallucinations. To overcome these issues, in this paper, we propose BRIDGE, a new learnable and reference-free image captioning metric that employs a novel module to map visual features into dense vectors and integrates them into multi-modal pseudo-captions which are built during the evaluation process. This approach results in a multimodal metric that properly incorporates information from the input image without relying on reference captions, bridging the gap between human judgment and machine-generated image captions. Experiments spanning several datasets demonstrate that our proposal achieves state-of-the-art results compared to existing reference-free evaluation scores. Our source code and trained models are publicly available at: https://github.com/aimagelab/bridge-score.

This paper examines the problems of severe image-text misalignment and high redundancy in the widely-used large-scale Vision-Language Pre-Training (VLP) datasets. To address these issues, we propose an efficient and straightforward Vision-Language learning algorithm called TL;DR, which aims to compress the existing large VLP data into a small, high-quality set. Our approach consists of two major steps. First, a codebook-based encoder-decoder captioner is developed to select representative samples. Second, a new caption is generated to complement the original captions for selected samples, mitigating the text-image misalignment problem while maintaining uniqueness. As the result, TL;DR enables us to reduce the large dataset into a small set of high-quality data, which can serve as an alternative pre-training dataset. This algorithm significantly speeds up the time-consuming pretraining process. Specifically, TL;DR can compress the mainstream VLP datasets at a high ratio, e.g., reduce well-cleaned CC3M dataset from 2.82M to 0.67M (sim24\%) and noisy YFCC15M from 15M to 2.5M (sim16.7\%). Extensive experiments with three popular VLP models over seven downstream tasks show that VLP model trained on the compressed dataset provided by TL;DR can perform similar or even better results compared with training on the full-scale dataset. The code will be made available at https://github.com/showlab/datacentric.vlp.

We address the challenge of representing long captions in vision-language models, such as CLIP. By design these models are limited by fixed, absolute positional encodings, restricting inputs to a maximum of 77 tokens and hindering performance on tasks requiring longer descriptions. Although recent work has attempted to overcome this limit, their proposed approaches struggle to model token relationships over longer distances and simply extend to a fixed new token length. Instead, we propose a generalizable method, named TULIP, able to upgrade the token length to any length for CLIP-like models. We do so by improving the architecture with relative position encodings, followed by a training procedure that (i) distills the original CLIP text encoder into an encoder with relative position encodings and (ii) enhances the model for aligning longer captions with images. By effectively encoding captions longer than the default 77 tokens, our model outperforms baselines on cross-modal tasks such as retrieval and text-to-image generation.

Image captioning systems are unable to generate fine-grained captions as they are trained on data that is either noisy (alt-text) or generic (human annotations). This is further exacerbated by maximum likelihood training that encourages generation of frequently occurring phrases. Previous works have tried to address this limitation by fine-tuning captioners with a self-retrieval (SR) reward. However, we find that SR fine-tuning has a tendency to reduce caption faithfulness and even hallucinate. In this work, we circumvent this bottleneck by improving the MLE initialization of the captioning system and designing a curriculum for the SR fine-tuning process. To this extent, we present (1) Visual Caption Boosting, a novel framework to instill fine-grainedness in generic image captioning datasets while remaining anchored in human annotations; and (2) BagCurri, a carefully designed training curriculum that more optimally leverages the contrastive nature of the self-retrieval reward. Jointly, they enable the captioner to describe fine-grained aspects in the image while preserving faithfulness to ground-truth captions. Our approach outperforms previous work by +8.9% on SR against 99 random distractors (RD100) (Dessi et al., 2023); and +7.6% on ImageCoDe. Additionally, existing metrics to evaluate captioning systems fail to reward diversity or evaluate a model's fine-grained understanding ability. Our third contribution addresses this by proposing self-retrieval from the lens of evaluation. We introduce TrueMatch, a benchmark comprising bags of highly similar images that uses SR to assess the captioner's ability to capture subtle visual distinctions. We evaluate and compare several state-of-the-art open-source MLLMs on TrueMatch, and find that our SR approach outperforms them all by a significant margin (e.g. +4.8% - 7.1% over Cambrian) while having 1-2 orders of magnitude fewer parameters.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Methods for designing organic materials with desired properties have high potential impact across fields such as medicine, renewable energy, petrochemical engineering, and agriculture. However, using generative modeling to design substances with desired properties is difficult because candidate compounds must satisfy multiple constraints, including synthetic accessibility and other metrics that are intuitive to domain experts but challenging to quantify. We propose C5T5, a novel self-supervised pretraining method that enables transformers to make zero-shot select-and-replace edits, altering organic substances towards desired property values. C5T5 operates on IUPAC names -- a standardized molecular representation that intuitively encodes rich structural information for organic chemists but that has been largely ignored by the ML community. Our technique requires no edited molecule pairs to train and only a rough estimate of molecular properties, and it has the potential to model long-range dependencies and symmetric molecular structures more easily than graph-based methods. C5T5 also provides a powerful interface to domain experts: it grants users fine-grained control over the generative process by selecting and replacing IUPAC name fragments, which enables experts to leverage their intuitions about structure-activity relationships. We demonstrate C5T5's effectiveness on four physical properties relevant for drug discovery, showing that it learns successful and chemically intuitive strategies for altering molecules towards desired property values.

Image captioning has long been regarded as a fundamental task in visual understanding. Recently, however, few large vision-language model (LVLM) research discusses model's image captioning performance because of the outdated short-caption benchmarks and unreliable evaluation metrics. In this work, we propose to benchmark detail image caption task by curating high-quality evaluation datasets annotated by human experts, GPT-4V and Gemini-1.5-Pro. We also design a more reliable caption evaluation metric called CAPTURE (CAPtion evaluation by exTracting and coUpling coRE information). CAPTURE extracts visual elements, e.g., objects, attributes and relations from captions, and then matches these elements through three stages, achieving the highest consistency with expert judgements over other rule-based or model-based caption metrics. The proposed benchmark and metric provide reliable evaluation for LVLM's detailed image captioning ability. Guided by this evaluation, we further explore to unleash LVLM's detail caption capabilities by synthesizing high-quality data through a five-stage data construction pipeline. Our pipeline only uses a given LVLM itself and other open-source tools, without any human or GPT-4V annotation in the loop. Experiments show that the proposed data construction strategy significantly improves model-generated detail caption data quality for LVLMs with leading performance, and the data quality can be further improved in a self-looping paradigm. All code and dataset will be publicly available at https://github.com/foundation-multimodal-models/CAPTURE.

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

In this work, we aim to analyze and optimize the EnCLAP framework, a state-of-the-art model in automated audio captioning. We investigate the impact of modifying the acoustic encoder components, explore pretraining with different dataset scales, and study the effectiveness of a reranking scheme. Through extensive experimentation and quantitative analysis of generated captions, we develop EnCLAP++, an enhanced version that significantly surpasses the original.

When describing an image, reading text in the visual scene is crucial to understand the key information. Recent work explores the TextCaps task, i.e. image captioning with reading Optical Character Recognition (OCR) tokens, which requires models to read text and cover them in generated captions. Existing approaches fail to generate accurate descriptions because of their (1) poor reading ability; (2) inability to choose the crucial words among all extracted OCR tokens; (3) repetition of words in predicted captions. To this end, we propose a Confidence-aware Non-repetitive Multimodal Transformers (CNMT) to tackle the above challenges. Our CNMT consists of a reading, a reasoning and a generation modules, in which Reading Module employs better OCR systems to enhance text reading ability and a confidence embedding to select the most noteworthy tokens. To address the issue of word redundancy in captions, our Generation Module includes a repetition mask to avoid predicting repeated word in captions. Our model outperforms state-of-the-art models on TextCaps dataset, improving from 81.0 to 93.0 in CIDEr. Our source code is publicly available.

Image captioning and cross-modal retrieval are examples of tasks that involve the joint analysis of visual and linguistic information. In connection to remote sensing imagery, these tasks can help non-expert users in extracting relevant Earth observation information for a variety of applications. Still, despite some previous efforts, the development and application of vision and language models to the remote sensing domain have been hindered by the relatively small size of the available datasets and models used in previous studies. In this work, we propose RS-CapRet, a Vision and Language method for remote sensing tasks, in particular image captioning and text-image retrieval. We specifically propose to use a highly capable large decoder language model together with image encoders adapted to remote sensing imagery through contrastive language-image pre-training. To bridge together the image encoder and language decoder, we propose training simple linear layers with examples from combining different remote sensing image captioning datasets, keeping the other parameters frozen. RS-CapRet can then generate descriptions for remote sensing images and retrieve images from textual descriptions, achieving SOTA or competitive performance with existing methods. Qualitative results illustrate that RS-CapRet can effectively leverage the pre-trained large language model to describe remote sensing images, retrieve them based on different types of queries, and also show the ability to process interleaved sequences of images and text in a dialogue manner.

State-of-The-Art (SoTA) image captioning models often rely on the Microsoft COCO (MS-COCO) dataset for training. This dataset contains annotations provided by human annotators, who typically produce captions averaging around ten tokens. However, this constraint presents a challenge in effectively capturing complex scenes and conveying detailed information. Furthermore, captioning models tend to exhibit bias towards the ``average'' caption, which captures only the more general aspects. What would happen if we were able to automatically generate longer captions, thereby making them more detailed? Would these captions, evaluated by humans, be more or less representative of the image content compared to the original MS-COCO captions? In this paper, we present a novel approach to address previous challenges by showcasing how captions generated from different SoTA models can be effectively fused, resulting in richer captions. Our proposed method leverages existing models from the literature, eliminating the need for additional training. Instead, it utilizes an image-text based metric to rank the captions generated by SoTA models for a given image. Subsequently, the top two captions are fused using a Large Language Model (LLM). Experimental results demonstrate the effectiveness of our approach, as the captions generated by our model exhibit higher consistency with human judgment when evaluated on the MS-COCO test set. By combining the strengths of various SoTA models, our method enhances the quality and appeal of image captions, bridging the gap between automated systems and the rich, informative nature of human-generated descriptions. This advance opens up new possibilities for generating captions that are more suitable for the training of both vision-language and captioning models.

Image captioning is a crucial task with applications in a wide range of domains, including healthcare and education. Despite extensive research on English image captioning datasets, the availability of such datasets for Vietnamese remains limited, with only two existing datasets. In this study, we introduce KTVIC, a comprehensive Vietnamese Image Captioning dataset focused on the life domain, covering a wide range of daily activities. This dataset comprises 4,327 images and 21,635 Vietnamese captions, serving as a valuable resource for advancing image captioning in the Vietnamese language. We conduct experiments using various deep neural networks as the baselines on our dataset, evaluating them using the standard image captioning metrics, including BLEU, METEOR, CIDEr, and ROUGE. Our findings underscore the effectiveness of the proposed dataset and its potential contributions to the field of image captioning in the Vietnamese context.

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction~(MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions~(PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales~(i.e., chain numbers). Specifically, we propose \textsc{PromptMSP}, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models. The code, data and checkpoints are released at https://github.com/zqgao22/PromptMSP.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Pretraining general-purpose visual features has become a crucial part of tackling many computer vision tasks. While one can learn such features on the extensively-annotated ImageNet dataset, recent approaches have looked at ways to allow for noisy, fewer, or even no annotations to perform such pretraining. Starting from the observation that captioned images are easily crawlable, we argue that this overlooked source of information can be exploited to supervise the training of visual representations. To do so, motivated by the recent progresses in language models, we introduce {\em image-conditioned masked language modeling} (ICMLM) -- a proxy task to learn visual representations over image-caption pairs. ICMLM consists in predicting masked words in captions by relying on visual cues. To tackle this task, we propose hybrid models, with dedicated visual and textual encoders, and we show that the visual representations learned as a by-product of solving this task transfer well to a variety of target tasks. Our experiments confirm that image captions can be leveraged to inject global and localized semantic information into visual representations. Project website: https://europe.naverlabs.com/icmlm.

While an important problem in the vision community is to design algorithms that can automatically caption images, few publicly-available datasets for algorithm development directly address the interests of real users. Observing that people who are blind have relied on (human-based) image captioning services to learn about images they take for nearly a decade, we introduce the first image captioning dataset to represent this real use case. This new dataset, which we call VizWiz-Captions, consists of over 39,000 images originating from people who are blind that are each paired with five captions. We analyze this dataset to (1) characterize the typical captions, (2) characterize the diversity of content found in the images, and (3) compare its content to that found in eight popular vision datasets. We also analyze modern image captioning algorithms to identify what makes this new dataset challenging for the vision community. We publicly-share the dataset with captioning challenge instructions at https://vizwiz.org

This paper presents a novel approach to Zero-Shot Action Recognition. Recent works have explored the detection and classification of objects to obtain semantic information from videos with remarkable performance. Inspired by them, we propose using video captioning methods to extract semantic information about objects, scenes, humans, and their relationships. To the best of our knowledge, this is the first work to represent both videos and labels with descriptive sentences. More specifically, we represent videos using sentences generated via video captioning methods and classes using sentences extracted from documents acquired through search engines on the Internet. Using these representations, we build a shared semantic space employing BERT-based embedders pre-trained in the paraphrasing task on multiple text datasets. The projection of both visual and semantic information onto this space is straightforward, as they are sentences, enabling classification using the nearest neighbor rule. We demonstrate that representing videos and labels with sentences alleviates the domain adaptation problem. Additionally, we show that word vectors are unsuitable for building the semantic embedding space of our descriptions. Our method outperforms the state-of-the-art performance on the UCF101 dataset by 3.3 p.p. in accuracy under the TruZe protocol and achieves competitive results on both the UCF101 and HMDB51 datasets under the conventional protocol (0/50\% - training/testing split). Our code is available at https://github.com/valterlej/zsarcap.

Textual and semantic comprehension of images is essential for generating proper captions. The comprehension requires detection of objects, modeling of relations between them, an assessment of the semantics of the scene and, finally, representing the extracted knowledge in a language space. To achieve rich language capabilities while ensuring good image-language mappings, pretrained language models (LMs) were conditioned on pretrained multi-modal (image-text) models that allow for image inputs. This requires an alignment of the image representation of the multi-modal model with the language representations of a generative LM. However, it is not clear how to best transfer semantics detected by the vision encoder of the multi-modal model to the LM. We introduce two novel ways of constructing a linear mapping that successfully transfers semantics between the embedding spaces of the two pretrained models. The first aligns the embedding space of the multi-modal language encoder with the embedding space of the pretrained LM via token correspondences. The latter leverages additional data that consists of image-text pairs to construct the mapping directly from vision to language space. Using our semantic mappings, we unlock image captioning for LMs without access to gradient information. By using different sources of data we achieve strong captioning performance on MS-COCO and Flickr30k datasets. Even in the face of limited data, our method partly exceeds the performance of other zero-shot and even finetuned competitors. Our ablation studies show that even LMs at a scale of merely 250M parameters can generate decent captions employing our semantic mappings. Our approach makes image captioning more accessible for institutions with restricted computational resources.

Fine-grained few-shot entity extraction in the chemical domain faces two unique challenges. First, compared with entity extraction tasks in the general domain, sentences from chemical papers usually contain more entities. Moreover, entity extraction models usually have difficulty extracting entities of long-tailed types. In this paper, we propose Chem-FINESE, a novel sequence-to-sequence (seq2seq) based few-shot entity extraction approach, to address these two challenges. Our Chem-FINESE has two components: a seq2seq entity extractor to extract named entities from the input sentence and a seq2seq self-validation module to reconstruct the original input sentence from extracted entities. Inspired by the fact that a good entity extraction system needs to extract entities faithfully, our new self-validation module leverages entity extraction results to reconstruct the original input sentence. Besides, we design a new contrastive loss to reduce excessive copying during the extraction process. Finally, we release ChemNER+, a new fine-grained chemical entity extraction dataset that is annotated by domain experts with the ChemNER schema. Experiments in few-shot settings with both ChemNER+ and CHEMET datasets show that our newly proposed framework has contributed up to 8.26% and 6.84% absolute F1-score gains respectively.

Large language models (LLMs)-based image captioning has the capability of describing objects not explicitly observed in training data; yet novel objects occur frequently, necessitating the requirement of sustaining up-to-date object knowledge for open-world comprehension. Instead of relying on large amounts of data and scaling up network parameters, we introduce a highly effective retrieval-augmented image captioning method that prompts LLMs with object names retrieved from External Visual--name memory (EVCap). We build ever-changing object knowledge memory using objects' visuals and names, enabling us to (i) update the memory at a minimal cost and (ii) effortlessly augment LLMs with retrieved object names utilizing a lightweight and fast-to-train model. Our model, which was trained only on the COCO dataset, can be adapted to out-domain data without additional fine-tuning or retraining. Our comprehensive experiments conducted on various benchmarks and synthetic commonsense-violating data demonstrate that EVCap, comprising solely 3.97M trainable parameters, exhibits superior performance compared to other methods of equivalent model size scale. Notably, it achieves competitive performance against specialist SOTAs with an enormous number of parameters. Our code is available at https://jiaxuan-li.github.io/EVCap.

We propose a method that can generate an unambiguous description (known as a referring expression) of a specific object or region in an image, and which can also comprehend or interpret such an expression to infer which object is being described. We show that our method outperforms previous methods that generate descriptions of objects without taking into account other potentially ambiguous objects in the scene. Our model is inspired by recent successes of deep learning methods for image captioning, but while image captioning is difficult to evaluate, our task allows for easy objective evaluation. We also present a new large-scale dataset for referring expressions, based on MS-COCO. We have released the dataset and a toolbox for visualization and evaluation, see https://github.com/mjhucla/Google_Refexp_toolbox

In recent years, automatic generation of image descriptions (captions), that is, image captioning, has attracted a great deal of attention. In this paper, we particularly consider generating Japanese captions for images. Since most available caption datasets have been constructed for English language, there are few datasets for Japanese. To tackle this problem, we construct a large-scale Japanese image caption dataset based on images from MS-COCO, which is called STAIR Captions. STAIR Captions consists of 820,310 Japanese captions for 164,062 images. In the experiment, we show that a neural network trained using STAIR Captions can generate more natural and better Japanese captions, compared to those generated using English-Japanese machine translation after generating English captions.

We propose a simple yet effective image captioning framework that can determine the quality of an image and notify the user of the reasons for any flaws in the image. Our framework first determines the quality of images and then generates captions using only those images that are determined to be of high quality. The user is notified by the flaws feature to retake if image quality is low, and this cycle is repeated until the input image is deemed to be of high quality. As a component of the framework, we trained and evaluated a low-quality image detection model that simultaneously learns difficulty in recognizing images and individual flaws, and we demonstrated that our proposal can explain the reasons for flaws with a sufficient score. We also evaluated a dataset with low-quality images removed by our framework and found improved values for all four common metrics (e.g., BLEU-4, METEOR, ROUGE-L, CIDEr), confirming an improvement in general-purpose image captioning capability. Our framework would assist the visually impaired, who have difficulty judging image quality.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

Image captioning bridges the gap between vision and language by automatically generating natural language descriptions for images. Traditional image captioning methods often overlook the preferences and characteristics of users. Personalized image captioning solves this problem by incorporating user prior knowledge into the model, such as writing styles and preferred vocabularies. Most existing methods emphasize the user context fusion process by memory networks or transformers. However, these methods ignore the distinct domains of each dataset. Therefore, they need to update the entire caption model parameters when meeting new samples, which is time-consuming and calculation-intensive. To address this challenge, we propose a novel personalized image captioning framework that leverages user context to consider personality factors. Additionally, our framework utilizes the prefix-tuning paradigm to extract knowledge from a frozen large language model, reducing the gap between different language domains. Specifically, we employ CLIP to extract the visual features of an image and align the semantic space using a query-guided mapping network. By incorporating the transformer layer, we merge the visual features with the user's contextual prior knowledge to generate informative prefixes. Moreover, we employ GPT-2 as the frozen large language model. With a small number of parameters to be trained, our model performs efficiently and effectively. Our model outperforms existing baseline models on Instagram and YFCC100M datasets across five evaluation metrics, demonstrating its superiority, including twofold improvements in metrics such as BLEU-4 and CIDEr.

This paper focuses on creating synthetic data to improve the quality of image captions. Existing works typically have two shortcomings. First, they caption images from scratch, ignoring existing alt-text metadata, and second, lack transparency if the captioners' training data (e.g. GPT) is unknown. In this paper, we study a principled approach Altogether based on the key idea to edit and re-align existing alt-texts associated with the images. To generate training data, we perform human annotation where annotators start with the existing alt-text and re-align it to the image content in multiple rounds, consequently constructing captions with rich visual concepts. This differs from prior work that carries out human annotation as a one-time description task solely based on images and annotator knowledge. We train a captioner on this data that generalizes the process of re-aligning alt-texts at scale. Our results show our Altogether approach leads to richer image captions that also improve text-to-image generation and zero-shot image classification tasks.

In this report, we introduce NICE (New frontiers for zero-shot Image Captioning Evaluation) project and share the results and outcomes of 2023 challenge. This project is designed to challenge the computer vision community to develop robust image captioning models that advance the state-of-the-art both in terms of accuracy and fairness. Through the challenge, the image captioning models were tested using a new evaluation dataset that includes a large variety of visual concepts from many domains. There was no specific training data provided for the challenge, and therefore the challenge entries were required to adapt to new types of image descriptions that had not been seen during training. This report includes information on the newly proposed NICE dataset, evaluation methods, challenge results, and technical details of top-ranking entries. We expect that the outcomes of the challenge will contribute to the improvement of AI models on various vision-language tasks.

When automatically generating a sentence description for an image or video, it often remains unclear how well the generated caption is grounded, that is whether the model uses the correct image regions to output particular words, or if the model is hallucinating based on priors in the dataset and/or the language model. The most common way of relating image regions with words in caption models is through an attention mechanism over the regions that are used as input to predict the next word. The model must therefore learn to predict the attentional weights without knowing the word it should localize. This is difficult to train without grounding supervision since recurrent models can propagate past information and there is no explicit signal to force the captioning model to properly ground the individual decoded words. In this work, we help the model to achieve this via a novel cyclical training regimen that forces the model to localize each word in the image after the sentence decoder generates it, and then reconstruct the sentence from the localized image region(s) to match the ground-truth. Our proposed framework only requires learning one extra fully-connected layer (the localizer), a layer that can be removed at test time. We show that our model significantly improves grounding accuracy without relying on grounding supervision or introducing extra computation during inference, for both image and video captioning tasks. Code is available at https://github.com/chihyaoma/cyclical-visual-captioning .

Image captioning models tend to describe images in an object-centric way, emphasising visible objects. But image descriptions can also abstract away from objects and describe the type of scene depicted. In this paper, we explore the potential of a state-of-the-art Vision and Language model, VinVL, to caption images at the scene level using (1) a novel dataset which pairs images with both object-centric and scene descriptions. Through (2) an in-depth analysis of the effect of the fine-tuning, we show (3) that a small amount of curated data suffices to generate scene descriptions without losing the capability to identify object-level concepts in the scene; the model acquires a more holistic view of the image compared to when object-centric descriptions are generated. We discuss the parallels between these results and insights from computational and cognitive science research on scene perception.

Pretrained visual-language models have demonstrated impressive zero-shot abilities in image captioning, when accompanied by hand-crafted prompts. Meanwhile, hand-crafted prompts utilize human prior knowledge to guide the model. However, due to the diversity between different domains, such hand-crafted prompt that provide invariant prior knowledge may result in mode collapse for some domains. Some researches attempted to incorporate expert knowledge and instruction datasets, but the results were costly and led to hallucinations. In this paper, we propose an unsupervised prompt learning method to improve Generalization of Image Captioning (GeneIC), which learns a domain-specific prompt vector for the target domain without requiring annotated data. GeneIC aligns visual and language modalities with a pre-trained Contrastive Language-Image Pre-Training (CLIP) model, thus optimizing the domain-specific prompt vector from two aspects: attribute and semantic consistency. Specifically, GeneIC first generates attribute-transferred images with differing attributes, while retaining semantic similarity with original images. Then, GeneIC uses CLIP to measure the similarity between the images and the generated sentences. By exploring the variable and invariant features in the original images and attribute-transferred images, attribute consistency constrains the attribute change direction of both images and sentences to learn domain-specific knowledge. The semantic consistency directly measures the similarity between the generated sentences and images to ensure the accuracy and comprehensiveness of the generated sentences. Consequently, GeneIC only optimizes the prompt vectors, which effectively retains the knowledge in the large model and introduces domain-specific knowledge.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Video paragraph captioning aims to generate a multi-sentence description of an untrimmed video with several temporal event locations in coherent storytelling. Following the human perception process, where the scene is effectively understood by decomposing it into visual (e.g. human, animal) and non-visual components (e.g. action, relations) under the mutual influence of vision and language, we first propose a visual-linguistic (VL) feature. In the proposed VL feature, the scene is modeled by three modalities including (i) a global visual environment; (ii) local visual main agents; (iii) linguistic scene elements. We then introduce an autoregressive Transformer-in-Transformer (TinT) to simultaneously capture the semantic coherence of intra- and inter-event contents within a video. Finally, we present a new VL contrastive loss function to guarantee learnt embedding features are matched with the captions semantics. Comprehensive experiments and extensive ablation studies on ActivityNet Captions and YouCookII datasets show that the proposed Visual-Linguistic Transformer-in-Transform (VLTinT) outperforms prior state-of-the-art methods on accuracy and diversity. Source code is made publicly available at: https://github.com/UARK-AICV/VLTinT.

We propose Visual News Captioner, an entity-aware model for the task of news image captioning. We also introduce Visual News, a large-scale benchmark consisting of more than one million news images along with associated news articles, image captions, author information, and other metadata. Unlike the standard image captioning task, news images depict situations where people, locations, and events are of paramount importance. Our proposed method can effectively combine visual and textual features to generate captions with richer information such as events and entities. More specifically, built upon the Transformer architecture, our model is further equipped with novel multi-modal feature fusion techniques and attention mechanisms, which are designed to generate named entities more accurately. Our method utilizes much fewer parameters while achieving slightly better prediction results than competing methods. Our larger and more diverse Visual News dataset further highlights the remaining challenges in captioning news images.

Recent advances in retrieval-augmented models for image captioning highlight the benefit of retrieving related captions for efficient, lightweight models with strong domain-transfer capabilities. While these models demonstrate the success of retrieval augmentation, retrieval models are still far from perfect in practice: the retrieved information can sometimes mislead the model, resulting in incorrect generation and worse performance. In this paper, we analyze the robustness of a retrieval-augmented captioning model SmallCap. Our analysis shows that the model is sensitive to tokens that appear in the majority of the retrieved captions, and the input attribution shows that those tokens are likely copied into the generated output. Given these findings, we propose to train the model by sampling retrieved captions from more diverse sets. This decreases the chance that the model learns to copy majority tokens, and improves both in-domain and cross-domain performance.

Training Large Multimodality Models (LMMs) relies on descriptive image caption that connects image and language. Existing methods either distill the caption from the LMM models or construct the captions from the internet images or by human. We propose to leverage off-the-shelf visual specialists, which were trained from annotated images initially not for image captioning, for enhancing the image caption. Our approach, named DCE, explores object low-level and fine-grained attributes (e.g., depth, emotion and fine-grained categories) and object relations (e.g., relative location and human-object-interaction (HOI)), and combine the attributes into the descriptive caption. Experiments demonstrate that such visual specialists are able to improve the performance for visual understanding tasks as well as reasoning that benefits from more accurate visual understanding. We will release the source code and the pipeline so that other visual specialists are easily combined into the pipeline. The complete source code of DCE pipeline and datasets will be available at https://github.com/syp2ysy/DCE.

Despite the success of various text generation metrics such as BERTScore, it is still difficult to evaluate the image captions without enough reference captions due to the diversity of the descriptions. In this paper, we introduce a new metric UMIC, an Unreferenced Metric for Image Captioning which does not require reference captions to evaluate image captions. Based on Vision-and-Language BERT, we train UMIC to discriminate negative captions via contrastive learning. Also, we observe critical problems of the previous benchmark dataset (i.e., human annotations) on image captioning metric, and introduce a new collection of human annotations on the generated captions. We validate UMIC on four datasets, including our new dataset, and show that UMIC has a higher correlation than all previous metrics that require multiple references. We release the benchmark dataset and pre-trained models to compute the UMIC.

Instructional videos are an excellent source for learning multimodal representations by leveraging video-subtitle pairs extracted with automatic speech recognition systems (ASR) from the audio signal in the videos. However, in contrast to human-annotated captions, both speech and subtitles naturally differ from the visual content of the videos and thus provide only noisy supervision for multimodal learning. As a result, large-scale annotation-free web video training data remains sub-optimal for training text-video models. In this work, we propose to leverage the capability of large language models (LLMs) to obtain fine-grained video descriptions aligned with videos. Specifically, we prompt an LLM to create plausible video descriptions based on ASR narrations of the video for a large-scale instructional video dataset. To this end, we introduce a prompting method that is able to take into account a longer text of subtitles, allowing us to capture context beyond a single sentence. To align the captions to the video temporally, we prompt the LLM to generate timestamps for each produced caption based on the subtitles. In this way, we obtain human-style video captions at scale without human supervision. We apply our method to the subtitles of the HowTo100M dataset, creating a new large-scale dataset, HowToCaption. Our evaluation shows that the resulting captions not only significantly improve the performance over many different benchmark datasets for text-video retrieval but also lead to a disentangling of textual narration from the audio, boosting performance in text-video-audio tasks.

Memes are a widely popular tool for web users to express their thoughts using visual metaphors. Understanding memes requires recognizing and interpreting visual metaphors with respect to the text inside or around the meme, often while employing background knowledge and reasoning abilities. We present the task of meme captioning and release a new dataset, MemeCap. Our dataset contains 6.3K memes along with the title of the post containing the meme, the meme captions, the literal image caption, and the visual metaphors. Despite the recent success of vision and language (VL) models on tasks such as image captioning and visual question answering, our extensive experiments using state-of-the-art VL models show that they still struggle with visual metaphors, and perform substantially worse than humans.

3D dense captioning is a task involving the localization of objects and the generation of descriptions for each object in a 3D scene. Recent approaches have attempted to incorporate contextual information by modeling relationships with object pairs or aggregating the nearest neighbor features of an object. However, the contextual information constructed in these scenarios is limited in two aspects: first, objects have multiple positional relationships that exist across the entire global scene, not only near the object itself. Second, it faces with contradicting objectives--where localization and attribute descriptions are generated better with tight localization, while descriptions involving global positional relations are generated better with contextualized features of the global scene. To overcome this challenge, we introduce BiCA, a transformer encoder-decoder pipeline that engages in 3D dense captioning for each object with Bi-directional Contextual Attention. Leveraging parallelly decoded instance queries for objects and context queries for non-object contexts, BiCA generates object-aware contexts, where the contexts relevant to each object is summarized, and context-aware objects, where the objects relevant to the summarized object-aware contexts are aggregated. This extension relieves previous methods from the contradicting objectives, enhancing both localization performance and enabling the aggregation of contextual features throughout the global scene; thus improving caption generation performance simultaneously. Extensive experiments on two of the most widely-used 3D dense captioning datasets demonstrate that our proposed method achieves a significant improvement over prior methods.

Existing automatic captioning methods for visual content face challenges such as lack of detail, content hallucination, and poor instruction following. In this work, we propose VisualFactChecker (VFC), a flexible training-free pipeline that generates high-fidelity and detailed captions for both 2D images and 3D objects. VFC consists of three steps: 1) proposal, where image-to-text captioning models propose multiple initial captions; 2) verification, where a large language model (LLM) utilizes tools such as object detection and VQA models to fact-check proposed captions; 3) captioning, where an LLM generates the final caption by summarizing caption proposals and the fact check verification results. In this step, VFC can flexibly generate captions in various styles following complex instructions. We conduct comprehensive captioning evaluations using four metrics: 1) CLIP-Score for image-text similarity; 2) CLIP-Image-Score for measuring the image-image similarity between the original and the reconstructed image generated by a text-to-image model using the caption. 3) human study on Amazon Mechanical Turk; 4) GPT-4V for fine-grained evaluation. Evaluation results show that VFC outperforms state-of-the-art open-sourced captioning methods for 2D images on the COCO dataset and 3D assets on the Objaverse dataset. Our study demonstrates that by combining open-source models into a pipeline, we can attain captioning capability comparable to proprietary models such as GPT-4V, despite being over 10x smaller in model size.

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

Evaluating the quality of automatically generated image descriptions is challenging, requiring metrics that capture various aspects such as grammaticality, coverage, correctness, and truthfulness. While human evaluation offers valuable insights, its cost and time-consuming nature pose limitations. Existing automated metrics like BLEU, ROUGE, METEOR, and CIDEr aim to bridge this gap but often show weak correlations with human judgment. We address this challenge by introducing a novel evaluation framework rooted in a modern large language model (LLM), such as GPT-4 or Gemini, capable of image generation. In our proposed framework, we begin by feeding an input image into a designated image captioning model, chosen for evaluation, to generate a textual description. Using this description, an LLM then creates a new image. By extracting features from both the original and LLM-created images, we measure their similarity using a designated similarity metric. A high similarity score suggests that the image captioning model has accurately generated textual descriptions, while a low similarity score indicates discrepancies, revealing potential shortcomings in the model's performance. Human-annotated reference captions are not required in our proposed evaluation framework, which serves as a valuable tool for evaluating the effectiveness of image captioning models. Its efficacy is confirmed through human evaluation.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Describing images with text is a fundamental problem in vision-language research. Current studies in this domain mostly focus on single image captioning. However, in various real applications (e.g., image editing, difference interpretation, and retrieval), generating relational captions for two images, can also be very useful. This important problem has not been explored mostly due to lack of datasets and effective models. To push forward the research in this direction, we first introduce a new language-guided image editing dataset that contains a large number of real image pairs with corresponding editing instructions. We then propose a new relational speaker model based on an encoder-decoder architecture with static relational attention and sequential multi-head attention. We also extend the model with dynamic relational attention, which calculates visual alignment while decoding. Our models are evaluated on our newly collected and two public datasets consisting of image pairs annotated with relationship sentences. Experimental results, based on both automatic and human evaluation, demonstrate that our model outperforms all baselines and existing methods on all the datasets.

This report introduces a solution to the Topic 1 Zero-shot Image Captioning of 2024 NICE : New frontiers for zero-shot Image Captioning Evaluation. In contrast to NICE 2023 datasets, this challenge involves new annotations by humans with significant differences in caption style and content. Therefore, we enhance image captions effectively through retrieval augmentation and caption grading methods. At the data level, we utilize high-quality captions generated by image caption models as training data to address the gap in text styles. At the model level, we employ OFA (a large-scale visual-language pre-training model based on handcrafted templates) to perform the image captioning task. Subsequently, we propose caption-level strategy for the high-quality caption data generated by the image caption models and integrate them with retrieval augmentation strategy into the template to compel the model to generate higher quality, more matching, and semantically enriched captions based on the retrieval augmentation prompts. Our approach achieves a CIDEr score of 234.11.

Modern image captioning system relies heavily on extracting knowledge from images to capture the concept of a static story. In this paper, we propose a textual visual context dataset for captioning, in which the publicly available dataset COCO Captions (Lin et al., 2014) has been extended with information about the scene (such as objects in the image). Since this information has a textual form, it can be used to leverage any NLP task, such as text similarity or semantic relation methods, into captioning systems, either as an end-to-end training strategy or a post-processing based approach.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already been described in the literature. These models learn a message passing algorithm and aggregation procedure to compute a function of their entire input graph. At this point, the next step is to find a particularly effective variant of this general approach and apply it to chemical prediction benchmarks until we either solve them or reach the limits of the approach. In this paper, we reformulate existing models into a single common framework we call Message Passing Neural Networks (MPNNs) and explore additional novel variations within this framework. Using MPNNs we demonstrate state of the art results on an important molecular property prediction benchmark; these results are strong enough that we believe future work should focus on datasets with larger molecules or more accurate ground truth labels.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

Video captioning is a challenging task since it requires generating sentences describing various diverse and complex videos. Existing video captioning models lack adequate visual representation due to the neglect of the existence of gaps between videos and texts. To bridge this gap, in this paper, we propose a CLIP4Caption framework that improves video captioning based on a CLIP-enhanced video-text matching network (VTM). This framework is taking full advantage of the information from both vision and language and enforcing the model to learn strongly text-correlated video features for text generation. Besides, unlike most existing models using LSTM or GRU as the sentence decoder, we adopt a Transformer structured decoder network to effectively learn the long-range visual and language dependency. Additionally, we introduce a novel ensemble strategy for captioning tasks. Experimental results demonstrate the effectiveness of our method on two datasets: 1) on MSR-VTT dataset, our method achieved a new state-of-the-art result with a significant gain of up to 10% in CIDEr; 2) on the private test data, our method ranking 2nd place in the ACM MM multimedia grand challenge 2021: Pre-training for Video Understanding Challenge. It is noted that our model is only trained on the MSR-VTT dataset.

Open-vocabulary scene understanding aims to localize and recognize unseen categories beyond the annotated label space. The recent breakthrough of 2D open-vocabulary perception is largely driven by Internet-scale paired image-text data with rich vocabulary concepts. However, this success cannot be directly transferred to 3D scenarios due to the inaccessibility of large-scale 3D-text pairs. To this end, we propose to distill knowledge encoded in pre-trained vision-language (VL) foundation models through captioning multi-view images from 3D, which allows explicitly associating 3D and semantic-rich captions. Further, to foster coarse-to-fine visual-semantic representation learning from captions, we design hierarchical 3D-caption pairs, leveraging geometric constraints between 3D scenes and multi-view images. Finally, by employing contrastive learning, the model learns language-aware embeddings that connect 3D and text for open-vocabulary tasks. Our method not only remarkably outperforms baseline methods by 25.8% sim 44.7% hIoU and 14.5% sim 50.4% hAP_{50} in open-vocabulary semantic and instance segmentation, but also shows robust transferability on challenging zero-shot domain transfer tasks. See the project website at https://dingry.github.io/projects/PLA.

The application of video captioning models aims at translating the content of videos by using accurate natural language. Due to the complex nature inbetween object interaction in the video, the comprehensive understanding of spatio-temporal relations of objects remains a challenging task. Existing methods often fail in generating sufficient feature representations of video content. In this paper, we propose a video captioning model based on dual graphs and gated fusion: we adapt two types of graphs to generate feature representations of video content and utilize gated fusion to further understand these different levels of information. Using a dual-graphs model to generate appearance features and motion features respectively can utilize the content correlation in frames to generate various features from multiple perspectives. Among them, dual-graphs reasoning can enhance the content correlation in frame sequences to generate advanced semantic features; The gated fusion, on the other hand, aggregates the information in multiple feature representations for comprehensive video content understanding. The experiments conducted on worldly used datasets MSVD and MSR-VTT demonstrate state-of-the-art performance of our proposed approach.

With the surge in available data from various modalities, there is a growing need to bridge the gap between different data types. In this work, we introduce a novel approach to learn cross-modal representations between image data and molecular representations for drug discovery. We propose EMM and IMM, two innovative loss functions built on top of CLIP that leverage weak supervision and cross sites replicates in High-Content Screening. Evaluating our model against known baseline on cross-modal retrieval, we show that our proposed approach allows to learn better representations and mitigate batch effect. In addition, we also present a preprocessing method for the JUMP-CP dataset that effectively reduce the required space from 85Tb to a mere usable 7Tb size, still retaining all perturbations and most of the information content.

The availability of large-scale image captioning and visual question answering datasets has contributed significantly to recent successes in vision-and-language pre-training. However, these datasets are often collected with overrestrictive requirements inherited from their original target tasks (e.g., image caption generation), which limit the resulting dataset scale and diversity. We take a step further in pushing the limits of vision-and-language pre-training data by relaxing the data collection pipeline used in Conceptual Captions 3M (CC3M) [Sharma et al. 2018] and introduce the Conceptual 12M (CC12M), a dataset with 12 million image-text pairs specifically meant to be used for vision-and-language pre-training. We perform an analysis of this dataset and benchmark its effectiveness against CC3M on multiple downstream tasks with an emphasis on long-tail visual recognition. Our results clearly illustrate the benefit of scaling up pre-training data for vision-and-language tasks, as indicated by the new state-of-the-art results on both the nocaps and Conceptual Captions benchmarks.

Existing work has observed that current text-to-image systems do not accurately reflect explicit spatial relations between objects such as 'left of' or 'below'. We hypothesize that this is because explicit spatial relations rarely appear in the image captions used to train these models. We propose an automatic method that, given existing images, generates synthetic captions that contain 14 explicit spatial relations. We introduce the Spatial Relation for Generation (SR4G) dataset, which contains 9.9 millions image-caption pairs for training, and more than 60 thousand captions for evaluation. In order to test generalization we also provide an 'unseen' split, where the set of objects in the train and test captions are disjoint. SR4G is the first dataset that can be used to spatially fine-tune text-to-image systems. We show that fine-tuning two different Stable Diffusion models (denoted as SD_{SR4G}) yields up to 9 points improvements in the VISOR metric. The improvement holds in the 'unseen' split, showing that SD_{SR4G} is able to generalize to unseen objects. SD_{SR4G} improves the state-of-the-art with fewer parameters, and avoids complex architectures. Our analysis shows that improvement is consistent for all relations. The dataset and the code will be publicly available.

Text-to-image diffusion models achieved a remarkable leap in capabilities over the last few years, enabling high-quality and diverse synthesis of images from a textual prompt. However, even the most advanced models often struggle to precisely follow all of the directions in their prompts. The vast majority of these models are trained on datasets consisting of (image, caption) pairs where the images often come from the web, and the captions are their HTML alternate text. A notable example is the LAION dataset, used by Stable Diffusion and other models. In this work we observe that these captions are often of low quality, and argue that this significantly affects the model's capability to understand nuanced semantics in the textual prompts. We show that by relabeling the corpus with a specialized automatic captioning model and training a text-to-image model on the recaptioned dataset, the model benefits substantially across the board. First, in overall image quality: e.g. FID 14.84 vs. the baseline of 17.87, and 64.3% improvement in faithful image generation according to human evaluation. Second, in semantic alignment, e.g. semantic object accuracy 84.34 vs. 78.90, counting alignment errors 1.32 vs. 1.44 and positional alignment 62.42 vs. 57.60. We analyze various ways to relabel the corpus and provide evidence that this technique, which we call RECAP, both reduces the train-inference discrepancy and provides the model with more information per example, increasing sample efficiency and allowing the model to better understand the relations between captions and images.

While current visual captioning models have achieved impressive performance, they often assume that the image is well-captured and provides a complete view of the scene. In real-world scenarios, however, a single image may not offer a good viewpoint, hindering fine-grained scene understanding. To overcome this limitation, we propose a novel task called Embodied Captioning, which equips visual captioning models with navigation capabilities, enabling them to actively explore the scene and reduce visual ambiguity from suboptimal viewpoints. Specifically, starting at a random viewpoint, an agent must navigate the environment to gather information from different viewpoints and generate a comprehensive paragraph describing all objects in the scene. To support this task, we build the ET-Cap dataset with Kubric simulator, consisting of 10K 3D scenes with cluttered objects and three annotated paragraphs per scene. We propose a Cascade Embodied Captioning model (CaBOT), which comprises of a navigator and a captioner, to tackle this task. The navigator predicts which actions to take in the environment, while the captioner generates a paragraph description based on the whole navigation trajectory. Extensive experiments demonstrate that our model outperforms other carefully designed baselines. Our dataset, codes and models are available at https://aim3-ruc.github.io/ExploreAndTell.

We introduce a formal information-theoretic framework for image captioning by regarding it as a representation learning task. Our framework defines three key objectives: task sufficiency, minimal redundancy, and human interpretability. Building upon this foundation, we propose a novel Pyramid of Captions (PoCa) method, which constructs caption pyramids by generating localized captions for zoomed-in image patches and integrating them with global caption information using large language models. This approach leverages intuition that the detailed examination of local patches can reduce error risks and address inaccuracies in global captions, either by correcting the hallucination or adding missing details. Based on our theoretical framework, we formalize this intuition and provide formal proof demonstrating the effectiveness of PoCa under certain assumptions. Empirical tests with various image captioning models and large language models show that PoCa consistently yields more informative and semantically aligned captions, maintaining brevity and interpretability.