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3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization

arXiv.org Artificial Intelligence

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.


Open-Vocabulary Part-Based Grasping

arXiv.org Artificial Intelligence

Many robotic applications require to grasp objects not arbitrarily but at a very specific object part. This is especially important for manipulation tasks beyond simple pick-and-place scenarios or in robot-human interactions, such as object handovers. We propose AnyPart, a practical system that combines open-vocabulary object detection, open-vocabulary part segmentation and 6DOF grasp pose prediction to infer a grasp pose on a specific part of an object in 800 milliseconds. We contribute two new datasets for the task of open-vocabulary part-based grasping, a hand-segmented dataset containing 1014 object-part segmentations, and a dataset of real-world scenarios gathered during our robot trials for individual objects and table-clearing tasks. We evaluate AnyPart on a mobile manipulator robot using a set of 28 common household objects over 360 grasping trials. AnyPart is capable of producing successful grasps 69.52 %, when ignoring robot-based grasp failures, AnyPart predicts a grasp location on the correct part 88.57 % of the time.


Computational and Statistical Guarantees for Tensor-on-Tensor Regression with Tensor Train Decomposition

arXiv.org Artificial Intelligence

Recently, a tensor-on-tensor (ToT) regression model has been proposed to generalize tensor recovery, encompassing scenarios like scalar-on-tensor regression and tensor-on-vector regression. However, the exponential growth in tensor complexity poses challenges for storage and computation in ToT regression. To overcome this hurdle, tensor decompositions have been introduced, with the tensor train (TT)-based ToT model proving efficient in practice due to reduced memory requirements, enhanced computational efficiency, and decreased sampling complexity. Despite these practical benefits, a disparity exists between theoretical analysis and real-world performance. In this paper, we delve into the theoretical and algorithmic aspects of the TT-based ToT regression model. Assuming the regression operator satisfies the restricted isometry property (RIP), we conduct an error analysis for the solution to a constrained least-squares optimization problem. This analysis includes upper error bound and minimax lower bound, revealing that such error bounds polynomially depend on the order $N+M$. To efficiently find solutions meeting such error bounds, we propose two optimization algorithms: the iterative hard thresholding (IHT) algorithm (employing gradient descent with TT-singular value decomposition (TT-SVD)) and the factorization approach using the Riemannian gradient descent (RGD) algorithm. When RIP is satisfied, spectral initialization facilitates proper initialization, and we establish the linear convergence rate of both IHT and RGD.


A novel method for identifying rice seed purity based on hybrid machine learning algorithms

arXiv.org Artificial Intelligence

In the grain industry, the identification of seed purity is a crucial task as it is an important factor in evaluating the quality of seeds. For rice seeds, this property allows for the reduction of unexpected influences of other varieties on rice yield, nutrient composition, and price. However, in practice, they are often mixed with seeds from others. This study proposes a novel method for automatically identifying the rice seed purity of a certain rice variety based on hybrid machine learning algorithms. The main idea is to use deep learning architectures for extracting important features from the raw data and then use machine learning algorithms for classification. Several experiments are conducted following a practical implementation to evaluate the performance of the proposed model. The obtained results show that the novel method improves significantly the performance of existing methods. Thus, it can be applied to design effective identification systems for rice seed purity.


Introducing GenCeption for Multimodal LLM Benchmarking: You May Bypass Annotations

arXiv.org Artificial Intelligence

Multimodal Large Language Models (MLLMs) are commonly evaluated using costly annotated multimodal benchmarks. However, these benchmarks often struggle to keep pace with the rapidly advancing requirements of MLLM evaluation. We propose GenCeption, a novel and annotation-free MLLM evaluation framework that merely requires unimodal data to assess inter-modality semantic coherence and inversely reflects the models' inclination to hallucinate. Analogous to the popular DrawCeption game, GenCeption initiates with a non-textual sample and undergoes a series of iterative description and generation steps. Semantic drift across iterations is quantified using the GC@T metric. Our empirical findings validate GenCeption's efficacy, showing strong correlations with popular MLLM benchmarking results. GenCeption may be extended to mitigate training data contamination by utilizing ubiquitous, previously unseen unimodal data.


Governance of Generative Artificial Intelligence for Companies

arXiv.org Artificial Intelligence

Generative Artificial Intelligence (GenAI), specifically large language models like ChatGPT, has swiftly entered organizations without adequate governance, posing both opportunities and risks. Despite extensive debates on GenAI's transformative nature and regulatory measures, limited research addresses organizational governance, encompassing technical and business perspectives. Our review paper fills this gap by surveying recent works with the purpose of developing a framework for GenAI governance within companies. This framework outlines the scope, objectives, and governance mechanisms tailored to harness business opportunities as well as mitigate risks associated with GenAI integration. Our research contributes a focused approach to GenAI governance, offering practical insights for companies navigating the challenges of GenAI adoption and highlighting research gaps.


Set the Clock: Temporal Alignment of Pretrained Language Models

arXiv.org Artificial Intelligence

Language models (LMs) are trained on web text originating from many points in time and, in general, without any explicit temporal grounding. This work investigates the temporal chaos of pretrained LMs and explores various methods to align their internal knowledge to a target time, which we call "temporal alignment." To do this, we first automatically construct a dataset containing 20K time-sensitive questions and their answers for each year from 2000 to 2023. Based on this dataset, we empirically show that pretrained LMs (e.g., LLaMa2), despite having a recent pretraining cutoff (e.g., 2022), mostly answer questions using earlier knowledge (e.g., in 2019). We then develop several methods, from prompting to finetuning, to align LMs to use their most recent knowledge when answering questions, and investigate various factors in this alignment. Our experiments demonstrate that aligning LLaMa2 to the year 2022 can enhance its performance by up to 62% according to that year's answers. This improvement occurs even without explicitly mentioning time information, indicating the possibility of aligning models' internal sense of time after pretraining. Finally, we find that alignment to a historical time is also possible, with up to 2.8$\times$ the performance of the unaligned LM in 2010 if finetuning models to that year. These findings hint at the sophistication of LMs' internal knowledge organization and the necessity of tuning them properly.


Self-Expansion of Pre-trained Models with Mixture of Adapters for Continual Learning

arXiv.org Artificial Intelligence

Continual learning (CL) aims to continually accumulate knowledge from a non-stationary data stream without catastrophic forgetting of learned knowledge, requiring a balance between stability and adaptability. Relying on the generalizable representation in pre-trained models (PTMs), PTM-based CL methods perform effective continual adaptation on downstream tasks by adding learnable adapters or prompts upon the frozen PTMs. However, many existing PTM-based CL methods use restricted adaptation on a fixed set of these modules to avoid forgetting, suffering from limited CL ability. Periodically adding task-specific modules results in linear model growth rate and impaired knowledge reuse. We propose Self-Expansion of pre-trained models with Modularized Adaptation (SEMA), a novel approach to enhance the control of stability-plasticity balance in PTM-based CL. SEMA automatically decides to reuse or add adapter modules on demand in CL, depending on whether significant distribution shift that cannot be handled is detected at different representation levels. We design modular adapter consisting of a functional adapter and a representation descriptor. The representation descriptors are trained as a distribution shift indicator and used to trigger self-expansion signals. For better composing the adapters, an expandable weighting router is learned jointly for mixture of adapter outputs. SEMA enables better knowledge reuse and sub-linear expansion rate. Extensive experiments demonstrate the effectiveness of the proposed self-expansion method, achieving state-of-the-art performance compared to PTM-based CL methods without memory rehearsal.


ProgGen: Generating Named Entity Recognition Datasets Step-by-step with Self-Reflexive Large Language Models

arXiv.org Artificial Intelligence

Although Large Language Models (LLMs) exhibit remarkable adaptability across domains, these models often fall short in structured knowledge extraction tasks such as named entity recognition (NER). This paper explores an innovative, cost-efficient strategy to harness LLMs with modest NER capabilities for producing superior NER datasets. Our approach diverges from the basic class-conditional prompts by instructing LLMs to self-reflect on the specific domain, thereby generating domain-relevant attributes (such as category and emotions for movie reviews), which are utilized for creating attribute-rich training data. Furthermore, we preemptively generate entity terms and then develop NER context data around these entities, effectively bypassing the LLMs' challenges with complex structures. Our experiments across both general and niche domains reveal significant performance enhancements over conventional data generation methods while being more cost-effective than existing alternatives.


WARDEN: Multi-Directional Backdoor Watermarks for Embedding-as-a-Service Copyright Protection

arXiv.org Artificial Intelligence

Embedding as a Service (EaaS) has become a widely adopted solution, which offers feature extraction capabilities for addressing various downstream tasks in Natural Language Processing (NLP). Prior studies have shown that EaaS can be prone to model extraction attacks; nevertheless, this concern could be mitigated by adding backdoor watermarks to the text embeddings and subsequently verifying the attack models post-publication. Through the analysis of the recent watermarking strategy for EaaS, EmbMarker, we design a novel CSE (Clustering, Selection, Elimination) attack that removes the backdoor watermark while maintaining the high utility of embeddings, indicating that the previous watermarking approach can be breached. In response to this new threat, we propose a new protocol to make the removal of watermarks more challenging by incorporating multiple possible watermark directions. Our defense approach, WARDEN, notably increases the stealthiness of watermarks and has been empirically shown to be effective against CSE attack.