OpenRaiser/Intern-Atlas huggingface dataset:
SAFE setup for generative molecular design
Venue: arXiv cs.LG 2024
Year: 2024

SMILES-based molecular generative models have been pivotal in drug design but face challenges in fragment-constrained tasks. To address this, the Sequential Attachment-based Fragment Embedding (SAFE) representation was recently introduced as an alternative that streamlines those tasks. In this study, we investigate the optimal setups for training SAFE generative models, focusing on dataset size, data augmentation through randomization, model architecture, and bond disconnection algorithms. We found that larger, more diverse datasets improve performance, with the LLaMA architecture using Rotary Positional Embedding proving most robust. SAFE-based models also consistently outperform SMILES-based approaches in scaffold decoration and linker design, particularly with BRICS decomposition yielding the best results. These insights highlight key factors that significantly impact the efficacy of SAFE-based generative models.
Characterization of $n$-Dimensional Toric and Burst-Error-Correcting Quantum Codes from Lattice Codes
Venue: arXiv cs.IT 2024
Year: 2024

Quantum error correction is essential for the development of any scalable quantum computer. In this work we introduce a generalization of a quantum interleaving method for combating clusters of errors in toric quantum error-correcting codes. We present new $n$-dimensional toric quantum codes, where $n\geq 5$, which are featured by lattice codes and apply the proposed quantum interleaving method to such new $n$-dimensional toric quantum codes. Through the application of this method to these novel $n$-dimensional toric quantum codes we derive new $n$-dimensional quantum burst-error-correcting codes. Consequently, $n$-dimensional toric quantum codes and burst-error-correcting quantum codes are provided offering both a good code rate and a significant coding gain when it comes to toric quantum codes. Another important consequence from the presented $n$-dimensional toric quantum codes is that if the Golomb and Welch conjecture in \cite{perfcodes} regarding the Lee sphere in $n$ dimensions for the respective close packings holds true, then it follows that these $n$-dimensional toric quantum codes are the only possible ones to be obtained from lattice codes. Moreover, such a methodology can be applied for burst error correction in cases involving localized errors, quantum data storage and quantum channels with memory.
That was not what I was aiming at! Differentiating human intent and outcome in a physically dynamic throwing task
Venue: arXiv cs.RO 2024
Year: 2024

Recognising intent in collaborative human robot tasks can improve team performance and human perception of robots. Intent can differ from the observed outcome in the presence of mistakes which are likely in physically dynamic tasks. We created a dataset of 1227 throws of a ball at a target from 10 participants and observed that 47% of throws were mistakes with 16% completely missing the target. Our research leverages facial images capturing the person's reaction to the outcome of a throw to predict when the resulting throw is a mistake and then we determine the actual intent of the throw. The approach we propose for outcome prediction performs 38% better than the two-stream architecture used previously for this task on front-on videos. In addition, we propose a 1-D CNN model which is used in conjunction with priors learned from the frequency of mistakes to provide an end-to-end pipeline for outcome and intent recognition in this throwing task.
FL-DABE-BC: A Privacy-Enhanced, Decentralized Authentication, and Secure Communication for Federated Learning Framework with Decentralized Attribute-Based Encryption and Blockchain for IoT Scenarios
Venue: arXiv cs.CR 2024
Year: 2024

This study proposes an advanced Federated Learning (FL) framework designed to enhance data privacy and security in IoT environments by integrating Decentralized Attribute-Based Encryption (DABE), Homomorphic Encryption (HE), Secure Multi-Party Computation (SMPC), and Blockchain technology. Unlike traditional FL, our framework enables secure, decentralized authentication and encryption directly on IoT devices using DABE, allowing sensitive data to remain locally encrypted. Homomorphic Encryption permits computations on encrypted data, and SMPC ensures privacy in collaborative computations, while Blockchain technology provides transparent, immutable record-keeping for all transactions and model updates. Local model weights are encrypted and transmitted to fog layers for aggregation using HE and SMPC, then iteratively refined by the central server using differential privacy to safeguard against data leakage. This secure, privacy-preserving FL framework delivers a robust solution for efficient model training and real-time analytics across distributed IoT devices, offering significant advancements in secure decentralized learning for IoT applications.
Access control in a distributed micro-cloud environment
Venue: arXiv cs.CR 2024
Year: 2024

Proliferation of systems that generate enormous amounts of data and operate in real time has led researchers to rethink the current organization of the cloud. Many proposed solutions consist of a number of small data centers in the vicinity of data sources. That creates a highly complex environment, where strict access control is essential. Recommended access control models frequently belong to the Attribute-Based Access Control (ABAC) family. Flexibility and dynamic nature of these models come at the cost of high policy management complexity. In this paper, we explore whether the administrative overhead can be lowered with resource hierarchies. We propose an ABAC model that incorporates user and object hierarchies. We develop a policy engine that supports the model and present a distributed cloud use case. Findings in this paper suggest that resource hierarchies simplify the administration of ABAC models, which is a necessary step towards their further inclusion in real-world systems.
Learning from Response not Preference: A Stackelberg Approach for LLM Detoxification using Non-parallel Data
Venue: arXiv cs.CL 2024
Year: 2024

Text detoxification, a variant of style transfer tasks, finds useful applications in online social media. This work presents a fine-tuning method that only uses non-parallel data to turn large language models (LLM) into a detoxification rewritter. We model the fine-tuning process as a Stackelberg game between an LLM (leader) and a toxicity screener (follower), which is a binary style classifier (toxic or non-toxic). The LLM aims to align its preference according to the screener and generate paraphases passing the screening. The primary challenge of non-parallel data fine-tuning is incomplete preference. In the case of unsuccessful paraphrases, the classifier cannot establish a preference between the input and paraphrase, as they belong to the same toxic style. Hence, preference-alignment fine-tuning methods, such as direct preference optimization (DPO), no longer apply. To address the challenge of incomplete preference, we propose Stackelberg response optimization (SRO), adapted from DPO, to enable the LLM to learn from the follower's response. The gist is that SRO decreases the likelihood of generating the paraphrase if it fails the follower's screening while performing DPO on the pair of the toxic input and its paraphrase when the latter passes the screening. Experiments indicate that the SRO-fine-tunned LLM achieves satisfying performance comparable to state-of-the-art models regarding style accuracy, content similarity, and fluency. The overall detoxification performance surpasses other computing methods and matches the human reference. Additional empirical evidence suggests that SRO is sensitive to the screener's feedback, and a slight perturbation leads to a significant performance drop. We release the code and LLM models at \url{https://github.com/XXXinhong/Detoxification_LLM}.
Predicting Mortality and Functional Status Scores of Traumatic Brain Injury Patients using Supervised Machine Learning
Venue: arXiv cs.LG 2024
Year: 2024

Traumatic brain injury (TBI) presents a significant public health challenge, often resulting in mortality or lasting disability. Predicting outcomes such as mortality and Functional Status Scale (FSS) scores can enhance treatment strategies and inform clinical decision-making. This study applies supervised machine learning (ML) methods to predict mortality and FSS scores using a real-world dataset of 300 pediatric TBI patients from the University of Colorado School of Medicine. The dataset captures clinical features, including demographics, injury mechanisms, and hospitalization outcomes. Eighteen ML models were evaluated for mortality prediction, and thirteen models were assessed for FSS score prediction. Performance was measured using accuracy, ROC AUC, F1-score, and mean squared error. Logistic regression and Extra Trees models achieved high precision in mortality prediction, while linear regression demonstrated the best FSS score prediction. Feature selection reduced 103 clinical variables to the most relevant, enhancing model efficiency and interpretability. This research highlights the role of ML models in identifying high-risk patients and supporting personalized interventions, demonstrating the potential of data-driven analytics to improve TBI care and integrate into clinical workflows.
Wavelet-based Mamba with Fourier Adjustment for Low-light Image Enhancement
Venue: arXiv cs.CV 2024
Year: 2024

Frequency information (e.g., Discrete Wavelet Transform and Fast Fourier Transform) has been widely applied to solve the issue of Low-Light Image Enhancement (LLIE). However, existing frequency-based models primarily operate in the simple wavelet or Fourier space of images, which lacks utilization of valid global and local information in each space. We found that wavelet frequency information is more sensitive to global brightness due to its low-frequency component while Fourier frequency information is more sensitive to local details due to its phase component. In order to achieve superior preliminary brightness enhancement by optimally integrating spatial channel information with low-frequency components in the wavelet transform, we introduce channel-wise Mamba, which compensates for the long-range dependencies of CNNs and has lower complexity compared to Diffusion and Transformer models. So in this work, we propose a novel Wavelet-based Mamba with Fourier Adjustment model called WalMaFa, consisting of a Wavelet-based Mamba Block (WMB) and a Fast Fourier Adjustment Block (FFAB). We employ an Encoder-Latent-Decoder structure to accomplish the end-to-end transformation. Specifically, WMB is adopted in the Encoder and Decoder to enhance global brightness while FFAB is adopted in the Latent to fine-tune local texture details and alleviate ambiguity. Extensive experiments demonstrate that our proposed WalMaFa achieves state-of-the-art performance with fewer computational resources and faster speed. Code is now available at: https://github.com/mcpaulgeorge/WalMaFa.
Deep Learning Based Dense Retrieval: A Comparative Study
Venue: arXiv cs.CL 2024
Year: 2024

Dense retrievers have achieved state-of-the-art performance in various information retrieval tasks, but their robustness against tokenizer poisoning remains underexplored. In this work, we assess the vulnerability of dense retrieval systems to poisoned tokenizers by evaluating models such as BERT, Dense Passage Retrieval (DPR), Contriever, SimCSE, and ANCE. We find that supervised models like BERT and DPR experience significant performance degradation when tokenizers are compromised, while unsupervised models like ANCE show greater resilience. Our experiments reveal that even small perturbations can severely impact retrieval accuracy, highlighting the need for robust defenses in critical applications.
Few-shot Open Relation Extraction with Gaussian Prototype and Adaptive Margin
Venue: arXiv cs.CV 2024
Year: 2024

Few-shot relation extraction with none-of-the-above (FsRE with NOTA) aims at predicting labels in few-shot scenarios with unknown classes. FsRE with NOTA is more challenging than the conventional few-shot relation extraction task, since the boundaries of unknown classes are complex and difficult to learn. Meta-learning based methods, especially prototype-based methods, are the mainstream solutions to this task. They obtain the classification boundary by learning the sample distribution of each class. However, their performance is limited because few-shot overfitting and NOTA boundary confusion lead to misclassification between known and unknown classes. To this end, we propose a novel framework based on Gaussian prototype and adaptive margin named GPAM for FsRE with NOTA, which includes three modules, semi-factual representation, GMM-prototype metric learning and decision boundary learning. The first two modules obtain better representations to solve the few-shot problem through debiased information enhancement and Gaussian space distance measurement. The third module learns more accurate classification boundaries and prototypes through adaptive margin and negative sampling. In the training procedure of GPAM, we use contrastive learning loss to comprehensively consider the effects of range and margin on the classification of known and unknown classes to ensure the model's stability and robustness. Sufficient experiments and ablations on the FewRel dataset show that GPAM surpasses previous prototype methods and achieves state-of-the-art performance.
Embedded Nonlocal Operator Regression (ENOR): Quantifying model error in learning nonlocal operators
Venue: arXiv cs.LG 2024
Year: 2024

Nonlocal, integral operators have become an efficient surrogate for bottom-up homogenization, due to their ability to represent long-range dependence and multiscale effects. However, the nonlocal homogenized model has unavoidable discrepancy from the microscale model. Such errors accumulate and propagate in long-term simulations, making the resultant prediction unreliable. To develop a robust and reliable bottom-up homogenization framework, we propose a new framework, which we coin Embedded Nonlocal Operator Regression (ENOR), to learn a nonlocal homogenized surrogate model and its structural model error. This framework provides discrepancy-adaptive uncertainty quantification for homogenized material response predictions in long-term simulations. The method is built on Nonlocal Operator Regression (NOR), an optimization-based nonlocal kernel learning approach, together with an embedded model error term in the trainable kernel. Then, Bayesian inference is employed to infer the model error term parameters together with the kernel parameters. To make the problem computationally feasible, we use a multilevel delayed acceptance Markov chain Monte Carlo (MLDA-MCMC) method, enabling efficient Bayesian model calibration and model error estimation. We apply this technique to predict long-term wave propagation in a heterogeneous one-dimensional bar, and compare its performance with additive noise models. Owing to its ability to capture model error, the learned ENOR achieves improved estimation of posterior predictive uncertainty.
The maximum storage capacity of open-loop written RRAM is around 4 bits
Venue: arXiv cs.ET 2024
Year: 2024

There have been a plethora of research on multi-level memory devices, where the resistive random-access memory (RRAM) is a prominent example. Although it is easy to write an RRAM device into multiple (even quasi-continuous) states, it suffers from the inherent variations that should limit the storage capacity, especially in the open-loop writing scenario. There have been many experimental results in this regard, however, it lacks a comprehensive analysis of the valid multi-bit storage capability, especially in theoretical terms. The absence of such an insight usually results in misleading conclusions that either exaggerate or underestimate the storage capacity of RRAM devices. Here, by the concept of information theory, we present a model for evaluating the storage capacity of open-loop written RRAM. Based on the experimental results in the literature and the test results of our own devices, we have carefully examined the effects of number of pre-defined levels, conductance variation, and conductance range, on the storage capacity. The analysis leads to a conclusion that the maximum capacity of RRAM devices is around 4 bits.
Improving Speech-based Emotion Recognition with Contextual Utterance Analysis and LLMs
Venue: arXiv cs.CL 2024
Year: 2024

Speech Emotion Recognition (SER) focuses on identifying emotional states from spoken language. The 2024 IEEE SLT-GenSEC Challenge on Post Automatic Speech Recognition (ASR) Emotion Recognition tasks participants to explore the capabilities of large language models (LLMs) for emotion recognition using only text data. We propose a novel approach that first refines all available transcriptions to ensure data reliability. We then segment each complete conversation into smaller dialogues and use these dialogues as context to predict the emotion of the target utterance within the dialogue. Finally, we investigated different context lengths and prompting techniques to improve prediction accuracy. Our best submission exceeded the baseline by 20% in unweighted accuracy, achieving the best performance in the challenge. All our experiments' codes, prediction results, and log files are publicly available.
Maintaining Informative Coherence: Migrating Hallucinations in Large Language Models via Absorbing Markov Chains
Venue: arXiv cs.CL 2024
Year: 2024

Large Language Models (LLMs) are powerful tools for text generation, translation, and summarization, but they often suffer from hallucinations-instances where they fail to maintain the fidelity and coherence of contextual information during decoding, sometimes overlooking critical details due to their sampling strategies and inherent biases from training data and fine-tuning discrepancies. These hallucinations can propagate through the web, affecting the trustworthiness of information disseminated online. To address this issue, we propose a novel decoding strategy that leverages absorbing Markov chains to quantify the significance of contextual information and measure the extent of information loss during generation. By considering all possible paths from the first to the last token, our approach enhances the reliability of model outputs without requiring additional training or external data. Evaluations on datasets including TruthfulQA, FACTOR, and HaluEval highlight the superior performance of our method in mitigating hallucinations, underscoring the necessity of ensuring accurate information flow in web-based applications.
Uncovering Capabilities of Model Pruning in Graph Contrastive Learning
Venue: arXiv cs.LG 2024
Year: 2024

Graph contrastive learning has achieved great success in pre-training graph neural networks without ground-truth labels. Leading graph contrastive learning follows the classical scheme of contrastive learning, forcing model to identify the essential information from augmented views. However, general augmented views are produced via random corruption or learning, which inevitably leads to semantics alteration. Although domain knowledge guided augmentations alleviate this issue, the generated views are domain specific and undermine the generalization. In this work, motivated by the firm representation ability of sparse model from pruning, we reformulate the problem of graph contrastive learning via contrasting different model versions rather than augmented views. We first theoretically reveal the superiority of model pruning in contrast to data augmentations. In practice, we take original graph as input and dynamically generate a perturbed graph encoder to contrast with the original encoder by pruning its transformation weights. Furthermore, considering the integrity of node embedding in our method, we are capable of developing a local contrastive loss to tackle the hard negative samples that disturb the model training. We extensively validate our method on various benchmarks regarding graph classification via unsupervised and transfer learning. Compared to the state-of-the-art (SOTA) works, better performance can always be obtained by the proposed method.
ThunderKittens: Simple, Fast, and Adorable AI Kernels
Venue: arXiv cs.LG 2024
Year: 2024

The challenge of mapping AI architectures to GPU hardware is creating a critical bottleneck in AI progress. Despite substantial efforts, hand-written custom kernels fail to meet their theoretical performance thresholds, even on well-established operations like linear attention. The diverse hardware capabilities of GPUs might suggest that we need a wide variety of techniques to achieve high performance. However, our work explores whether a small number of key abstractions can drastically simplify the process. We present ThunderKittens (TK), a framework for writing performant AI kernels while remaining easy to use and maintain. Our abstractions map to the three levels of the GPU hierarchy: (1) at the warp-level, we provide 16x16 matrix tiles as basic data structures and PyTorch-like parallel compute operations over tiles, (2) at the thread-block level, we provide a template for overlapping asynchronous operations across parallel warps, and (3) at the grid-level, we provide support to help hide the block launch and tear-down, and memory costs. We show the value of TK by providing kernels that match or outperform prior kernels for a range of AI operations. We match CuBLAS and FlashAttention-3 on GEMM and attention inference performance and outperform the strongest baselines by $10-40\%$ on attention backwards, $8\times$ on state space models, and $14\times$ on linear attention.
Prototypical Extreme Multi-label Classification with a Dynamic Margin Loss
Venue: arXiv cs.LG 2024
Year: 2024

Extreme Multi-label Classification (XMC) methods predict relevant labels for a given query in an extremely large label space. Recent works in XMC address this problem using deep encoders that project text descriptions to an embedding space suitable for recovering the closest labels. However, learning deep models can be computationally expensive in large output spaces, resulting in a trade-off between high performing brute-force approaches and efficient solutions. In this paper, we propose PRIME, a XMC method that employs a novel prototypical contrastive learning technique to reconcile efficiency and performance surpassing brute-force approaches. We frame XMC as a data-to-prototype prediction task where label prototypes aggregate information from related queries. More precisely, we use a shallow transformer encoder that we coin as Label Prototype Network, which enriches label representations by aggregating text-based embeddings, label centroids and learnable free vectors. We jointly train a deep encoder and the Label Prototype Network using an adaptive triplet loss objective that better adapts to the high granularity and ambiguity of extreme label spaces. PRIME achieves state-of-the-art results in several public benchmarks of different sizes and domains, while keeping the model efficient.