OpenRaiser/Intern-Atlas huggingface dataset:
Graph Multi-Similarity Learning for Molecular Property Prediction
Venue: arXiv cs.LG 2024
Year: 2024

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative similarities) between molecules. However, current molecular representation learning methods fall short in exploring multi-similarity and often underestimate the complexity of relationships between molecules. Additionally, previous multi-similarity approaches require the specification of positive and negative pairs to attribute distinct predefined weights to different relative similarities, which can introduce potential bias. In this work, we introduce Graph Multi-Similarity Learning for Molecular Property Prediction (GraphMSL) framework, along with a novel approach to formulate a generalized multi-similarity metric without the need to define positive and negative pairs. In each of the chemical modality spaces (e.g.,molecular depiction image, fingerprint, NMR, and SMILES) under consideration, we first define a self-similarity metric (i.e., similarity between an anchor molecule and another molecule), and then transform it into a generalized multi-similarity metric for the anchor through a pair weighting function. GraphMSL validates the efficacy of the multi-similarity metric across MoleculeNet datasets. Furthermore, these metrics of all modalities are integrated into a multimodal multi-similarity metric, which showcases the potential to improve the performance. Moreover, the focus of the model can be redirected or customized by altering the fusion function. Last but not least, GraphMSL proves effective in drug discovery evaluations through post-hoc analyses of the learnt representations.
Navigating the OverKill in Large Language Models
Venue: arXiv cs.CL 2024
Year: 2024

Large language models are meticulously aligned to be both helpful and harmless. However, recent research points to a potential overkill which means models may refuse to answer benign queries. In this paper, we investigate the factors for overkill by exploring how models handle and determine the safety of queries. Our findings reveal the presence of shortcuts within models, leading to an over-attention of harmful words like 'kill' and prompts emphasizing safety will exacerbate overkill. Based on these insights, we introduce Self-Contrastive Decoding (Self-CD), a training-free and model-agnostic strategy, to alleviate this phenomenon. We first extract such over-attention by amplifying the difference in the model's output distributions when responding to system prompts that either include or omit an emphasis on safety. Then we determine the final next-token predictions by downplaying the over-attention from the model via contrastive decoding. Empirical results indicate that our method has achieved an average reduction of the refusal rate by 20\% while having almost no impact on safety.
Covering All Bases: The Next Inning in DNA Sequencing Efficiency
Venue: arXiv cs.IT 2024
Year: 2024

DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal error-correcting code pairings with DNA storage systems to minimize coverage depth. Conducted within random access settings, the study provides theoretical analyses and experimental simulations to examine the expectation and probability distribution of samples needed for files recovery. Structured into sections covering definitions, analyses, lower bounds, and comparative evaluations of coding schemes, the paper unveils insights into effective coding schemes for optimizing DNA storage systems.
A primer on synthetic health data
Venue: arXiv cs.LG 2024
Year: 2024

Recent advances in deep generative models have greatly expanded the potential to create realistic synthetic health datasets. These synthetic datasets aim to preserve the characteristics, patterns, and overall scientific conclusions derived from sensitive health datasets without disclosing patient identity or sensitive information. Thus, synthetic data can facilitate safe data sharing that supports a range of initiatives including the development of new predictive models, advanced health IT platforms, and general project ideation and hypothesis development. However, many questions and challenges remain, including how to consistently evaluate a synthetic dataset's similarity and predictive utility in comparison to the original real dataset and risk to privacy when shared. Additional regulatory and governance issues have not been widely addressed. In this primer, we map the state of synthetic health data, including generation and evaluation methods and tools, existing examples of deployment, the regulatory and ethical landscape, access and governance options, and opportunities for further development.
Contextual Feature Extraction Hierarchies Converge in Large Language Models and the Brain
Venue: arXiv cs.CL 2024
Year: 2024

Recent advancements in artificial intelligence have sparked interest in the parallels between large language models (LLMs) and human neural processing, particularly in language comprehension. While prior research has established similarities in the representation of LLMs and the brain, the underlying computational principles that cause this convergence, especially in the context of evolving LLMs, remain elusive. Here, we examined a diverse selection of high-performance LLMs with similar parameter sizes to investigate the factors contributing to their alignment with the brain's language processing mechanisms. We find that as LLMs achieve higher performance on benchmark tasks, they not only become more brain-like as measured by higher performance when predicting neural responses from LLM embeddings, but also their hierarchical feature extraction pathways map more closely onto the brain's while using fewer layers to do the same encoding. We also compare the feature extraction pathways of the LLMs to each other and identify new ways in which high-performing models have converged toward similar hierarchical processing mechanisms. Finally, we show the importance of contextual information in improving model performance and brain similarity. Our findings reveal the converging aspects of language processing in the brain and LLMs and offer new directions for developing models that align more closely with human cognitive processing.
Joint Transceiver Optimization for MmWave/THz MU-MIMO ISAC Systems
Venue: arXiv cs.IT 2024
Year: 2024

In this paper, we consider the problem of joint transceiver design for millimeter wave (mmWave)/Terahertz (THz) multi-user MIMO integrated sensing and communication (ISAC) systems. Such a problem is formulated into a nonconvex optimization problem, with the objective of maximizing a weighted sum of communication users' rates and the passive radar's signal-to-clutter-and-noise-ratio (SCNR). By exploring a low-dimensional subspace property of the optimal precoder, a low-complexity block-coordinate-descent (BCD)-based algorithm is proposed. Our analysis reveals that the hybrid analog/digital beamforming structure can attain the same performance as that of a fully digital precoder, provided that the number of radio frequency (RF) chains is no less than the number of resolvable signal paths. Also, through expressing the precoder as a sum of a communication-precoder and a sensing-precoder, we develop an analytical solution to the joint transceiver design problem by generalizing the idea of block-diagonalization (BD) to the ISAC system. Simulation results show that with a proper tradeoff parameter, the proposed methods can achieve a decent compromise between communication and sensing, where the performance of each communication/sensing task experiences only a mild performance loss as compared with the performance attained by optimizing exclusively for a single task.
Deductive Beam Search: Decoding Deducible Rationale for Chain-of-Thought Reasoning
Venue: arXiv cs.CL 2024
Year: 2024

Recent advancements have significantly augmented the reasoning capabilities of Large Language Models (LLMs) through various methodologies, especially chain-of-thought (CoT) reasoning. However, previous methods fail to address reasoning errors in intermediate steps, leading to accumulative errors. In this paper, we propose Deductive Beam Search (DBS), which seamlessly integrates CoT and deductive reasoning with step-wise beam search for LLMs. Our approach deploys a verifier, verifying the deducibility of a reasoning step and its premises, thus alleviating the error accumulation. Furthermore, we introduce a scalable and labor-free data construction method to amplify our model's verification capabilities. Extensive experiments demonstrate that our approach significantly enhances the base performance of LLMs of various scales (7B, 13B, 70B, and ChatGPT) across 8 reasoning datasets from 3 diverse reasoning genres, including arithmetic, commonsense, and symbolic. Moreover, our analysis proves DBS's capability of detecting diverse and subtle reasoning errors and robustness on different model scales.
Computing the forcing spectrum of outerplanar graphs in polynomial time
Venue: arXiv cs.DM 2024
Year: 2024

The forcing number of a graph with a perfect matching $M$ is the minimum number of edges in $M$ whose endpoints need to be deleted, such that the remaining graph only has a single perfect matching. This number is of great interest in theoretical chemistry, since it conveys information about the structural properties of several interesting molecules. On the other hand, in bipartite graphs the forcing number corresponds to the famous feedback vertex set problem in digraphs. Determining the complexity of finding the smallest forcing number of a given planar graph is still a widely open and important question in this area, originally proposed by Afshani, Hatami, and Mahmoodian in 2004. We take a first step towards the resolution of this question by providing an algorithm that determines the set of all possible forcing numbers of an outerplanar graph in polynomial time. This is the first polynomial-time algorithm concerning this problem for a class of graphs of comparable or greater generality.
Predicting suicidal behavior among Indian adults using childhood trauma, mental health questionnaires and machine learning cascade ensembles
Venue: arXiv cs.LG 2024
Year: 2024

Among young adults, suicide is India's leading cause of death, accounting for an alarming national suicide rate of around 16%. In recent years, machine learning algorithms have emerged to predict suicidal behavior using various behavioral traits. But to date, the efficacy of machine learning algorithms in predicting suicidal behavior in the Indian context has not been explored in literature. In this study, different machine learning algorithms and ensembles were developed to predict suicide behavior based on childhood trauma, different mental health parameters, and other behavioral factors. The dataset was acquired from 391 individuals from a wellness center in India. Information regarding their childhood trauma, psychological wellness, and other mental health issues was acquired through standardized questionnaires. Results revealed that cascade ensemble learning methods using a support vector machine, decision trees, and random forest were able to classify suicidal behavior with an accuracy of 95.04% using data from childhood trauma and mental health questionnaires. The study highlights the potential of using these machine learning ensembles to identify individuals with suicidal tendencies so that targeted interinterventions could be provided efficiently.
High-Performance Data Mapping for BNNs on PCM-based Integrated Photonics
Venue: arXiv cs.AR 2024
Year: 2024

State-of-the-Art (SotA) hardware implementations of Deep Neural Networks (DNNs) incur high latencies and costs. Binary Neural Networks (BNNs) are potential alternative solutions to realize faster implementations without losing accuracy. In this paper, we first present a new data mapping, called TacitMap, suited for BNNs implemented based on a Computation-In-Memory (CIM) architecture. TacitMap maximizes the use of available parallelism, while CIM architecture eliminates the data movement overhead. We then propose a hardware accelerator based on optical phase change memory (oPCM) called EinsteinBarrier. Ein-steinBarrier incorporates TacitMap and adds an extra dimension for parallelism through wavelength division multiplexing, leading to extra latency reduction. The simulation results show that, compared to the SotA CIM baseline, TacitMap and EinsteinBarrier significantly improve execution time by up to ~154x and ~3113x, respectively, while also maintaining the energy consumption within 60% of that in the CIM baseline.
Towards Physical Plausibility in Neuroevolution Systems
Venue: arXiv cs.NE 2024
Year: 2024

The increasing usage of Artificial Intelligence (AI) models, especially Deep Neural Networks (DNNs), is increasing the power consumption during training and inference, posing environmental concerns and driving the need for more energy-efficient algorithms and hardware solutions. This work addresses the growing energy consumption problem in Machine Learning (ML), particularly during the inference phase. Even a slight reduction in power usage can lead to significant energy savings, benefiting users, companies, and the environment. Our approach focuses on maximizing the accuracy of Artificial Neural Network (ANN) models using a neuroevolutionary framework whilst minimizing their power consumption. To do so, power consumption is considered in the fitness function. We introduce a new mutation strategy that stochastically reintroduces modules of layers, with power-efficient modules having a higher chance of being chosen. We introduce a novel technique that allows training two separate models in a single training step whilst promoting one of them to be more power efficient than the other while maintaining similar accuracy. The results demonstrate a reduction in power consumption of ANN models by up to 29.2% without a significant decrease in predictive performance.
Leveraging Human-Machine Interactions for Computer Vision Dataset Quality Enhancement
Venue: arXiv cs.CV 2024
Year: 2024

Large-scale datasets for single-label multi-class classification, such as \emph{ImageNet-1k}, have been instrumental in advancing deep learning and computer vision. However, a critical and often understudied aspect is the comprehensive quality assessment of these datasets, especially regarding potential multi-label annotation errors. In this paper, we introduce a lightweight, user-friendly, and scalable framework that synergizes human and machine intelligence for efficient dataset validation and quality enhancement. We term this novel framework \emph{Multilabelfy}. Central to Multilabelfy is an adaptable web-based platform that systematically guides annotators through the re-evaluation process, effectively leveraging human-machine interactions to enhance dataset quality. By using Multilabelfy on the ImageNetV2 dataset, we found that approximately $47.88\%$ of the images contained at least two labels, underscoring the need for more rigorous assessments of such influential datasets. Furthermore, our analysis showed a negative correlation between the number of potential labels per image and model top-1 accuracy, illuminating a crucial factor in model evaluation and selection. Our open-source framework, Multilabelfy, offers a convenient, lightweight solution for dataset enhancement, emphasizing multi-label proportions. This study tackles major challenges in dataset integrity and provides key insights into model performance evaluation. Moreover, it underscores the advantages of integrating human expertise with machine capabilities to produce more robust models and trustworthy data development. The source code for Multilabelfy will be available at https://github.com/esla/Multilabelfy. \keywords{Computer Vision \and Dataset Quality Enhancement \and Dataset Validation \and Human-Computer Interaction \and Multi-label Annotation.}
Algorithmic Robust Forecast Aggregation
Venue: arXiv cs.LG 2024
Year: 2024

Forecast aggregation combines the predictions of multiple forecasters to improve accuracy. However, the lack of knowledge about forecasters' information structure hinders optimal aggregation. Given a family of information structures, robust forecast aggregation aims to find the aggregator with minimal worst-case regret compared to the omniscient aggregator. Previous approaches for robust forecast aggregation rely on heuristic observations and parameter tuning. We propose an algorithmic framework for robust forecast aggregation. Our framework provides efficient approximation schemes for general information aggregation with a finite family of possible information structures. In the setting considered by Arieli et al. (2018) where two agents receive independent signals conditioned on a binary state, our framework also provides efficient approximation schemes by imposing Lipschitz conditions on the aggregator or discrete conditions on agents' reports. Numerical experiments demonstrate the effectiveness of our method by providing a nearly optimal aggregator in the setting considered by Arieli et al. (2018).
Rapid post-disaster infrastructure damage characterisation enabled by remote sensing and deep learning technologies -- a tiered approach
Venue: arXiv cs.CV 2024
Year: 2024

Critical infrastructure, such as transport networks and bridges, are systematically targeted during wars and suffer damage during extensive natural disasters because it is vital for enabling connectivity and transportation of people and goods, and hence, underpins national and international economic growth. Mass destruction of transport assets, in conjunction with minimal or no accessibility in the wake of natural and anthropogenic disasters, prevents us from delivering rapid recovery and adaptation. As a result, systemic operability is drastically reduced, leading to low levels of resilience. Thus, there is a need for rapid assessment of its condition to allow for informed decision-making for restoration prioritisation. A solution to this challenge is to use technology that enables stand-off observations. Nevertheless, no methods exist for automated characterisation of damage at multiple scales, i.e. regional (e.g., network), asset (e.g., bridges), and structural (e.g., road pavement) scales. We propose a methodology based on an integrated, multi-scale tiered approach to fill this capability gap. In doing so, we demonstrate how automated damage characterisation can be enabled by fit-for-purpose digital technologies. Next, the methodology is applied and validated to a case study in Ukraine that includes 17 bridges, damaged by human targeted interventions. From regional to component scale, we deploy technology to integrate assessments using Sentinel-1 SAR images, crowdsourced information, and high-resolution images for deep learning to facilitate automatic damage detection and characterisation. For the first time, the interferometric coherence difference and semantic segmentation of images were deployed in a tiered multi-scale approach to improve the reliability of damage characterisations at different scales.
SNP-S3: Shared Network Pre-training and Significant Semantic Strengthening for Various Video-Text Tasks
Venue: arXiv cs.CV 2024
Year: 2024

We present a framework for learning cross-modal video representations by directly pre-training on raw data to facilitate various downstream video-text tasks. Our main contributions lie in the pre-training framework and proxy tasks. First, based on the shortcomings of two mainstream pixel-level pre-training architectures (limited applications or less efficient), we propose Shared Network Pre-training (SNP). By employing one shared BERT-type network to refine textual and cross-modal features simultaneously, SNP is lightweight and could support various downstream applications. Second, based on the intuition that people always pay attention to several "significant words" when understanding a sentence, we propose the Significant Semantic Strengthening (S3) strategy, which includes a novel masking and matching proxy task to promote the pre-training performance. Experiments conducted on three downstream video-text tasks and six datasets demonstrate that, we establish a new state-of-the-art in pixel-level video-text pre-training; we also achieve a satisfactory balance between the pre-training efficiency and the fine-tuning performance. The codebase are available at https://github.com/alipay/Ant-Multi-Modal-Framework/tree/main/prj/snps3_vtp.
M2-RAAP: A Multi-Modal Recipe for Advancing Adaptation-based Pre-training towards Effective and Efficient Zero-shot Video-text Retrieval
Venue: arXiv cs.CV 2024
Year: 2024

We present a Multi-Modal Recipe for Advancing Adaptation-based Pre-training towards effective and efficient zero-shot video-text retrieval, dubbed M2-RAAP. Upon popular image-text models like CLIP, most current adaptation-based video-text pre-training methods are confronted by three major issues, i.e., noisy data corpus, time-consuming pre-training, and limited performance gain. Towards this end, we conduct a comprehensive study including four critical steps in video-text pre-training. Specifically, we investigate 1) data filtering and refinement, 2) video input type selection, 3) temporal modeling, and 4) video feature enhancement. We then summarize this empirical study into the M2-RAAP recipe, where our technical contributions lie in 1) the data filtering and text re-writing pipeline resulting in 1M high-quality bilingual video-text pairs, 2) the replacement of video inputs with key-frames to accelerate pre-training, and 3) the Auxiliary-Caption-Guided (ACG) strategy to enhance video features. We conduct extensive experiments by adapting three image-text foundation models on two refined video-text datasets from different languages, validating the robustness and reproducibility of M2-RAAP for adaptation-based pre-training. Results demonstrate that M2-RAAP yields superior performance with significantly reduced data (-90%) and time consumption (-95%), establishing a new SOTA on four English zero-shot retrieval datasets and two Chinese ones. We are preparing our refined bilingual data annotations and codebase, which will be available at https://github.com/alipay/Ant-Multi-Modal-Framework/tree/main/prj/M2_RAAP.