Ajay Jaiswal

Ajay Jaiswal, Haoyu Ma, Tianlong Chen et al. · meta-ai

Pruning large neural networks to create high-quality, independently trainable sparse masks, which can maintain similar performance to their dense counterparts, is very desirable due to the reduced space and time complexity. As research effort is focused on increasingly sophisticated pruning methods that leads to sparse subnetworks trainable from the scratch, we argue for an orthogonal, under-explored theme: improving training techniques for pruned sub-networks, i.e. sparse training. Apart from the popular belief that only the quality of sparse masks matters for sparse training, in this paper we demonstrate an alternative opportunity: one can carefully customize the sparse training techniques to deviate from the default dense network training protocols, consisting of introducing ``ghost" neurons and skip connections at the early stage of training, and strategically modifying the initialization as well as labels. Our new sparse training recipe is generally applicable to improving training from scratch with various sparse masks. By adopting our newly curated techniques, we demonstrate significant performance gains across various popular datasets (CIFAR-10, CIFAR-100, TinyImageNet), architectures (ResNet-18/32/104, Vgg16, MobileNet), and sparse mask options (lottery ticket, SNIP/GRASP, SynFlow, or even randomly pruning), compared to the default training protocols, especially at high sparsity levels. Code is at https://github.com/VITA-Group/ToST

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Large pre-trained transformers are show-stealer in modern-day deep learning, and it becomes crucial to comprehend the parsimonious patterns that exist within them as they grow in scale. With exploding parameter counts, Lottery Ticket Hypothesis (LTH) and its variants, have lost their pragmatism in sparsifying them due to high computation and memory bottleneck of repetitive train-prune-retrain routine of iterative magnitude pruning (IMP) which worsens with increasing model size. This paper comprehensively studies induced sparse patterns across multiple large pre-trained vision and language transformers. We propose the existence of -- essential sparsity defined with a sharp dropping point beyond which the performance declines much faster w.r.t the rise of sparsity level, when we directly remove weights with the smallest magnitudes in one-shot without re-training. We also find essential sparsity to hold valid for N:M sparsity patterns as well as on modern-scale large language models (Vicuna-7B). We also present an intriguing emerging phenomenon of abrupt sparsification during the pre-training of BERT, i.e., BERT suddenly becomes heavily sparse in pre-training after certain iterations. Moreover, our observations also indicate a counter-intuitive finding that BERT trained with a larger amount of pre-training data tends to have a better ability to condense knowledge in comparatively relatively fewer parameters. Lastly, we investigate the effect of the pre-training loss on essential sparsity and discover that self-supervised learning (SSL) objectives trigger stronger emergent sparsification properties than supervised learning (SL). Our codes are available at \url{https://github.com/VITA-Group/essential_sparsity}.

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Large pre-trained transformers have been receiving explosive attention in the past few years, due to their wide adaptability for numerous downstream applications via fine-tuning, but their exponentially increasing parameter counts are becoming a primary hurdle to even just fine-tune them without industry-standard hardware. Recently, Lottery Ticket Hypothesis (LTH) and its variants, have been exploited to prune these large pre-trained models generating subnetworks that can achieve similar performance as their dense counterparts, but LTH pragmatism is enormously inhibited by repetitive full training and pruning routine of iterative magnitude pruning (IMP) which worsens with increasing model size. Motivated by the recent observations of model soups, which suggest that fine-tuned weights of multiple models can be merged to a better minima, we propose Instant Soup Pruning (ISP) to generate lottery ticket quality subnetworks, using a fraction of the original IMP cost by replacing the expensive intermediate pruning stages of IMP with computationally efficient weak mask generation and aggregation routine. More specifically, during the mask generation stage, ISP takes a small handful of iterations using varying training protocols and data subsets to generate many weak and noisy subnetworks, and superpose them to average out the noise creating a high-quality denoised subnetwork. Our extensive experiments and ablation on two popular large-scale pre-trained models: CLIP (unexplored in pruning till date) and BERT across multiple benchmark vision and language datasets validate the effectiveness of ISP compared to several state-of-the-art pruning methods. Codes are available at: \url{https://github.com/VITA-Group/instant_soup}

Ajay Jaiswal, Peihao Wang, Tianlong Chen et al.

Despite the enormous success of Graph Convolutional Networks (GCNs) in modeling graph-structured data, most of the current GCNs are shallow due to the notoriously challenging problems of over-smoothening and information squashing along with conventional difficulty caused by vanishing gradients and over-fitting. Previous works have been primarily focused on the study of over-smoothening and over-squashing phenomena in training deep GCNs. Surprisingly, in comparison with CNNs/RNNs, very limited attention has been given to understanding how healthy gradient flow can benefit the trainability of deep GCNs. In this paper, firstly, we provide a new perspective of gradient flow to understand the substandard performance of deep GCNs and hypothesize that by facilitating healthy gradient flow, we can significantly improve their trainability, as well as achieve state-of-the-art (SOTA) level performance from vanilla-GCNs. Next, we argue that blindly adopting the Glorot initialization for GCNs is not optimal, and derive a topology-aware isometric initialization scheme for vanilla-GCNs based on the principles of isometry. Additionally, contrary to ad-hoc addition of skip-connections, we propose to use gradient-guided dynamic rewiring of vanilla-GCNs} with skip connections. Our dynamic rewiring method uses the gradient flow within each layer during training to introduce on-demand skip-connections adaptively. We provide extensive empirical evidence across multiple datasets that our methods improve gradient flow in deep vanilla-GCNs and significantly boost their performance to comfortably compete and outperform many fancy state-of-the-art methods. Codes are available at: https://github.com/VITA-Group/GradientGCN.

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Graphs are omnipresent and GNNs are a powerful family of neural networks for learning over graphs. Despite their popularity, scaling GNNs either by deepening or widening suffers from prevalent issues of unhealthy gradients, over-smoothening, information squashing, which often lead to sub-standard performance. In this work, we are interested in exploring a principled way to scale GNNs capacity without deepening or widening, which can improve its performance across multiple small and large graphs. Motivated by the recent intriguing phenomenon of model soups, which suggest that fine-tuned weights of multiple large-language pre-trained models can be merged to a better minima, we argue to exploit the fundamentals of model soups to mitigate the aforementioned issues of memory bottleneck and trainability during GNNs scaling. More specifically, we propose not to deepen or widen current GNNs, but instead present a data-centric perspective of model soups tailored for GNNs, i.e., to build powerful GNNs. By dividing giant graph data, we build multiple independently and parallelly trained weaker GNNs (soup ingredient) without any intermediate communication, and combine their strength using a greedy interpolation soup procedure to achieve state-of-the-art performance. Compared to concurrent distributed GNN training works such as Jiong et. al. 2023, we train each soup ingredient by sampling different subgraphs per epoch and their respective sub-models are merged only after being fully trained (rather than intermediately so). Moreover, we provide a wide variety of model soup preparation techniques by leveraging state-of-the-art graph sampling and graph partitioning approaches that can handle large graphs. Codes are available at: \url{https://github.com/VITA-Group/graph_ladling}.

Ajay Jaiswal, Xingguang Zhang, Stanley H. Chan et al.

Image distortion by atmospheric turbulence is a stochastic degradation, which is a critical problem in long-range optical imaging systems. A number of research has been conducted during the past decades, including model-based and emerging deep-learning solutions with the help of synthetic data. Although fast and physics-grounded simulation tools have been introduced to help the deep-learning models adapt to real-world turbulence conditions recently, the training of such models only relies on the synthetic data and ground truth pairs. This paper proposes the Physics-integrated Restoration Network (PiRN) to bring the physics-based simulator directly into the training process to help the network to disentangle the stochasticity from the degradation and the underlying image. Furthermore, to overcome the ``average effect" introduced by deterministic models and the domain gap between the synthetic and real-world degradation, we further introduce PiRN with Stochastic Refinement (PiRN-SR) to boost its perceptual quality. Overall, our PiRN and PiRN-SR improve the generalization to real-world unknown turbulence conditions and provide a state-of-the-art restoration in both pixel-wise accuracy and perceptual quality. Our codes are available at \url{https://github.com/VITA-Group/PiRN}.

Feng Liu, Ryan Ashbaugh, Nicholas Chimitt et al. · gatech

Whole-body biometric recognition is an important area of research due to its vast applications in law enforcement, border security, and surveillance. This paper presents the end-to-end design, development and evaluation of FarSight, an innovative software system designed for whole-body (fusion of face, gait and body shape) biometric recognition. FarSight accepts videos from elevated platforms and drones as input and outputs a candidate list of identities from a gallery. The system is designed to address several challenges, including (i) low-quality imagery, (ii) large yaw and pitch angles, (iii) robust feature extraction to accommodate large intra-person variabilities and large inter-person similarities, and (iv) the large domain gap between training and test sets. FarSight combines the physics of imaging and deep learning models to enhance image restoration and biometric feature encoding. We test FarSight's effectiveness using the newly acquired IARPA Biometric Recognition and Identification at Altitude and Range (BRIAR) dataset. Notably, FarSight demonstrated a substantial performance increase on the BRIAR dataset, with gains of +11.82% Rank-20 identification and +11.3% TAR@1% FAR.

Ajay Jaiswal, Zhe Gan, Xianzhi Du et al.

Despite their remarkable achievements, modern Large Language Models (LLMs) face exorbitant computational and memory footprints. Recently, several works have shown significant success in training-free and data-free compression (pruning and quantization) of LLMs that achieve 50 - 60% sparsity and reduce the bit width to 3 or 4 bits per weight, with negligible degradation of perplexity over the uncompressed baseline. As recent research efforts are focused on developing increasingly sophisticated compression methods, our work takes a step back and re-evaluates the effectiveness of existing SoTA compression methods, which rely on a fairly simple and widely questioned metric, perplexity (even for dense LLMs). We introduce Knowledge-Intensive Compressed LLM BenchmarK (LLM-KICK), a collection of carefully curated tasks to redefine the evaluation protocol for compressed LLMs, which have significant alignment with their dense counterparts and perplexity fail to capture subtle change in their true capabilities. LLM-KICK unveils many favorable merits and unfortunate plights of current SoTA compression methods: all pruning methods suffer significant performance degradation, sometimes at trivial sparsity ratios (e.g., 25-30%), and fail for N:M sparsity in knowledge-intensive tasks; current quantization methods are more successful than pruning; yet, pruned LLMs even at $\geq 50$% sparsity are robust in-context retrieval and summarization systems; among others. LLM-KICK is designed to holistically access compressed LLMs' ability for language understanding, reasoning, generation, in-context retrieval, in-context summarization, etc. We hope our study can foster the development of better LLM compression methods. The reproduced codes are available at https://github.com/VITA-Group/llm-kick.

Wenqing Zheng, S P Sharan, Ajay Kumar Jaiswal et al.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

Ajay Jaiswal, Yifan Wang, Lu Yin et al.

Large Language Models' (LLMs) weight matrices can often be expressed in low-rank form with potential to relax memory and compute resource requirements. Unlike prior efforts that focus on developing novel matrix decompositions, in this work we study the non-uniform low-rank properties of weight matrices in LLMs through the lens of stabilizing gradient subspace. First, we provide a theoretical framework to understand the stabilization of gradient subspaces through Hessian analysis. Second, we empirically establish an important relationship between gradient dynamics and low-rank expressiveness of weight matrices. Our findings reveal that different LLM components exhibit varying levels of converged low-rank structures, necessitating variable rank reduction across them to minimize drop in performance due to compression. Drawing on this result, we present Weight Low-Rank Projection(WeLore) that unifies weight compression and memory-efficient fine-tuning into one, in a data-agnostic and one-shot manner. When used as a compression technique, WeLore categorizes weight matrices into Low-rank Components (LRCs) and Non-Low-rank Components (N-LRCs) and suitably encodes them for minimum performance loss. Our gradient dynamics perspective illustrates that LRCs tend to have better fine-tuning capabilities and their standalone fine-tuning can closely mimic and sometimes outperform the training loss trajectory and performance of full fine-tuning with notable memory and compute footprint reduction. Codes are available at https://github.com/VITA-Group/WeLore.

Tianlong Chen, Zhenyu Zhang, Ajay Jaiswal et al.

Despite their remarkable achievement, gigantic transformers encounter significant drawbacks, including exorbitant computational and memory footprints during training, as well as severe collapse evidenced by a high degree of parameter redundancy. Sparsely-activated Mixture-of-Experts (SMoEs) have shown promise to mitigate the issue of training efficiency, yet they are prone to (1) redundant experts due to representational collapse; and (2) poor expert scalability for inference and downstream fine-tuning, primarily due to overfitting of the learned routing policy to the number of activated experts during training. As recent research efforts are predominantly focused on improving routing policies to encourage expert specializations, this work focuses on exploring the overlooked scalability bottleneck of SMoEs and leveraging it to effectively scale dense transformers. To this end, we propose a new plug-and-play training framework, SMoE-Dropout, to enable scaling transformers to better accuracy in their full capacity without collapse. Specifically, SMoE-Dropout consists of a randomly initialized and fixed router network to activate experts and gradually increases the activated expert number as training progresses over time. Transformers trained by SMoE-Dropout naturally exhibit a self-slimmable property subject to resource availability, offering smooth and consistent performance boosts with an increase in activated experts during inference or fine-tuning. Our extensive experiments demonstrate the superior performance and substantial computation savings of SMoE-Dropout, compared to dense training baselines with equivalent parameter counts. In particular, our trained BERT outperforms its densely trained counterpart with consistent improvements of {1.03%, 0.78%, 1.09%} on challenging reasoning tasks {ASDiv-A, MAWPS, SVAMP}, respectively.

Zhiyuan Mao, Ajay Jaiswal, Zhangyang Wang et al.

Image restoration algorithms for atmospheric turbulence are known to be much more challenging to design than traditional ones such as blur or noise because the distortion caused by the turbulence is an entanglement of spatially varying blur, geometric distortion, and sensor noise. Existing CNN-based restoration methods built upon convolutional kernels with static weights are insufficient to handle the spatially dynamical atmospheric turbulence effect. To address this problem, in this paper, we propose a physics-inspired transformer model for imaging through atmospheric turbulence. The proposed network utilizes the power of transformer blocks to jointly extract a dynamical turbulence distortion map and restore a turbulence-free image. In addition, recognizing the lack of a comprehensive dataset, we collect and present two new real-world turbulence datasets that allow for evaluation with both classical objective metrics (e.g., PSNR and SSIM) and a new task-driven metric using text recognition accuracy. Both real testing sets and all related code will be made publicly available.

Lu Yin, Ajay Jaiswal, Shiwei Liu et al.

We present Junk DNA Hypothesis by adopting a novel task-centric angle for the pre-trained weights of large language models (LLMs). It has been believed that weights in LLMs contain significant redundancy, leading to the conception that a considerable chunk of the parameters can be removed by pruning without compromising performance. Contrary to this belief, this paper presents a counter-argument: small-magnitude weights of pre-trained model weights encode vital knowledge essential for tackling difficult downstream tasks - manifested as the monotonic relationship between the performance drop of downstream tasks across the difficulty spectrum, as we prune more pre-trained weights by magnitude. Moreover, we reveal that these seemingly inconsequential weights can result in irreparable loss of knowledge and performance degradation in difficult tasks, even when downstream continual training is allowed. Interestingly, our evaluations show that the other popular compression, namely quantization, fails to exhibit similar monotonic effect and does not as convincingly disentangle this task-difficulty information. To study formally, we introduce several quantifiable metrics to gauge the downstream task difficulty: (1) within the same task category, and (2) across different task categories. Our extensive experiments substantiate the Junk DNA Hypothesis across a diverse range of model sizes, tasks, datasets, and even pruning methods. Codes are available at: https://github.com/VITA-Group/Junk_DNA_Hypothesis.git.

Shiwei Liu, Tianlong Chen, Zhenyu Zhang et al.

Sparse Neural Networks (SNNs) have received voluminous attention predominantly due to growing computational and memory footprints of consistently exploding parameter count in large-scale models. Similar to their dense counterparts, recent SNNs generalize just as well and are equipped with numerous favorable benefits (e.g., low complexity, high scalability, and robustness), sometimes even better than the original dense networks. As research effort is focused on developing increasingly sophisticated sparse algorithms, it is startling that a comprehensive benchmark to evaluate the effectiveness of these algorithms has been highly overlooked. In absence of a carefully crafted evaluation benchmark, most if not all, sparse algorithms are evaluated against fairly simple and naive tasks (eg. CIFAR, ImageNet, GLUE, etc.), which can potentially camouflage many advantages as well unexpected predicaments of SNNs. In pursuit of a more general evaluation and unveiling the true potential of sparse algorithms, we introduce "Sparsity May Cry" Benchmark (SMC-Bench), a collection of carefully-curated 4 diverse tasks with 10 datasets, that accounts for capturing a wide range of domain-specific and sophisticated knowledge. Our systemic evaluation of the most representative sparse algorithms reveals an important obscured observation: the state-of-the-art magnitude- and/or gradient-based sparse algorithms seemingly fail to perform on SMC-Bench when applied out-of-the-box, sometimes at significantly trivial sparsity as low as 5%. By incorporating these well-thought and diverse tasks, SMC-Bench is designed to favor and encourage the development of more scalable and generalizable sparse algorithms.

Gregory Holste, Ziyu Jiang, Ajay Jaiswal et al.

Pruning has emerged as a powerful technique for compressing deep neural networks, reducing memory usage and inference time without significantly affecting overall performance. However, the nuanced ways in which pruning impacts model behavior are not well understood, particularly for long-tailed, multi-label datasets commonly found in clinical settings. This knowledge gap could have dangerous implications when deploying a pruned model for diagnosis, where unexpected model behavior could impact patient well-being. To fill this gap, we perform the first analysis of pruning's effect on neural networks trained to diagnose thorax diseases from chest X-rays (CXRs). On two large CXR datasets, we examine which diseases are most affected by pruning and characterize class "forgettability" based on disease frequency and co-occurrence behavior. Further, we identify individual CXRs where uncompressed and heavily pruned models disagree, known as pruning-identified exemplars (PIEs), and conduct a human reader study to evaluate their unifying qualities. We find that radiologists perceive PIEs as having more label noise, lower image quality, and higher diagnosis difficulty. This work represents a first step toward understanding the impact of pruning on model behavior in deep long-tailed, multi-label medical image classification. All code, model weights, and data access instructions can be found at https://github.com/VITA-Group/PruneCXR.

Zhenyu Zhang, Ajay Jaiswal, Lu Yin et al.

Training Large Language Models (LLMs) is memory-intensive due to the large number of parameters and associated optimization states. GaLore, a recent method, reduces memory usage by projecting weight gradients into a low-rank subspace without compromising performance. However, GaLore relies on time-consuming Singular Value Decomposition (SVD) operations to identify the subspace, and the frequent subspace updates lead to significant training time overhead. Moreover, GaLore offers minimal improvements in accuracy and efficiency compared to LoRA in more accessible fine-tuning scenarios. To address these limitations, we introduce Q-Galore, a novel approach that substantially reduces memory usage by combining quantization and low-rank projection, surpassing the benefits of GaLore. Our method is based on two key observations: (i) the gradient subspace exhibits diverse properties, with some layers converging early in training while others are subject to frequent changes; (ii) the projection matrices are highly resilient to low-bit quantization. Leveraging these insights, Q-GaLore adaptively updates the gradient subspace based on its convergence statistics, achieving comparable performance while significantly reducing the number of SVD operations. We maintain the projection matrices in INT4 format and weights in INT8 format, incorporating stochastic rounding to capture accumulated gradient information. This approach enables a high-precision training trajectory using only low-precision weights. We demonstrate that Q-GaLore achieves highly competitive performance with exceptional memory efficiency. At pre-training, Q-GaLore facilitates training a LLaMA-7B model from scratch on a single NVIDIA RTX 4060 Ti with only 16 GB memory. At fine-tuning, it reduces memory consumption by up to 50% compared to LoRA and GaLore, while consistently outperforming QLoRA at the same memory cost.

Ajay Jaiswal, Tianlong Chen, Justin F. Rousseau et al.

Deep neural networks (DNNs) have rapidly become a \textit{de facto} choice for medical image understanding tasks. However, DNNs are notoriously fragile to the class imbalance in image classification. We further point out that such imbalance fragility can be amplified when it comes to more sophisticated tasks such as pathology localization, as imbalances in such problems can have highly complex and often implicit forms of presence. For example, different pathology can have different sizes or colors (w.r.t.the background), different underlying demographic distributions, and in general different difficulty levels to recognize, even in a meticulously curated balanced distribution of training data. In this paper, we propose to use pruning to automatically and adaptively identify \textit{hard-to-learn} (HTL) training samples, and improve pathology localization by attending them explicitly, during training in \textit{supervised, semi-supervised, and weakly-supervised} settings. Our main inspiration is drawn from the recent finding that deep classification models have difficult-to-memorize samples and those may be effectively exposed through network pruning \cite{hooker2019compressed} - and we extend such observation beyond classification for the first time. We also present an interesting demographic analysis which illustrates HTLs ability to capture complex demographic imbalances. Our extensive experiments on the Skin Lesion Localization task in multiple training settings by paying additional attention to HTLs show significant improvement of localization performance by $\sim$2-3\%.

Ajay Jaiswal, Kumar Ashutosh, Justin F Rousseau et al.

AI-powered Medical Imaging has recently achieved enormous attention due to its ability to provide fast-paced healthcare diagnoses. However, it usually suffers from a lack of high-quality datasets due to high annotation cost, inter-observer variability, human annotator error, and errors in computer-generated labels. Deep learning models trained on noisy labelled datasets are sensitive to the noise type and lead to less generalization on the unseen samples. To address this challenge, we propose a Robust Stochastic Knowledge Distillation (RoS-KD) framework which mimics the notion of learning a topic from multiple sources to ensure deterrence in learning noisy information. More specifically, RoS-KD learns a smooth, well-informed, and robust student manifold by distilling knowledge from multiple teachers trained on overlapping subsets of training data. Our extensive experiments on popular medical imaging classification tasks (cardiopulmonary disease and lesion classification) using real-world datasets, show the performance benefit of RoS-KD, its ability to distill knowledge from many popular large networks (ResNet-50, DenseNet-121, MobileNet-V2) in a comparatively small network, and its robustness to adversarial attacks (PGD, FSGM). More specifically, RoS-KD achieves >2% and >4% improvement on F1-score for lesion classification and cardiopulmonary disease classification tasks, respectively, when the underlying student is ResNet-18 against recent competitive knowledge distillation baseline. Additionally, on cardiopulmonary disease classification task, RoS-KD outperforms most of the SOTA baselines by ~1% gain in AUC score.

Gregory Holste, Yiliang Zhou, Song Wang et al.

Many real-world image recognition problems, such as diagnostic medical imaging exams, are "long-tailed" $\unicode{x2013}$ there are a few common findings followed by many more relatively rare conditions. In chest radiography, diagnosis is both a long-tailed and multi-label problem, as patients often present with multiple findings simultaneously. While researchers have begun to study the problem of long-tailed learning in medical image recognition, few have studied the interaction of label imbalance and label co-occurrence posed by long-tailed, multi-label disease classification. To engage with the research community on this emerging topic, we conducted an open challenge, CXR-LT, on long-tailed, multi-label thorax disease classification from chest X-rays (CXRs). We publicly release a large-scale benchmark dataset of over 350,000 CXRs, each labeled with at least one of 26 clinical findings following a long-tailed distribution. We synthesize common themes of top-performing solutions, providing practical recommendations for long-tailed, multi-label medical image classification. Finally, we use these insights to propose a path forward involving vision-language foundation models for few- and zero-shot disease classification.

Tianhao Li, Sandesh Shetty, Advaith Kamath et al.

Large pre-trained language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology, has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Our proposed few-shot learning approach uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. Our experiments, which involved seven rare tissues from different cancer types, demonstrated that the LLM-based prediction model achieved significant accuracy with very few or zero samples. Our proposed model, the CancerGPT (with $\sim$ 124M parameters), was even comparable to the larger fine-tuned GPT-3 model (with $\sim$ 175B parameters). Our research is the first to tackle drug pair synergy prediction in rare tissues with limited data. We are also the first to utilize an LLM-based prediction model for biological reaction prediction tasks.

Ajay Jaiswal, Nurendra Choudhary, Ravinarayana Adkathimar et al.

Graph Neural Networks (GNNs) have attracted immense attention in the past decade due to their numerous real-world applications built around graph-structured data. On the other hand, Large Language Models (LLMs) with extensive pretrained knowledge and powerful semantic comprehension abilities have recently shown a remarkable ability to benefit applications using vision and text data. In this paper, we investigate how LLMs can be leveraged in a computationally efficient fashion to benefit rich graph-structured data, a modality relatively unexplored in LLM literature. Prior works in this area exploit LLMs to augment every node features in an ad-hoc fashion (not scalable for large graphs), use natural language to describe the complex structural information of graphs, or perform computationally expensive finetuning of LLMs in conjunction with GNNs. We propose E-LLaGNN (Efficient LLMs augmented GNNs), a framework with an on-demand LLM service that enriches message passing procedure of graph learning by enhancing a limited fraction of nodes from the graph. More specifically, E-LLaGNN relies on sampling high-quality neighborhoods using LLMs, followed by on-demand neighborhood feature enhancement using diverse prompts from our prompt catalog, and finally information aggregation using message passing from conventional GNN architectures. We explore several heuristics-based active node selection strategies to limit the computational and memory footprint of LLMs when handling millions of nodes. Through extensive experiments & ablation on popular graph benchmarks of varying scales (Cora, PubMed, ArXiv, & Products), we illustrate the effectiveness of our E-LLaGNN framework and reveal many interesting capabilities such as improved gradient flow in deep GNNs, LLM-free inference ability etc.

Runjin Chen, Tong Zhao, Ajay Jaiswal et al.

Graph Neural Networks (GNNs) have empowered the advance in graph-structured data analysis. Recently, the rise of Large Language Models (LLMs) like GPT-4 has heralded a new era in deep learning. However, their application to graph data poses distinct challenges due to the inherent difficulty of translating graph structures to language. To this end, we introduce the Large Language and Graph Assistant (LLaGA), an innovative model that effectively integrates LLM capabilities to handle the complexities of graph-structured data. LLaGA retains the general-purpose nature of LLMs while adapting graph data into a format compatible with LLM input. LLaGA achieves this by reorganizing graph nodes to structure-aware sequences and then mapping these into the token embedding space through a versatile projector. LLaGA excels in versatility, generalizability and interpretability, allowing it to perform consistently well across different datasets and tasks, extend its ability to unseen datasets or tasks, and provide explanations for graphs. Our extensive experiments across popular graph benchmarks show that LLaGA delivers outstanding performance across four datasets and three tasks using one single model, surpassing state-of-the-art graph models in both supervised and zero-shot scenarios. Our code is available at \url{https://github.com/VITA-Group/LLaGA}.

Tianhao Chen, Xin Xu, Zijing Liu et al.

Modern Large Language Models, such as the LLaMA, Qwen and DeepSeek series, predominantly adopt the Pre-LayerNorm (Pre-LN) Transformer architecture. While being stable during pretraining and scalable to large model sizes, Pre-LN suffers from an exponential growth in activation variance across layers, causing the shortcut to dominate over sub-layer outputs in the residual connection and limiting the learning capacity of deeper layers. To mitigate this issue, we propose Gradient-Preserving Activation Scaling (GPAS), a simple technique that can be used in combination with existing approaches. GPAS works by scaling down the intermediate activations while keeping their gradients unchanged. This leaves information in the activations intact, and avoids the gradient vanishing problem associated with gradient downscaling. Extensive experiments across various model sizes from 71M to 1B show that GPAS achieves consistent performance gains. Beyond enhancing Pre-LN Transformers, GPAS also shows promise in improving alternative architectures such as Sandwich-LN and DeepNorm, demonstrating its versatility and potential for improving training dynamics in a wide range of settings. Our code is available at https://github.com/dandingsky/GPAS.

Awais Naeem, Tianhao Li, Huang-Ru Liao et al.

Accurate diagnosis and prognosis assisted by pathology images are essential for cancer treatment selection and planning. Despite the recent trend of adopting deep-learning approaches for analyzing complex pathology images, they fall short as they often overlook the domain-expert understanding of tissue structure and cell composition. In this work, we focus on a challenging Open-ended Pathology VQA (PathVQA-Open) task and propose a novel framework named Path-RAG, which leverages HistoCartography to retrieve relevant domain knowledge from pathology images and significantly improves performance on PathVQA-Open. Admitting the complexity of pathology image analysis, Path-RAG adopts a human-centered AI approach by retrieving domain knowledge using HistoCartography to select the relevant patches from pathology images. Our experiments suggest that domain guidance can significantly boost the accuracy of LLaVA-Med from 38% to 47%, with a notable gain of 28% for H&E-stained pathology images in the PathVQA-Open dataset. For longer-form question and answer pairs, our model consistently achieves significant improvements of 32.5% in ARCH-Open PubMed and 30.6% in ARCH-Open Books on H\&E images. Our code and dataset is available here (https://github.com/embedded-robotics/path-rag).

Yan Han, Chongyan Chen, Liyan Tang et al.

Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. In this paper, we develop an end-to-end framework, ChexRadiNet, that can utilize the radiomics features to improve the abnormality classification performance. Specifically, ChexRadiNet first applies a light-weight but efficient triplet-attention mechanism to classify the chest X-rays and highlight the abnormal regions. Then it uses the generated class activation map to extract radiomic features, which further guides our model to learn more robust image features. After a number of iterations and with the help of radiomic features, our framework can converge to more accurate image regions. We evaluate the ChexRadiNet framework using three public datasets: NIH ChestX-ray, CheXpert, and MIMIC-CXR. We find that ChexRadiNet outperforms the state-of-the-art on both disease detection (0.843 in AUC) and localization (0.679 in T(IoU) = 0.1). We will make the code publicly available at https://github.com/bionlplab/lung_disease_detection_amia2021, with the hope that this method can facilitate the development of automatic systems with a higher-level understanding of the radiological world.

Junyuan Hong, Jinhao Duan, Chenhui Zhang et al. · berkeley

Compressing high-capability Large Language Models (LLMs) has emerged as a favored strategy for resource-efficient inferences. While state-of-the-art (SoTA) compression methods boast impressive advancements in preserving benign task performance, the potential risks of compression in terms of safety and trustworthiness have been largely neglected. This study conducts the first, thorough evaluation of three (3) leading LLMs using five (5) SoTA compression techniques across eight (8) trustworthiness dimensions. Our experiments highlight the intricate interplay between compression and trustworthiness, revealing some interesting patterns. We find that quantization is currently a more effective approach than pruning in achieving efficiency and trustworthiness simultaneously. For instance, a 4-bit quantized model retains the trustworthiness of its original counterpart, but model pruning significantly degrades trustworthiness, even at 50% sparsity. Moreover, employing quantization within a moderate bit range could unexpectedly improve certain trustworthiness dimensions such as ethics and fairness. Conversely, extreme quantization to very low bit levels (3 bits) tends to reduce trustworthiness significantly. This increased risk cannot be uncovered by looking at benign performance alone, in turn, mandating comprehensive trustworthiness evaluation in practice. These findings culminate in practical recommendations for simultaneously achieving high utility, efficiency, and trustworthiness in LLMs. Code and models are available at https://decoding-comp-trust.github.io.

Ajay Jaiswal, Bodun Hu, Lu Yin et al.

Autoregressive Large Language Models (e.g., LLaMa, GPTs) are omnipresent achieving remarkable success in language understanding and generation. However, such impressive capability typically comes with a substantial model size, which presents significant challenges for autoregressive token-by-token generation. To mitigate computation overload incurred during generation, several early-exit and layer-dropping strategies have been proposed. Despite some promising success due to the redundancy across LLMs layers on metrics like Rough-L/BLUE, our careful knowledge-intensive evaluation unveils issues such as generation collapse, hallucination of wrong facts, and noticeable performance drop even at the trivial exit ratio of 10-15% of layers. We attribute these errors primarily to ineffective handling of the KV cache through state copying during early-exit. In this work, we observed the saturation of computationally expensive feed-forward blocks of LLM layers and proposed FFN-SkipLLM, which is a novel fine-grained skip strategy of autoregressive LLMs. More specifically, FFN-SkipLLM is an input-adaptive feed-forward skipping strategy that can skip 25-30% of FFN blocks of LLMs with marginal change in performance on knowledge-intensive generation tasks without any requirement to handle KV cache. Our extensive experiments and ablation across benchmarks like MT-Bench, Factoid-QA, and variable-length text summarization illustrate how our simple and ease-at-use method can facilitate faster autoregressive decoding.

Adarsh Kappiyath, Abhra Chaudhuri, Ajay Jaiswal et al.

Ranking samples by fine-grained estimates of spuriosity (the degree to which spurious cues are present) has recently been shown to significantly benefit bias mitigation, over the traditional binary biased-\textit{vs}-unbiased partitioning of train sets. However, this spuriosity ranking comes with the requirement of human supervision. In this paper, we propose a debiasing framework based on our novel \ul{Se}lf-Guided \ul{B}ias \ul{Ra}nking (\emph{Sebra}), that mitigates biases (spurious correlations) via an automatic ranking of data points by spuriosity within their respective classes. Sebra leverages a key local symmetry in Empirical Risk Minimization (ERM) training -- the ease of learning a sample via ERM inversely correlates with its spuriousity; the fewer spurious correlations a sample exhibits, the harder it is to learn, and vice versa. However, globally across iterations, ERM tends to deviate from this symmetry. Sebra dynamically steers ERM to correct this deviation, facilitating the sequential learning of attributes in increasing order of difficulty, \ie, decreasing order of spuriosity. As a result, the sequence in which Sebra learns samples naturally provides spuriousity rankings. We use the resulting fine-grained bias characterization in a contrastive learning framework to mitigate biases from multiple sources. Extensive experiments show that Sebra consistently outperforms previous state-of-the-art unsupervised debiasing techniques across multiple standard benchmarks, including UrbanCars, BAR, CelebA, and ImageNet-1K. Code, pre-trained models, and training logs are available at https://kadarsh22.github.io/sebra_iclr25/.

Ajay Jaiswal, Liyan Tang, Meheli Ghosh et al.

Radiology reports are unstructured and contain the imaging findings and corresponding diagnoses transcribed by radiologists which include clinical facts and negated and/or uncertain statements. Extracting pathologic findings and diagnoses from radiology reports is important for quality control, population health, and monitoring of disease progress. Existing works, primarily rely either on rule-based systems or transformer-based pre-trained model fine-tuning, but could not take the factual and uncertain information into consideration, and therefore generate false-positive outputs. In this work, we introduce three sedulous augmentation techniques which retain factual and critical information while generating augmentations for contrastive learning. We introduce RadBERT-CL, which fuses these information into BlueBert via a self-supervised contrastive loss. Our experiments on MIMIC-CXR show superior performance of RadBERT-CL on fine-tuning for multi-class, multi-label report classification. We illustrate that when few labeled data are available, RadBERT-CL outperforms conventional SOTA transformers (BERT/BlueBert) by significantly larger margins (6-11%). We also show that the representations learned by RadBERT-CL can capture critical medical information in the latent space.

Ajay Jaiswal, Tianhao Li, Cyprian Zander et al.

Computer-aided diagnosis plays a salient role in more accessible and accurate cardiopulmonary diseases classification and localization on chest radiography. Millions of people get affected and die due to these diseases without an accurate and timely diagnosis. Recently proposed contrastive learning heavily relies on data augmentation, especially positive data augmentation. However, generating clinically-accurate data augmentations for medical images is extremely difficult because the common data augmentation methods in computer vision, such as sharp, blur, and crop operations, can severely alter the clinical settings of medical images. In this paper, we proposed a novel and simple data augmentation method based on patient metadata and supervised knowledge to create clinically accurate positive and negative augmentations for chest X-rays. We introduce an end-to-end framework, SCALP, which extends the self-supervised contrastive approach to a supervised setting. Specifically, SCALP pulls together chest X-rays from the same patient (positive keys) and pushes apart chest X-rays from different patients (negative keys). In addition, it uses ResNet-50 along with the triplet-attention mechanism to identify cardiopulmonary diseases, and Grad-CAM++ to highlight the abnormal regions. Our extensive experiments demonstrate that SCALP outperforms existing baselines with significant margins in both classification and localization tasks. Specifically, the average classification AUCs improve from 82.8% (SOTA using DenseNet-121) to 83.9% (SCALP using ResNet-50), while the localization results improve on average by 3.7% over different IoU thresholds.

Ajay Kumar Jaiswal, Haoyu Ma, Tianlong Chen et al.

Lottery Ticket Hypothesis (LTH) suggests that a dense neural network contains a sparse sub-network that can match the performance of the original dense network when trained in isolation from scratch. Most works retrain the sparse sub-network with the same training protocols as its dense network, such as initialization, architecture blocks, and training recipes. However, till now it is unclear that whether these training protocols are optimal for sparse networks. In this paper, we demonstrate that it is unnecessary for spare retraining to strictly inherit those properties from the dense network. Instead, by plugging in purposeful "tweaks" of the sparse subnetwork architecture or its training recipe, its retraining can be significantly improved than the default, especially at high sparsity levels. Combining all our proposed "tweaks" can yield the new state-of-the-art performance of LTH, and these modifications can be easily adapted to other sparse training algorithms in general. Specifically, we have achieved a significant and consistent performance gain of1.05% - 4.93% for ResNet18 on CIFAR-100 over vanilla-LTH. Moreover, our methods are shown to generalize across datasets (CIFAR10, CIFAR100, TinyImageNet) and architectures (Vgg16, ResNet-18/ResNet-34, MobileNet). All codes will be publicly available.

Mayank Raj, Ajay Jaiswal, Rohit R. R et al.

This paper describes our system (Solomon) details and results of participation in the SemEval 2020 Task 11 "Detection of Propaganda Techniques in News Articles"\cite{DaSanMartinoSemeval20task11}. We participated in Task "Technique Classification" (TC) which is a multi-class classification task. To address the TC task, we used RoBERTa based transformer architecture for fine-tuning on the propaganda dataset. The predictions of RoBERTa were further fine-tuned by class-dependent-minority-class classifiers. A special classifier, which employs dynamically adapted Least Common Sub-sequence algorithm, is used to adapt to the intricacies of repetition class. Compared to the other participating systems, our submission is ranked 4th on the leaderboard.