arXiv subjects

Ali Ghodsi

Publications and source records attributed to Ali Ghodsi.

At least 19 recordsLinked to original sources

arXiv2026

GraphPI: Efficient Protein Inference with Graph Neural Networks

The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs in various applications. Despite these strides, its application in protein inference is impeded by the scarcity of extensively labeled datasets, a challenge compounded by the high costs and complexities of accurate protein annotation. In this study, we introduce GraphPI, a novel framework that treats protein inference as a node classification problem. We treat proteins as interconnected nodes within a protein-peptide-PSM graph, utilizing a Graph Neural Network-based architecture to elucidate their interrelations. To address label scarcity, we train the model on a set of unlabeled public protein datasets with pseudo-labels derived from an existing protein inference algorithm, enhanced by self-training to iteratively refine labels based on confidence scores. Contrary to prevalent methodologies necessitating dataset-specific training, our research illustrates that GraphPI, due to the well normalized nature of Percolator features, exhibits universal applicability without dataset-specific fine-tuning, a feature that not only mitigates the risk of overfitting but also enhances computational efficiency. Our empirical experiments reveal notable performance on various test datasets and deliver significantly reduced computation times compared to common protein inference algorithms.

cs.LG↗

arXiv2026

Auto-Regressive Masked Diffusion Models

Masked diffusion models (MDMs) have emerged as a promising approach for language modeling, yet they face a performance gap compared to autoregressive models (ARMs) and require more training iterations. In this work, we present the Auto-Regressive Masked Diffusion (ARMD) model, an architecture designed to close this gap by unifying the training efficiency of autoregressive models with the parallel generation capabilities of diffusion-based models. Our key insight is to reframe the masked diffusion process as a block-wise causal model. This perspective allows us to design a strictly causal, permutation-equivariant architecture that computes all conditional probabilities across multiple denoising steps in a single, parallel forward pass. The resulting architecture supports efficient, autoregressive-style decoding and a progressive permutation training scheme, allowing the model to learn both canonical left-to-right and random token orderings. Leveraging this flexibility, we introduce a novel strided parallel generation strategy that accelerates inference by generating tokens in parallel streams while maintaining global coherence. Empirical results demonstrate that ARMD achieves state-of-the-art performance on standard language modeling benchmarks, outperforming established diffusion baselines while requiring significantly fewer training steps. Furthermore, it establishes a new benchmark for parallel text generation, effectively bridging the performance gap between parallel and sequential decoding.

cs.LG↗

arXiv2025

How Many Heads Make an SSM? A Unified Framework for Attention and State Space Models

Sequence modeling has produced diverse architectures -- from classical recurrent neural networks to modern Transformers and state space models (SSMs) -- yet a unified theoretical understanding of expressivity and trainability trade-offs remains limited. We introduce a unified framework that represents a broad class of sequence maps via an input-dependent effective interaction operator $W_{ij}(X)$, making explicit two recurring construction patterns: (i) the Unified Factorized Framework (Explicit) (attention-style mixing), in which $W_{ij}(X)$ varies through scalar coefficients applied to shared value maps, and (ii) Structured Dynamics (Implicit) (state-space recurrences), in which $W_{ij}$ is induced by a latent dynamical system. Using this framework, we derive three theoretical results. First, we establish the Interaction Rank Gap: models in the Unified Factorized Framework, such as single-head attention, are constrained to a low-dimensional operator span and cannot represent certain structured dynamical maps. Second, we prove an Equivalence (Head-Count) Theorem showing that, within our multi-head factorized class, representing a linear SSM whose lag operators span a $k$-dimensional subspace on length-$n$ sequences requires and is achievable with $H=k$ heads. Third, we prove a Gradient Highway Result, showing that attention layers admit inputs with distance-independent gradient paths, whereas stable linear dynamics exhibit distance-dependent gradient attenuation. Together, these results formalize a fundamental trade-off between algebraic expressivity (interaction/operator span) and long-range gradient propagation, providing theoretical grounding for modern sequence architecture design.

cs.LG↗

arXiv2024

Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing

Data-Independent Acquisition (DIA) was introduced to improve sensitivity to cover all peptides in a range rather than only sampling high-intensity peaks as in Data-Dependent Acquisition (DDA) mass spectrometry. However, it is not very clear how useful DIA data is for de novo peptide sequencing as the DIA data are marred with coeluted peptides, high noises, and varying data quality. We present a new deep learning method DIANovo, and address each of these difficulties, and improves the previous established systems by a large margin, via equipping the model with a deeper understanding of coeluted DIA spectra. This paper also provides criteria about when DIA data could be used for de novo peptide sequencing and when not to by providing a comparison between DDA and DIA, in both de novo and database search mode. We find that while DIA excels with narrow isolation windows on older-generation instruments, it loses its advantage with wider windows. However, with Orbitrap Astral, DIA consistently outperforms DDA due to narrow window mode enabled. We also provide a theoretical explanation of this phenomenon, emphasizing the critical role of the signal-to-noise profile in the successful application of de novo sequencing.

q-bio.BM↗

arXiv2024

EchoAtt: Attend, Copy, then Adjust for More Efficient Large Language Models

Large Language Models (LLMs), with their increasing depth and number of parameters, have demonstrated outstanding performance across a variety of natural language processing tasks. However, this growth in scale leads to increased computational demands, particularly during inference and fine-tuning. To address these challenges, we introduce EchoAtt, a novel framework aimed at optimizing transformer-based models by analyzing and leveraging the similarity of attention patterns across layers. Our analysis reveals that many inner layers in LLMs, especially larger ones, exhibit highly similar attention matrices. By exploiting this similarity, EchoAtt enables the sharing of attention matrices in less critical layers, significantly reducing computational requirements without compromising performance. We incorporate this approach within a knowledge distillation setup, where a pre-trained teacher model guides the training of a smaller student model. The student model selectively shares attention matrices in layers with high similarity while inheriting key parameters from the teacher. Our best results with TinyLLaMA-1.1B demonstrate that EchoAtt improves inference speed by 15\%, training speed by 25\%, and reduces the number of parameters by approximately 4\%, all while improving zero-shot performance. These findings highlight the potential of attention matrix sharing to enhance the efficiency of LLMs, making them more practical for real-time and resource-limited applications.

cs.CL↗

arXiv2024

S2D: Sorted Speculative Decoding For More Efficient Deployment of Nested Large Language Models

Deployment of autoregressive large language models (LLMs) is costly, and as these models increase in size, the associated costs will become even more considerable. Consequently, different methods have been proposed to accelerate the token generation process and reduce costs. Speculative decoding (SD) is among the most promising approaches to speed up the LLM decoding process by verifying multiple tokens in parallel and using an auxiliary smaller draft model to generate the possible tokens. In SD, usually, one draft model is used to serve a specific target model; however, in practice, LLMs are diverse, and we might need to deal with many target models or more than one target model simultaneously. In this scenario, it is not clear which draft model should be used for which target model, and searching among different draft models or training customized draft models can further increase deployment costs. In this paper, we first introduce a novel multi-target scenario for the deployment of draft models for faster inference. Then, we present a novel, more efficient sorted speculative decoding mechanism that outperforms regular baselines in multi-target settings. We evaluated our method on Spec-Bench in different settings, including base models such as Vicuna 7B, 13B, and LLama Chat 70B. Our results suggest that our draft models perform better than baselines for multiple target models at the same time.

cs.CL↗

arXiv2024

Learning Chemotherapy Drug Action via Universal Physics-Informed Neural Networks

Quantitative systems pharmacology (QSP) is widely used to assess drug effects and toxicity before the drug goes to clinical trial. However, significant manual distillation of the literature is needed in order to construct a QSP model. Parameters may need to be fit, and simplifying assumptions of the model need to be made. In this work, we apply Universal Physics-Informed Neural Networks (UPINNs) to learn unknown components of various differential equations that model chemotherapy pharmacodynamics. We learn three commonly employed chemotherapeutic drug actions (log-kill, Norton-Simon, and E_max) from synthetic data. Then, we use the UPINN method to fit the parameters for several synthetic datasets simultaneously. Finally, we learn the net proliferation rate in a model of doxorubicin (a chemotherapeutic) pharmacodynamics. As these are only toy examples, we highlight the usefulness of UPINNs in learning unknown terms in pharmacodynamic and pharmacokinetic models.

q-bio.QM↗

arXiv2024

Orchid: Flexible and Data-Dependent Convolution for Sequence Modeling

In the rapidly evolving field of deep learning, the demand for models that are both expressive and computationally efficient has never been more critical. This paper introduces Orchid, a novel architecture designed to address the quadratic complexity of traditional attention mechanisms without compromising the ability to capture long-range dependencies and in-context learning. At the core of this architecture lies a new data-dependent global convolution layer, which contextually adapts its kernel conditioned on input sequence using a dedicated conditioning neural network. We design two simple conditioning networks that maintain shift equivariance in our data-dependent convolution operation. The dynamic nature of the proposed convolution kernel grants Orchid high expressivity while maintaining quasilinear scalability for long sequences. We evaluate the proposed model across multiple domains, including language modeling and image classification, to highlight its performance and generality. Our experiments demonstrate that this architecture not only outperforms traditional attention-based architectures such as BERT and Vision Transformers with smaller model sizes, but also extends the feasible sequence length beyond the limitations of the dense attention layers. This achievement represents a significant step towards more efficient and scalable deep learning models for sequence modeling. The code is available at https://github.com/Karami-m/orchid.

cs.LG↗

arXiv2024

QDyLoRA: Quantized Dynamic Low-Rank Adaptation for Efficient Large Language Model Tuning

Finetuning large language models requires huge GPU memory, restricting the choice to acquire Larger models. While the quantized version of the Low-Rank Adaptation technique, named QLoRA, significantly alleviates this issue, finding the efficient LoRA rank is still challenging. Moreover, QLoRA is trained on a pre-defined rank and, therefore, cannot be reconfigured for its lower ranks without requiring further fine-tuning steps. This paper proposes QDyLoRA -Quantized Dynamic Low-Rank Adaptation-, as an efficient quantization approach for dynamic low-rank adaptation. Motivated by Dynamic LoRA, QDyLoRA is able to efficiently finetune LLMs on a set of pre-defined LoRA ranks. QDyLoRA enables fine-tuning Falcon-40b for ranks 1 to 64 on a single 32 GB V100-GPU through one round of fine-tuning. Experimental results show that QDyLoRA is competitive to QLoRA and outperforms when employing its optimal rank.

cs.LG↗

arXiv2024

WERank: Towards Rank Degradation Prevention for Self-Supervised Learning Using Weight Regularization

A common phenomena confining the representation quality in Self-Supervised Learning (SSL) is dimensional collapse (also known as rank degeneration), where the learned representations are mapped to a low dimensional subspace of the representation space. The State-of-the-Art SSL methods have shown to suffer from dimensional collapse and fall behind maintaining full rank. Recent approaches to prevent this problem have proposed using contrastive losses, regularization techniques, or architectural tricks. We propose WERank, a new regularizer on the weight parameters of the network to prevent rank degeneration at different layers of the network. We provide empirical evidence and mathematical justification to demonstrate the effectiveness of the proposed regularization method in preventing dimensional collapse. We verify the impact of WERank on graph SSL where dimensional collapse is more pronounced due to the lack of proper data augmentation. We empirically demonstrate that WERank is effective in helping BYOL to achieve higher rank during SSL pre-training and consequently downstream accuracy during evaluation probing. Ablation studies and experimental analysis shed lights on the underlying factors behind the performance gains of the proposed approach.

cs.LG↗

arXiv2024

Scalable Graph Self-Supervised Learning

In regularization Self-Supervised Learning (SSL) methods for graphs, computational complexity increases with the number of nodes in graphs and embedding dimensions. To mitigate the scalability of non-contrastive graph SSL, we propose a novel approach to reduce the cost of computing the covariance matrix for the pre-training loss function with volume-maximization terms. Our work focuses on reducing the cost associated with the loss computation via graph node or dimension sampling. We provide theoretical insight into why dimension sampling would result in accurate loss computations and support it with mathematical derivation of the novel approach. We develop our experimental setup on the node-level graph prediction tasks, where SSL pre-training has shown to be difficult due to the large size of real world graphs. Our experiments demonstrate that the cost associated with the loss computation can be reduced via node or dimension sampling without lowering the downstream performance. Our results demonstrate that sampling mostly results in improved downstream performance. Ablation studies and experimental analysis are provided to untangle the role of the different factors in the experimental setup.

cs.LG↗

arXiv2023

Sorted LLaMA: Unlocking the Potential of Intermediate Layers of Large Language Models for Dynamic Inference

Large language models (LLMs) have revolutionized natural language processing (NLP) by excelling at understanding and generating human-like text. However, their widespread deployment can be prohibitively expensive. SortedNet is a recent training technique for enabling dynamic inference by leveraging the modularity in networks and sorting sub-models based on computation/accuracy in a nested manner. We extend SortedNet to generative NLP tasks, making large language models dynamic without any Pre-Training and by only replacing Standard Fine-Tuning (SFT) with Sorted Fine-Tuning (SoFT). Our approach boosts model efficiency, eliminating the need for multiple models for various scenarios during inference. We show that this approach can unlock the power of intermediate layers of transformers in generating the target output. Our sub-models remain integral components of the original model, minimizing storage requirements and transition costs between different computational/latency budgets. The efficacy of our proposed method was demonstrated by applying it to tune LLaMA 2 13B on the Stanford Alpaca dataset for instruction following and TriviaQA for closed-book question answering. Our results show the superior performance of sub-models in comparison to Standard Fine-Tuning and SFT+ICT (Early-Exit), all achieved with efficient tuning and without additional memory usage during inference.

cs.CL↗

arXiv2023

SortedNet: A Scalable and Generalized Framework for Training Modular Deep Neural Networks

Deep neural networks (DNNs) must cater to a variety of users with different performance needs and budgets, leading to the costly practice of training, storing, and maintaining numerous user/task-specific models. There are solutions in the literature to deal with single dynamic or many-in-one models instead of many individual networks; however, they suffer from significant drops in performance, lack of generalization across different model architectures or different dimensions (e.g. depth, width, attention blocks), heavy model search requirements during training, and training a limited number of sub-models. To address these limitations, we propose SortedNet, a generalized and scalable training solution to harness the inherent modularity of DNNs. Thanks to a generalized nested architecture (which we refer as \textit{sorted} architecture in this paper) with shared parameters and its novel update scheme combining random sub-model sampling and a new gradient accumulation mechanism, SortedNet enables the training of sub-models simultaneously along with the training of the main model (without any significant extra training or inference overhead), simplifies dynamic model selection, customizes deployment during inference, and reduces the model storage requirement significantly. The versatility and scalability of SortedNet are validated through various architectures and tasks, including LLaMA, BERT, RoBERTa (NLP tasks), ResNet and MobileNet (image classification) demonstrating its superiority over existing dynamic training methods. For example, we introduce a novel adaptive self-speculative approach based on sorted-training to accelerate large language models decoding. Moreover, SortedNet is able to train 160 sub-models at once, achieving at least 96\% of the original model's performance.

cs.LG↗

arXiv2023

Recurrent Neural Networks and Long Short-Term Memory Networks: Tutorial and Survey

This is a tutorial paper on Recurrent Neural Network (RNN), Long Short-Term Memory Network (LSTM), and their variants. We start with a dynamical system and backpropagation through time for RNN. Then, we discuss the problems of gradient vanishing and explosion in long-term dependencies. We explain close-to-identity weight matrix, long delays, leaky units, and echo state networks for solving this problem. Then, we introduce LSTM gates and cells, history and variants of LSTM, and Gated Recurrent Units (GRU). Finally, we introduce bidirectional RNN, bidirectional LSTM, and the Embeddings from Language Model (ELMo) network, for processing a sequence in both directions.

cs.LG↗

arXiv2023

DyLoRA: Parameter Efficient Tuning of Pre-trained Models using Dynamic Search-Free Low-Rank Adaptation

With the ever-growing size of pretrained models (PMs), fine-tuning them has become more expensive and resource-hungry. As a remedy, low-rank adapters (LoRA) keep the main pretrained weights of the model frozen and just introduce some learnable truncated SVD modules (so-called LoRA blocks) to the model. While LoRA blocks are parameter-efficient, they suffer from two major problems: first, the size of these blocks is fixed and cannot be modified after training (for example, if we need to change the rank of LoRA blocks, then we need to re-train them from scratch); second, optimizing their rank requires an exhaustive search and effort. In this work, we introduce a dynamic low-rank adaptation (DyLoRA) technique to address these two problems together. Our DyLoRA method trains LoRA blocks for a range of ranks instead of a single rank by sorting the representation learned by the adapter module at different ranks during training. We evaluate our solution on different natural language understanding (GLUE benchmark) and language generation tasks (E2E, DART and WebNLG) using different pretrained models such as RoBERTa and GPT with different sizes. Our results show that we can train dynamic search-free models with DyLoRA at least 4 to 7 times (depending to the task) faster than LoRA without significantly compromising performance. Moreover, our models can perform consistently well on a much larger range of ranks compared to LoRA.

cs.CL↗

arXiv2023

Do we need Label Regularization to Fine-tune Pre-trained Language Models?

Knowledge Distillation (KD) is a prominent neural model compression technique that heavily relies on teacher network predictions to guide the training of a student model. Considering the ever-growing size of pre-trained language models (PLMs), KD is often adopted in many NLP tasks involving PLMs. However, it is evident that in KD, deploying the teacher network during training adds to the memory and computational requirements of training. In the computer vision literature, the necessity of the teacher network is put under scrutiny by showing that KD is a label regularization technique that can be replaced with lighter teacher-free variants such as the label-smoothing technique. However, to the best of our knowledge, this issue is not investigated in NLP. Therefore, this work concerns studying different label regularization techniques and whether we actually need them to improve the fine-tuning of smaller PLM networks on downstream tasks. In this regard, we did a comprehensive set of experiments on different PLMs such as BERT, RoBERTa, and GPT with more than 600 distinct trials and ran each configuration five times. This investigation led to a surprising observation that KD and other label regularization techniques do not play any meaningful role over regular fine-tuning when the student model is pre-trained. We further explore this phenomenon in different settings of NLP and computer vision tasks and demonstrate that pre-training itself acts as a kind of regularization, and additional label regularization is unnecessary.

cs.LG↗

arXiv2023

Improved knowledge distillation by utilizing backward pass knowledge in neural networks

Knowledge distillation (KD) is one of the prominent techniques for model compression. In this method, the knowledge of a large network (teacher) is distilled into a model (student) with usually significantly fewer parameters. KD tries to better-match the output of the student model to that of the teacher model based on the knowledge extracts from the forward pass of the teacher network. Although conventional KD is effective for matching the two networks over the given data points, there is no guarantee that these models would match in other areas for which we do not have enough training samples. In this work, we address that problem by generating new auxiliary training samples based on extracting knowledge from the backward pass of the teacher in the areas where the student diverges greatly from the teacher. We compute the difference between the teacher and the student and generate new data samples that maximize the divergence. This is done by perturbing data samples in the direction of the gradient of the difference between the student and the teacher. Augmenting the training set by adding this auxiliary improves the performance of KD significantly and leads to a closer match between the student and the teacher. Using this approach, when data samples come from a discrete domain, such as applications of natural language processing (NLP) and language understanding, is not trivial. However, we show how this technique can be used successfully in such applications. We evaluated the performance of our method on various tasks in computer vision and NLP domains and got promising results.

cs.LG↗

arXiv2022

Improving Generalization of Pre-trained Language Models via Stochastic Weight Averaging

Knowledge Distillation (KD) is a commonly used technique for improving the generalization of compact Pre-trained Language Models (PLMs) on downstream tasks. However, such methods impose the additional burden of training a separate teacher model for every new dataset. Alternatively, one may directly work on the improvement of the optimization procedure of the compact model toward better generalization. Recent works observe that the flatness of the local minimum correlates well with better generalization. In this work, we adapt Stochastic Weight Averaging (SWA), a method encouraging convergence to a flatter minimum, to fine-tuning PLMs. We conduct extensive experiments on various NLP tasks (text classification, question answering, and generation) and different model architectures and demonstrate that our adaptation improves the generalization without extra computation cost. Moreover, we observe that this simple optimization technique is able to outperform the state-of-the-art KD methods for compact models.

cs.CL↗