OpenRaiser/Intern-Atlas huggingface dataset:
The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA
Venue: arXiv cs.LG 2024
Year: 2024

This study introduces a systematic framework to compare the efficacy of Large Language Models (LLMs) for fine-tuning across various cheminformatics tasks. Employing a uniform training methodology, we assessed three well-known models-RoBERTa, BART, and LLaMA-on their ability to predict molecular properties using the Simplified Molecular Input Line Entry System (SMILES) as a universal molecular representation format. Our comparative analysis involved pre-training 18 configurations of these models, with varying parameter sizes and dataset scales, followed by fine-tuning them on six benchmarking tasks from DeepChem. We maintained consistent training environments across models to ensure reliable comparisons. This approach allowed us to assess the influence of model type, size, and training dataset size on model performance. Specifically, we found that LLaMA-based models generally offered the lowest validation loss, suggesting their superior adaptability across tasks and scales. However, we observed that absolute validation loss is not a definitive indicator of model performance - contradicts previous research - at least for fine-tuning tasks: instead, model size plays a crucial role. Through rigorous replication and validation, involving multiple training and fine-tuning cycles, our study not only delineates the strengths and limitations of each model type but also provides a robust methodology for selecting the most suitable LLM for specific cheminformatics applications. This research underscores the importance of considering model architecture and dataset characteristics in deploying AI for molecular property prediction, paving the way for more informed and effective utilization of AI in drug discovery and related fields.
SimEndoGS: Efficient Data-driven Scene Simulation using Robotic Surgery Videos via Physics-embedded 3D Gaussians
Venue: arXiv cs.RO 2024
Year: 2024

Surgical scene simulation plays a crucial role in surgical education and simulator-based robot learning. Traditional approaches for creating these environments with surgical scene involve a labor-intensive process where designers hand-craft tissues models with textures and geometries for soft body simulations. This manual approach is not only time-consuming but also limited in the scalability and realism. In contrast, data-driven simulation offers a compelling alternative. It has the potential to automatically reconstruct 3D surgical scenes from real-world surgical video data, followed by the application of soft body physics. This area, however, is relatively uncharted. In our research, we introduce 3D Gaussian as a learnable representation for surgical scene, which is learned from stereo endoscopic video. To prevent over-fitting and ensure the geometrical correctness of these scenes, we incorporate depth supervision and anisotropy regularization into the Gaussian learning process. Furthermore, we apply the Material Point Method, which is integrated with physical properties, to the 3D Gaussians to achieve realistic scene deformations. Our method was evaluated on our collected in-house and public surgical videos datasets. Results show that it can reconstruct and simulate surgical scenes from endoscopic videos efficiently-taking only a few minutes to reconstruct the surgical scene-and produce both visually and physically plausible deformations at a speed approaching real-time. The results demonstrate great potential of our proposed method to enhance the efficiency and variety of simulations available for surgical education and robot learning.
Bayesian Optimization with LLM-Based Acquisition Functions for Natural Language Preference Elicitation
Venue: arXiv cs.AI 2024
Year: 2024

Designing preference elicitation (PE) methodologies that can quickly ascertain a user's top item preferences in a cold-start setting is a key challenge for building effective and personalized conversational recommendation (ConvRec) systems. While large language models (LLMs) enable fully natural language (NL) PE dialogues, we hypothesize that monolithic LLM NL-PE approaches lack the multi-turn, decision-theoretic reasoning required to effectively balance the exploration and exploitation of user preferences towards an arbitrary item set. In contrast, traditional Bayesian optimization PE methods define theoretically optimal PE strategies, but cannot generate arbitrary NL queries or reason over content in NL item descriptions -- requiring users to express preferences via ratings or comparisons of unfamiliar items. To overcome the limitations of both approaches, we formulate NL-PE in a Bayesian Optimization (BO) framework that seeks to actively elicit NL feedback to identify the best recommendation. Key challenges in generalizing BO to deal with natural language feedback include determining: (a) how to leverage LLMs to model the likelihood of NL preference feedback as a function of item utilities, and (b) how to design an acquisition function for NL BO that can elicit preferences in the infinite space of language. We demonstrate our framework in a novel NL-PE algorithm, PEBOL, which uses: 1) Natural Language Inference (NLI) between user preference utterances and NL item descriptions to maintain Bayesian preference beliefs, and 2) BO strategies such as Thompson Sampling (TS) and Upper Confidence Bound (UCB) to steer LLM query generation. We numerically evaluate our methods in controlled simulations, finding that after 10 turns of dialogue, PEBOL can achieve an MRR@10 of up to 0.27 compared to the best monolithic LLM baseline's MRR@10 of 0.17, despite relying on earlier and smaller LLMs.
Progressive Feedforward Collapse of ResNet Training
Venue: arXiv cs.LG 2024
Year: 2024

Neural collapse (NC) is a simple and symmetric phenomenon for deep neural networks (DNNs) at the terminal phase of training, where the last-layer features collapse to their class means and form a simplex equiangular tight frame aligning with the classifier vectors. However, the relationship of the last-layer features to the data and intermediate layers during training remains unexplored. To this end, we characterize the geometry of intermediate layers of ResNet and propose a novel conjecture, progressive feedforward collapse (PFC), claiming the degree of collapse increases during the forward propagation of DNNs. We derive a transparent model for the well-trained ResNet according to that ResNet with weight decay approximates the geodesic curve in Wasserstein space at the terminal phase. The metrics of PFC indeed monotonically decrease across depth on various datasets. We propose a new surrogate model, multilayer unconstrained feature model (MUFM), connecting intermediate layers by an optimal transport regularizer. The optimal solution of MUFM is inconsistent with NC but is more concentrated relative to the input data. Overall, this study extends NC to PFC to model the collapse phenomenon of intermediate layers and its dependence on the input data, shedding light on the theoretical understanding of ResNet in classification problems.
Deep Learning Models in Speech Recognition: Measuring GPU Energy Consumption, Impact of Noise and Model Quantization for Edge Deployment
Venue: arXiv cs.SD 2024
Year: 2024

Recent transformer-based ASR models have achieved word-error rates (WER) below 4%, surpassing human annotator accuracy, yet they demand extensive server resources, contributing to significant carbon footprints. The traditional server-based architecture of ASR also presents privacy concerns, alongside reliability and latency issues due to network dependencies. In contrast, on-device (edge) ASR enhances privacy, boosts performance, and promotes sustainability by effectively balancing energy use and accuracy for specific applications. This study examines the effects of quantization, memory demands, and energy consumption on the performance of various ASR model inference on the NVIDIA Jetson Orin Nano. By analyzing WER and transcription speed across models using FP32, FP16, and INT8 quantization on clean and noisy datasets, we highlight the crucial trade-offs between accuracy, speeds, quantization, energy efficiency, and memory needs. We found that changing precision from fp32 to fp16 halves the energy consumption for audio transcription across different models, with minimal performance degradation. A larger model size and number of parameters neither guarantees better resilience to noise, nor predicts the energy consumption for a given transcription load. These, along with several other findings offer novel insights for optimizing ASR systems within energy- and memory-limited environments, crucial for the development of efficient on-device ASR solutions. The code and input data needed to reproduce the results in this article are open sourced are available on [https://github.com/zzadiues3338/ASR-energy-jetson].
Proven Runtime Guarantees for How the MOEA/D Computes the Pareto Front From the Subproblem Solutions
Venue: arXiv cs.NE 2024
Year: 2024

The decomposition-based multi-objective evolutionary algorithm (MOEA/D) does not directly optimize a given multi-objective function $f$, but instead optimizes $N + 1$ single-objective subproblems of $f$ in a co-evolutionary manner. It maintains an archive of all non-dominated solutions found and outputs it as approximation to the Pareto front. Once the MOEA/D found all optima of the subproblems (the $g$-optima), it may still miss Pareto optima of $f$. The algorithm is then tasked to find the remaining Pareto optima directly by mutating the $g$-optima. In this work, we analyze for the first time how the MOEA/D with only standard mutation operators computes the whole Pareto front of the OneMinMax benchmark when the $g$-optima are a strict subset of the Pareto front. For standard bit mutation, we prove an expected runtime of $O(n N \log n + n^{n/(2N)} N \log n)$ function evaluations. Especially for the second, more interesting phase when the algorithm start with all $g$-optima, we prove an $Ω(n^{(1/2)(n/N + 1)} \sqrt{N} 2^{-n/N})$ expected runtime. This runtime is super-polynomial if $N = o(n)$, since this leaves large gaps between the $g$-optima, which require costly mutations to cover. For power-law mutation with exponent $β\in (1, 2)$, we prove an expected runtime of $O\left(n N \log n + n^β \log n\right)$ function evaluations. The $O\left(n^β \log n\right)$ term stems from the second phase of starting with all $g$-optima, and it is independent of the number of subproblems $N$. This leads to a huge speedup compared to the lower bound for standard bit mutation. In general, our overall bound for power-law suggests that the MOEA/D performs best for $N = O(n^{β- 1})$, resulting in an $O(n^β\log n)$ bound. In contrast to standard bit mutation, smaller values of $N$ are better for power-law mutation, as it is capable of easily creating missing solutions.
Efficient and Flexible Method for Reducing Moderate-size Deep Neural Networks with Condensation
Venue: arXiv cs.LG 2024
Year: 2024

Neural networks have been extensively applied to a variety of tasks, achieving astounding results. Applying neural networks in the scientific field is an important research direction that is gaining increasing attention. In scientific applications, the scale of neural networks is generally moderate-size, mainly to ensure the speed of inference during application. Additionally, comparing neural networks to traditional algorithms in scientific applications is inevitable. These applications often require rapid computations, making the reduction of neural network sizes increasingly important. Existing work has found that the powerful capabilities of neural networks are primarily due to their non-linearity. Theoretical work has discovered that under strong non-linearity, neurons in the same layer tend to behave similarly, a phenomenon known as condensation. Condensation offers an opportunity to reduce the scale of neural networks to a smaller subnetwork with similar performance. In this article, we propose a condensation reduction algorithm to verify the feasibility of this idea in practical problems. Our reduction method can currently be applied to both fully connected networks and convolutional networks, achieving positive results. In complex combustion acceleration tasks, we reduced the size of the neural network to 41.7% of its original scale while maintaining prediction accuracy. In the CIFAR10 image classification task, we reduced the network size to 11.5% of the original scale, still maintaining a satisfactory validation accuracy. Our method can be applied to most trained neural networks, reducing computational pressure and improving inference speed.
Differentiable Particles for General-Purpose Deformable Object Manipulation
Venue: arXiv cs.RO 2024
Year: 2024

Deformable object manipulation is a long-standing challenge in robotics. While existing approaches often focus narrowly on a specific type of object, we seek a general-purpose algorithm, capable of manipulating many different types of objects: beans, rope, cloth, liquid, . . . . One key difficulty is a suitable representation, rich enough to capture object shape, dynamics for manipulation and yet simple enough to be acquired effectively from sensor data. Specifically, we propose Differentiable Particles (DiPac), a new algorithm for deformable object manipulation. DiPac represents a deformable object as a set of particles and uses a differentiable particle dynamics simulator to reason about robot manipulation. To find the best manipulation action, DiPac combines learning, planning, and trajectory optimization through differentiable trajectory tree optimization. Differentiable dynamics provides significant benefits and enable DiPac to (i) estimate the dynamics parameters efficiently, thereby narrowing the sim-to-real gap, and (ii) choose the best action by backpropagating the gradient along sampled trajectories. Both simulation and real-robot experiments show promising results. DiPac handles a variety of object types. By combining planning and learning, DiPac outperforms both pure model-based planning methods and pure data-driven learning methods. In addition, DiPac is robust and adapts to changes in dynamics, thereby enabling the transfer of an expert policy from one object to another with different physical properties, e.g., from a rigid rod to a deformable rope.
Multi-user ISAC through Stacked Intelligent Metasurfaces: New Algorithms and Experiments
Venue: arXiv cs.IT 2024
Year: 2024

This paper investigates a Stacked Intelligent Metasurfaces (SIM)-assisted Integrated Sensing and Communications (ISAC) system. An extended target model is considered, where the BS aims to estimate the complete target response matrix relative to the SIM. Under the constraints of minimum Signal-to-Interference-plus-Noise Ratio (SINR) for the communication users (CUs) and maximum transmit power, we jointly optimize the transmit beamforming at the base station (BS) and the end-to-end transmission matrix of the SIM, to minimize the Cramér-Rao Bound (CRB) for target estimation. Effective algorithms such as the alternating optimization (AO) and semidefinite relaxation (SDR) are employed to solve the non-convex SINR-constrained CRB minimization problem. Finally, we design and build an experimental platform for SIM, and evaluate the performance of the proposed algorithms for communication and sensing tasks.
CoViS-Net: A Cooperative Visual Spatial Foundation Model for Multi-Robot Applications
Venue: arXiv cs.RO 2024
Year: 2024

Autonomous robot operation in unstructured environments is often underpinned by spatial understanding through vision. Systems composed of multiple concurrently operating robots additionally require access to frequent, accurate and reliable pose estimates. In this work, we propose CoViS-Net, a decentralized visual spatial foundation model that learns spatial priors from data, enabling pose estimation as well as spatial comprehension. Our model is fully decentralized, platform-agnostic, executable in real-time using onboard compute, and does not require existing networking infrastructure. CoViS-Net provides relative pose estimates and a local bird's-eye-view (BEV) representation, even without camera overlap between robots (in contrast to classical methods). We demonstrate its use in a multi-robot formation control task across various real-world settings. We provide code, models and supplementary material online. https://proroklab.github.io/CoViS-Net/
Leveraging Procedural Generation for Learning Autonomous Peg-in-Hole Assembly in Space
Venue: arXiv cs.RO 2024
Year: 2024

The ability to autonomously assemble structures is crucial for the development of future space infrastructure. However, the unpredictable conditions of space pose significant challenges for robotic systems, necessitating the development of advanced learning techniques to enable autonomous assembly. In this study, we present a novel approach for learning autonomous peg-in-hole assembly in the context of space robotics. Our focus is on enhancing the generalization and adaptability of autonomous systems through deep reinforcement learning. By integrating procedural generation and domain randomization, we train agents in a highly parallelized simulation environment across a spectrum of diverse scenarios with the aim of acquiring a robust policy. The proposed approach is evaluated using three distinct reinforcement learning algorithms to investigate the trade-offs among various paradigms. We demonstrate the adaptability of our agents to novel scenarios and assembly sequences while emphasizing the potential of leveraging advanced simulation techniques for robot learning in space. Our findings set the stage for future advancements in intelligent robotic systems capable of supporting ambitious space missions and infrastructure development beyond Earth.
Error-Driven Uncertainty Aware Training
Venue: arXiv cs.LG 2024
Year: 2024

Neural networks are often overconfident about their predictions, which undermines their reliability and trustworthiness. In this work, we present a novel technique, named Error-Driven Uncertainty Aware Training (EUAT), which aims to enhance the ability of neural classifiers to estimate their uncertainty correctly, namely to be highly uncertain when they output inaccurate predictions and low uncertain when their output is accurate. The EUAT approach operates during the model's training phase by selectively employing two loss functions depending on whether the training examples are correctly or incorrectly predicted by the model. This allows for pursuing the twofold goal of i) minimizing model uncertainty for correctly predicted inputs and ii) maximizing uncertainty for mispredicted inputs, while preserving the model's misprediction rate. We evaluate EUAT using diverse neural models and datasets in the image recognition domains considering both non-adversarial and adversarial settings. The results show that EUAT outperforms existing approaches for uncertainty estimation (including other uncertainty-aware training techniques, calibration, ensembles, and DEUP) by providing uncertainty estimates that not only have higher quality when evaluated via statistical metrics (e.g., correlation with residuals) but also when employed to build binary classifiers that decide whether the model's output can be trusted or not and under distributional data shifts.
TRAMBA: A Hybrid Transformer and Mamba Architecture for Practical Audio and Bone Conduction Speech Super Resolution and Enhancement on Mobile and Wearable Platforms
Venue: arXiv cs.SD 2024
Year: 2024

We propose TRAMBA, a hybrid transformer and Mamba architecture for acoustic and bone conduction speech enhancement, suitable for mobile and wearable platforms. Bone conduction speech enhancement has been impractical to adopt in mobile and wearable platforms for several reasons: (i) data collection is labor-intensive, resulting in scarcity; (ii) there exists a performance gap between state of-art models with memory footprints of hundreds of MBs and methods better suited for resource-constrained systems. To adapt TRAMBA to vibration-based sensing modalities, we pre-train TRAMBA with audio speech datasets that are widely available. Then, users fine-tune with a small amount of bone conduction data. TRAMBA outperforms state-of-art GANs by up to 7.3% in PESQ and 1.8% in STOI, with an order of magnitude smaller memory footprint and an inference speed up of up to 465 times. We integrate TRAMBA into real systems and show that TRAMBA (i) improves battery life of wearables by up to 160% by requiring less data sampling and transmission; (ii) generates higher quality voice in noisy environments than over-the-air speech; (iii) requires a memory footprint of less than 20.0 MB.
Topics in the Study of the Pragmatic Functions of Phonetic Reduction in Dialog
Venue: arXiv cs.CL 2024
Year: 2024

Reduced articulatory precision is common in speech, but for dialog its acoustic properties and pragmatic functions have been little studied. We here try to remedy this gap. This technical report contains content that was omitted from the journal article (Ward et al. 2024, submitted). Specifically, we here report 1) lessons learned about annotating for perceived reduction, 2) the finding that, unlike in read speech, the correlates of reduction in dialog include high pitch, wide pitch range, and intensity, and 3) a baseline model for predicting reduction in dialog, using simple acoustic/prosodic features, that achieves correlations with human perceptions of 0.24 for English, and 0.17 for Spanish. We also provide examples of additional possible pragmatic functions of reduction in English, and various discussion, observations and speculations
Applying Transparent Shaping for Zero Trust Architecture Implementation in AWS: A Case Study
Venue: arXiv cs.CR 2024
Year: 2024

This study introduces a methodology integrating Zero Trust Architecture (ZTA) principles and Transparent Shaping into an AWS-hosted Online File Manager (OFM) application, enhancing security without substantial code modifications. We evaluate our approach with the Mozilla Observatory, highlighting significant security improvements and outlining a promising direction for applying Transparent Shaping and ZTA in cloud environments.
SATO: Stable Text-to-Motion Framework
Venue: arXiv cs.CV 2024
Year: 2024

Is the Text to Motion model robust? Recent advancements in Text to Motion models primarily stem from more accurate predictions of specific actions. However, the text modality typically relies solely on pre-trained Contrastive Language-Image Pretraining (CLIP) models. Our research has uncovered a significant issue with the text-to-motion model: its predictions often exhibit inconsistent outputs, resulting in vastly different or even incorrect poses when presented with semantically similar or identical text inputs. In this paper, we undertake an analysis to elucidate the underlying causes of this instability, establishing a clear link between the unpredictability of model outputs and the erratic attention patterns of the text encoder module. Consequently, we introduce a formal framework aimed at addressing this issue, which we term the Stable Text-to-Motion Framework (SATO). SATO consists of three modules, each dedicated to stable attention, stable prediction, and maintaining a balance between accuracy and robustness trade-off. We present a methodology for constructing an SATO that satisfies the stability of attention and prediction. To verify the stability of the model, we introduced a new textual synonym perturbation dataset based on HumanML3D and KIT-ML. Results show that SATO is significantly more stable against synonyms and other slight perturbations while keeping its high accuracy performance.