PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis

We present a comprehensive framework for predicting the effects of perturbations in single cells, designed to standardize benchmarking in this rapidly evolving field. Our framework, PerturBench, includes a user-friendly platform, diverse datasets, metrics for fair model comparison, and detailed performance analysis. Extensive evaluations of published and baseline models reveal limitations like mode or posterior collapse, and underscore the importance of rank metrics that assess the ordering of perturbations alongside traditional measures like RMSE. Our findings show that simple models can outperform more complex approaches. This benchmarking exercise sets new standards for model evaluation, supports robust model development, and advances the potential of these models to use high-throughput and high-content genetic and chemical screens for disease target discovery.

Learning Stable Robot Grasping with Transformer-based Tactile Control Policies

Measuring grasp stability is an important skill for dexterous robot manipulation tasks, which can be inferred from haptic information with a tactile sensor. Control policies have to detect rotational displacement and slippage from tactile feedback, and determine a re-grasp strategy in term of location and force. Classic stable grasp task only trains control policies to solve for re-grasp location with objects of fixed center of gravity. In this work, we propose a revamped version of stable grasp task that optimises both re-grasp location and gripping force for objects with unknown and moving center of gravity. We tackle this task with a model-free, end-to-end Transformer-based reinforcement learning framework. We show that our approach is able to solve both objectives after training in both simulation and in a real-world setup with zero-shot transfer. We also provide performance analysis of different models to understand the dynamics of optimizing two opposing objectives.

Analysis of Impulsive Interference in Digital Audio Broadcasting Systems in Electric Vehicles

Recently, new types of interference in electric vehicles (EVs), such as converters switching and/or battery chargers, have been found to degrade the performance of wireless digital transmission systems. Measurements show that such an interference is characterized by impulsive behavior and is widely varying in time. This paper uses recorded data from our EV testbed to analyze the impulsive interference in the digital audio broadcasting band. Moreover, we use our analysis to obtain a corresponding interference model. In particular, we studied the temporal characteristics of the interference and confirmed that its amplitude indeed exhibits an impulsive behavior. Our results show that impulsive events span successive received signal samples and thus indicate a bursty nature. To this end, we performed a data-driven modification of a well-established model for bursty impulsive interference, the Markov-Middleton model, to produce synthetic noise realization. We investigate the optimal symbol detector design based on the proposed model and show significant performance gains compared to the conventional detector based on the additive white Gaussian noise assumption.

Data-Driven Symbol Detection for Intersymbol Interference Channels with Bursty Impulsive Noise

We developed machine learning approaches for data-driven trellis-based soft symbol detection in coded transmission over intersymbol interference (ISI) channels in presence of bursty impulsive noise (IN), for example encountered in wireless digital broadcasting systems and vehicular communications. This enabled us to obtain optimized detectors based on the Bahl-Cocke-Jelinek-Raviv (BCJR) algorithm while circumventing the use of full channel state information (CSI) for computing likelihoods and trellis state transition probabilities. First, we extended the application of the neural network (NN)-aided BCJR, recently proposed for ISI channels with additive white Gaussian noise (AWGN). Although suitable for estimating likelihoods via labeling of transmission sequences, the BCJR-NN method does not provide a framework for learning the trellis state transitions. In addition to detection over the joint ISI and IN states we also focused on another scenario where trellis transitions are not trivial: detection for the ISI channel with AWGN with inaccurate knowledge of the channel memory at the receiver. Without access to the accurate state transition matrix, the BCJR- NN performance significantly degrades in both settings. To this end, we devised an alternative approach for data-driven BCJR detection based on the unsupervised learning of a hidden Markov model (HMM). The BCJR-HMM allowed us to optimize both the likelihood function and the state transition matrix without labeling. Moreover, we demonstrated the viability of a hybrid NN and HMM BCJR detection where NN is used for learning the likelihoods, while the state transitions are optimized via HMM. While reducing the required prior channel knowledge, the examined data-driven detectors with learned trellis state transitions achieve bit error rates close to the optimal full CSI-based BCJR, significantly outperforming detection with inaccurate CSI.

CPA-Enhancer: Chain-of-Thought Prompted Adaptive Enhancer for Object Detection under Unknown Degradations

Object detection methods under known single degradations have been extensively investigated. However, existing approaches require prior knowledge of the degradation type and train a separate model for each, limiting their practical applications in unpredictable environments. To address this challenge, we propose a chain-of-thought (CoT) prompted adaptive enhancer, CPA-Enhancer, for object detection under unknown degradations. Specifically, CPA-Enhancer progressively adapts its enhancement strategy under the step-by-step guidance of CoT prompts, that encode degradation-related information. To the best of our knowledge, it's the first work that exploits CoT prompting for object detection tasks. Overall, CPA-Enhancer is a plug-and-play enhancement model that can be integrated into any generic detectors to achieve substantial gains on degraded images, without knowing the degradation type priorly. Experimental results demonstrate that CPA-Enhancer not only sets the new state of the art for object detection but also boosts the performance of other downstream vision tasks under unknown degradations.

Multi-perspective Feedback-attention Coupling Model for Continuous-time Dynamic Graphs

Recently, representation learning over graph networks has gained popularity, with various models showing promising results. Despite this, several challenges persist: 1) most methods are designed for static or discrete-time dynamic graphs; 2) existing continuous-time dynamic graph algorithms focus on a single evolving perspective; and 3) many continuous-time dynamic graph approaches necessitate numerous temporal neighbors to capture long-term dependencies. In response, this paper introduces the Multi-Perspective Feedback-Attention Coupling (MPFA) model. MPFA incorporates information from both evolving and raw perspectives, efficiently learning the interleaved dynamics of observed processes. The evolving perspective employs temporal self-attention to distinguish continuously evolving temporal neighbors for information aggregation. Through dynamic updates, this perspective can capture long-term dependencies using a small number of temporal neighbors. Meanwhile, the raw perspective utilizes a feedback attention module with growth characteristic coefficients to aggregate raw neighborhood information. Experimental results on a self-organizing dataset and seven public datasets validate the efficacy and competitiveness of our proposed model.

Dynamic Link Prediction for New Nodes in Temporal Graph Networks

Modelling temporal networks for dynamic link prediction of new nodes has many real-world applications, such as providing relevant item recommendations to new customers in recommender systems and suggesting appropriate posts to new users on social platforms. Unlike old nodes, new nodes have few historical links, which poses a challenge for the dynamic link prediction task. Most existing dynamic models treat all nodes equally and are not specialized for new nodes, resulting in suboptimal performances. In this paper, we consider dynamic link prediction of new nodes as a few-shot problem and propose a novel model based on the meta-learning principle to effectively mitigate this problem. Specifically, we develop a temporal encoder with a node-level span memory to obtain a new node embedding, and then we use a predictor to determine whether the new node generates a link. To overcome the few-shot challenge, we incorporate the encoder-predictor into the meta-learning paradigm, which can learn two types of implicit information during the formation of the temporal network through span adaptation and node adaptation. The acquired implicit information can serve as model initialisation and facilitate rapid adaptation to new nodes through a fine-tuning process on just a few links. Experiments on three publicly available datasets demonstrate the superior performance of our model compared to existing state-of-the-art methods.

AbDiffuser: Full-Atom Generation of In-Vitro Functioning Antibodies

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel architecture for aligned proteins, and utilizes strong diffusion priors to improve the denoising process. Our approach improves protein diffusion by taking advantage of domain knowledge and physics-based constraints; handles sequence-length changes; and reduces memory complexity by an order of magnitude enabling backbone and side chain generation. We validate AbDiffuser in silico and in vitro. Numerical experiments showcase the ability of AbDiffuser to generate antibodies that closely track the sequence and structural properties of a reference set. Laboratory experiments confirm that all 16 HER2 antibodies discovered were expressed at high levels and that 57.1% of selected designs were tight binders.

Protein Discovery with Discrete Walk-Jump Sampling

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the maximum likelihood training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 35% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Investigating Vision Foundational Models for Tactile Representation Learning

Tactile representation learning (TRL) equips robots with the ability to leverage touch information, boosting performance in tasks such as environment perception and object manipulation. However, the heterogeneity of tactile sensors results in many sensor- and task-specific learning approaches. This limits the efficacy of existing tactile datasets, and the subsequent generalisability of any learning outcome. In this work, we investigate the applicability of vision foundational models to sensor-agnostic TRL, via a simple yet effective transformation technique to feed the heterogeneous sensor readouts into the model. Our approach recasts TRL as a computer vision (CV) problem, which permits the application of various CV techniques for tackling TRL-specific challenges. We evaluate our approach on multiple benchmark tasks, using datasets collected from four different tactile sensors. Empirically, we demonstrate significant improvements in task performance, model robustness, as well as cross-sensor and cross-task knowledge transferability with limited data requirements.