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Researcher profile

Ehsan Abbasnejad

Ehsan Abbasnejad contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningComputer VisionComputation and Languageeess.SPNeural and Evolutionary ComputingArtificial IntelligenceCryptography and Security

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Published work

12 published item(s)

preprint2026arXiv

What Makes a Representation Good for Single-Cell Perturbation Prediction?

Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an overlooked challenge: gene expression is dominated by perturbation-invariant information, while perturbation-specific signals are intrinsically sparse. As a result, learned representations either entangle invariant and perturbation-specific information, leading to spurious and non-generalizable predictors, or suppress perturbation-specific signals altogether, rendering them ineffective for prediction. To address this, we propose PerturbedVAE, a general framework designed to resolve this signal imbalance. The framework explicitly separates perturbation-specific information from dominant invariant structure and recovers causal representations to effectively utilize such information for prediction. We further provide an identifiability analysis that characterizes the conditions under which sparse perturbation effects can be reliably recovered, thereby clarifying how the framework can be concretely specified under such conditions. Empirically, PerturbedVAE achieves state-of-the-art performance on a widely used benchmark across multiple evaluation settings, yielding significant gains on out-of-distribution combinatorial predictions and uncovering interpretable perturbation-response programs.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Active Learning by Feature Mixing

The promise of active learning (AL) is to reduce labelling costs by selecting the most valuable examples to annotate from a pool of unlabelled data. Identifying these examples is especially challenging with high-dimensional data (e.g. images, videos) and in low-data regimes. In this paper, we propose a novel method for batch AL called ALFA-Mix. We identify unlabelled instances with sufficiently-distinct features by seeking inconsistencies in predictions resulting from interventions on their representations. We construct interpolations between representations of labelled and unlabelled instances then examine the predicted labels. We show that inconsistencies in these predictions help discovering features that the model is unable to recognise in the unlabelled instances. We derive an efficient implementation based on a closed-form solution to the optimal interpolation causing changes in predictions. Our method outperforms all recent AL approaches in 30 different settings on 12 benchmarks of images, videos, and non-visual data. The improvements are especially significant in low-data regimes and on self-trained vision transformers, where ALFA-Mix outperforms the state-of-the-art in 59% and 43% of the experiments respectively.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

EBMs vs. CL: Exploring Self-Supervised Visual Pretraining for Visual Question Answering

The availability of clean and diverse labeled data is a major roadblock for training models on complex tasks such as visual question answering (VQA). The extensive work on large vision-and-language models has shown that self-supervised learning is effective for pretraining multimodal interactions. In this technical report, we focus on visual representations. We review and evaluate self-supervised methods to leverage unlabeled images and pretrain a model, which we then fine-tune on a custom VQA task that allows controlled evaluation and diagnosis. We compare energy-based models (EBMs) with contrastive learning (CL). While EBMs are growing in popularity, they lack an evaluation on downstream tasks. We find that both EBMs and CL can learn representations from unlabeled images that enable training a VQA model on very little annotated data. In a simple setting similar to CLEVR, we find that CL representations also improve systematic generalization, and even match the performance of representations from a larger, supervised, ImageNet-pretrained model. However, we find EBMs to be difficult to train because of instabilities and high variability in their results. Although EBMs prove useful for OOD detection, other results on supervised energy-based training and uncertainty calibration are largely negative. Overall, CL currently seems a preferable option over EBMs.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Evading the Simplicity Bias: Training a Diverse Set of Models Discovers Solutions with Superior OOD Generalization

Neural networks trained with SGD were recently shown to rely preferentially on linearly-predictive features and can ignore complex, equally-predictive ones. This simplicity bias can explain their lack of robustness out of distribution (OOD). The more complex the task to learn, the more likely it is that statistical artifacts (i.e. selection biases, spurious correlations) are simpler than the mechanisms to learn. We demonstrate that the simplicity bias can be mitigated and OOD generalization improved. We train a set of similar models to fit the data in different ways using a penalty on the alignment of their input gradients. We show theoretically and empirically that this induces the learning of more complex predictive patterns. OOD generalization fundamentally requires information beyond i.i.d. examples, such as multiple training environments, counterfactual examples, or other side information. Our approach shows that we can defer this requirement to an independent model selection stage. We obtain SOTA results in visual recognition on biased data and generalization across visual domains. The method - the first to evade the simplicity bias - highlights the need for a better understanding and control of inductive biases in deep learning.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Predicting is not Understanding: Recognizing and Addressing Underspecification in Machine Learning

Machine learning (ML) models are typically optimized for their accuracy on a given dataset. However, this predictive criterion rarely captures all desirable properties of a model, in particular how well it matches a domain expert's understanding of a task. Underspecification refers to the existence of multiple models that are indistinguishable in their in-domain accuracy, even though they differ in other desirable properties such as out-of-distribution (OOD) performance. Identifying these situations is critical for assessing the reliability of ML models. We formalize the concept of underspecification and propose a method to identify and partially address it. We train multiple models with an independence constraint that forces them to implement different functions. They discover predictive features that are otherwise ignored by standard empirical risk minimization (ERM), which we then distill into a global model with superior OOD performance. Importantly, we constrain the models to align with the data manifold to ensure that they discover meaningful features. We demonstrate the method on multiple datasets in computer vision (collages, WILDS-Camelyon17, GQA) and discuss general implications of underspecification. Most notably, in-domain performance cannot serve for OOD model selection without additional assumptions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Progressive Class Semantic Matching for Semi-supervised Text Classification

Semi-supervised learning is a promising way to reduce the annotation cost for text-classification. Combining with pre-trained language models (PLMs), e.g., BERT, recent semi-supervised learning methods achieved impressive performance. In this work, we further investigate the marriage between semi-supervised learning and a pre-trained language model. Unlike existing approaches that utilize PLMs only for model parameter initialization, we explore the inherent topic matching capability inside PLMs for building a more powerful semi-supervised learning approach. Specifically, we propose a joint semi-supervised learning process that can progressively build a standard $K$-way classifier and a matching network for the input text and the Class Semantic Representation (CSR). The CSR will be initialized from the given labeled sentences and progressively updated through the training process. By means of extensive experiments, we show that our method can not only bring remarkable improvement to baselines, but also overall be more stable, and achieves state-of-the-art performance in semi-supervised text classification.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

TnT Attacks! Universal Naturalistic Adversarial Patches Against Deep Neural Network Systems

Deep neural networks are vulnerable to attacks from adversarial inputs and, more recently, Trojans to misguide or hijack the model's decision. We expose the existence of an intriguing class of spatially bounded, physically realizable, adversarial examples -- Universal NaTuralistic adversarial paTches -- we call TnTs, by exploring the superset of the spatially bounded adversarial example space and the natural input space within generative adversarial networks. Now, an adversary can arm themselves with a patch that is naturalistic, less malicious-looking, physically realizable, highly effective achieving high attack success rates, and universal. A TnT is universal because any input image captured with a TnT in the scene will: i) misguide a network (untargeted attack); or ii) force the network to make a malicious decision (targeted attack). Interestingly, now, an adversarial patch attacker has the potential to exert a greater level of control -- the ability to choose a location-independent, natural-looking patch as a trigger in contrast to being constrained to noisy perturbations -- an ability is thus far shown to be only possible with Trojan attack methods needing to interfere with the model building processes to embed a backdoor at the risk discovery; but, still realize a patch deployable in the physical world. Through extensive experiments on the large-scale visual classification task, ImageNet with evaluations across its entire validation set of 50,000 images, we demonstrate the realistic threat from TnTs and the robustness of the attack. We show a generalization of the attack to create patches achieving higher attack success rates than existing state-of-the-art methods. Our results show the generalizability of the attack to different visual classification tasks (CIFAR-10, GTSRB, PubFig) and multiple state-of-the-art deep neural networks such as WideResnet50, Inception-V3 and VGG-16.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Learning for Visual Navigation by Imagining the Success

Visual navigation is often cast as a reinforcement learning (RL) problem. Current methods typically result in a suboptimal policy that learns general obstacle avoidance and search behaviours. For example, in the target-object navigation setting, the policies learnt by traditional methods often fail to complete the task, even when the target is clearly within reach from a human perspective. In order to address this issue, we propose to learn to imagine a latent representation of the successful (sub-)goal state. To do so, we have developed a module which we call Foresight Imagination (ForeSIT). ForeSIT is trained to imagine the recurrent latent representation of a future state that leads to success, e.g. either a sub-goal state that is important to reach before the target, or the goal state itself. By conditioning the policy on the generated imagination during training, our agent learns how to use this imagination to achieve its goal robustly. Our agent is able to imagine what the (sub-)goal state may look like (in the latent space) and can learn to navigate towards that state. We develop an efficient learning algorithm to train ForeSIT in an on-policy manner and integrate it into our RL objective. The integration is not trivial due to the constantly evolving state representation shared between both the imagination and the policy. We, empirically, observe that our method outperforms the state-of-the-art methods by a large margin in the commonly accepted benchmark AI2THOR environment. Our method can be readily integrated or added to other model-free RL navigation frameworks.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

An Evolutionary Deep Learning Method for Short-term Wind Speed Prediction: A Case Study of the Lillgrund Offshore Wind Farm

Accurate short-term wind speed forecasting is essential for large-scale integration of wind power generation. However, the seasonal and stochastic characteristics of wind speed make forecasting a challenging task. This study uses a new hybrid evolutionary approach that uses a popular evolutionary search algorithm, CMA-ES, to tune the hyper-parameters of two Long short-term memory(LSTM) ANN models for wind prediction. The proposed hybrid approach is trained on data gathered from an offshore wind turbine installed in a Swedish wind farm located in the Baltic Sea. Two forecasting horizons including ten-minutes ahead (absolute short term) and one-hour ahead (short term) are considered in our experiments. Our experimental results indicate that the new approach is superior to five other applied machine learning models, i.e., polynomial neural network (PNN), feed-forward neural network (FNN), nonlinear autoregressive neural network (NAR) and adaptive neuro-fuzzy inference system (ANFIS), as measured by five performance criteria.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Gold Seeker: Information Gain from Policy Distributions for Goal-oriented Vision-and-Langauge Reasoning

As Computer Vision moves from a passive analysis of pixels to active analysis of semantics, the breadth of information algorithms need to reason over has expanded significantly. One of the key challenges in this vein is the ability to identify the information required to make a decision, and select an action that will recover it. We propose a reinforcement-learning approach that maintains a distribution over its internal information, thus explicitly representing the ambiguity in what it knows, and needs to know, towards achieving its goal. Potential actions are then generated according to this distribution. For each potential action a distribution of the expected outcomes is calculated, and the value of the potential information gain assessed. The action taken is that which maximizes the potential information gain. We demonstrate this approach applied to two vision-and-language problems that have attracted significant recent interest, visual dialog and visual query generation. In both cases, the method actively selects actions that will best reduce its internal uncertainty and outperforms its competitors in achieving the goal of the challenge.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Hybrid Neuro-Evolutionary Method for Predicting Wind Turbine Power Output

Reliable wind turbine power prediction is imperative to the planning, scheduling and control of wind energy farms for stable power production. In recent years Machine Learning (ML) methods have been successfully applied in a wide range of domains, including renewable energy. However, due to the challenging nature of power prediction in wind farms, current models are far short of the accuracy required by industry. In this paper, we deploy a composite ML approach--namely a hybrid neuro-evolutionary algorithm--for accurate forecasting of the power output in wind-turbine farms. We use historical data in the supervisory control and data acquisition (SCADA) systems as input to estimate the power output from an onshore wind farm in Sweden. At the beginning stage, the k-means clustering method and an Autoencoder are employed, respectively, to detect and filter noise in the SCADA measurements. Next, with the prior knowledge that the underlying wind patterns are highly non-linear and diverse, we combine a self-adaptive differential evolution (SaDE) algorithm as a hyper-parameter optimizer, and a recurrent neural network (RNN) called Long Short-term memory (LSTM) to model the power curve of a wind turbine in a farm. Two short time forecasting horizons, including ten-minutes ahead and one-hour ahead, are considered in our experiments. We show that our approach outperforms its counterparts.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

On the Value of Out-of-Distribution Testing: An Example of Goodhart's Law

Out-of-distribution (OOD) testing is increasingly popular for evaluating a machine learning system's ability to generalize beyond the biases of a training set. OOD benchmarks are designed to present a different joint distribution of data and labels between training and test time. VQA-CP has become the standard OOD benchmark for visual question answering, but we discovered three troubling practices in its current use. First, most published methods rely on explicit knowledge of the construction of the OOD splits. They often rely on ``inverting'' the distribution of labels, e.g. answering mostly 'yes' when the common training answer is 'no'. Second, the OOD test set is used for model selection. Third, a model's in-domain performance is assessed after retraining it on in-domain splits (VQA v2) that exhibit a more balanced distribution of labels. These three practices defeat the objective of evaluating generalization, and put into question the value of methods specifically designed for this dataset. We show that embarrassingly-simple methods, including one that generates answers at random, surpass the state of the art on some question types. We provide short- and long-term solutions to avoid these pitfalls and realize the benefits of OOD evaluation.

0 citations0 reviewsNo code linkedOpen access