Erinc Merdivan

Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer et al.

Recent advances in Artificial Intelligence have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, text, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of protein modality encoders in a lightweight fine-tuning scheme that focuses on pairwise alignment with sequence data rather than requiring full matches. This novel approach comprises a mix of Graph Neural Networks and transformer architectures. It demonstrates strong performance in retrieval tasks and showcases the efficacy of multi-modal systems in Protein Machine Learning through a broad spectrum of downstream baselines, including enzyme function prediction and binding site analysis. Furthermore, OneProt enables the transfer of representational information from specialized encoders to the sequence encoder, enhancing capabilities for distinguishing evolutionarily related and unrelated sequences and exhibiting representational properties where evolutionarily related proteins align in similar directions within the latent space. In addition, we extensively investigate modality ablations to identify the encoders that contribute most to predictive performance, highlighting the significance of the binding site encoder, which has not been used in similar models previously. This work expands the horizons of multi-modal protein models, paving the way for transformative applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Erinc Merdivan, Sten Hanke, Matthieu Geist

Recent successful deep reinforcement learning algorithms, such as Trust Region Policy Optimization (TRPO) or Proximal Policy Optimization (PPO), are fundamentally variations of conservative policy iteration (CPI). These algorithms iterate policy evaluation followed by a softened policy improvement step. As so, they are naturally on-policy. In this paper, we propose to combine (any kind of) soft greediness with Modified Policy Iteration (MPI). The proposed abstract framework applies repeatedly: (i) a partial policy evaluation step that allows off-policy learning and (ii) any softened greedy step. Our contribution can be seen as a new generic tool for the deep reinforcement learning toolbox. As a proof of concept, we instantiate this framework with the PPO greediness. Comparison to the original PPO shows that our algorithm is much more sample efficient. We also show that it is competitive with the state-of-art off-policy algorithm Soft Actor Critic (SAC).

Erinc Merdivan, Anastasios Vafeiadis, Dimitrios Kalatzis et al.

We propose a new approach to natural language understanding in which we consider the input text as an image and apply 2D Convolutional Neural Networks to learn the local and global semantics of the sentences from the variations ofthe visual patterns of words. Our approach demonstrates that it is possible to get semantically meaningful features from images with text without using optical character recognition and sequential processing pipelines, techniques that traditional Natural Language Understanding algorithms require. To validate our approach, we present results for two applications: text classification and dialog modeling. Using a 2D Convolutional Neural Network, we were able to outperform the state-of-art accuracy results of non-Latin alphabet-based text classification and achieved promising results for eight text classification datasets. Furthermore, our approach outperformed the memory networks when using out of vocabulary entities fromtask 4 of the bAbI dialog dataset.

Deepika Singh, Erinc Merdivan, Ismini Psychoula et al.

Human activity recognition using smart home sensors is one of the bases of ubiquitous computing in smart environments and a topic undergoing intense research in the field of ambient assisted living. The increasingly large amount of data sets calls for machine learning methods. In this paper, we introduce a deep learning model that learns to classify human activities without using any prior knowledge. For this purpose, a Long Short Term Memory (LSTM) Recurrent Neural Network was applied to three real world smart home datasets. The results of these experiments show that the proposed approach outperforms the existing ones in terms of accuracy and performance.

Ismini Psychoula, Erinc Merdivan, Deepika Singh et al.

In the era of Internet of Things (IoT) technologies the potential for privacy invasion is becoming a major concern especially in regards to healthcare data and Ambient Assisted Living (AAL) environments. Systems that offer AAL technologies make extensive use of personal data in order to provide services that are context-aware and personalized. This makes privacy preservation a very important issue especially since the users are not always aware of the privacy risks they could face. A lot of progress has been made in the deep learning field, however, there has been lack of research on privacy preservation of sensitive personal data with the use of deep learning. In this paper we focus on a Long Short Term Memory (LSTM) Encoder-Decoder, which is a principal component of deep learning, and propose a new encoding technique that allows the creation of different AAL data views, depending on the access level of the end user and the information they require access to. The efficiency and effectiveness of the proposed method are demonstrated with experiments on a simulated AAL dataset. Qualitatively, we show that the proposed model learns privacy operations such as disclosure, deletion and generalization and can perform encoding and decoding of the data with almost perfect recovery.