Leonid Yavits

Zuher Jahshan, Can Alkan, Leonid Yavits

Real-time viral genome detection, taxonomic classification and phylogenetic analysis are critical for efficient tracking and control of viral pandemics such as Covid-19. However, the unprecedented and still growing amounts of viral genome data create a computational bottleneck, which effectively prevents the real-time pandemic tracking. For genomic tracing to work effectively, each new viral genome sequence must be placed in its pangenomic context. Re-inferring the full phylogeny of SARS-CoV-2, with datasets containing millions of samples, is prohibitively slow even using powerful computational resources. We are attempting to alleviate the computational bottleneck by modifying and applying Vision Transformer, a recently developed neural network model for image recognition, to taxonomic classification and placement of viral genomes, such as SARS-CoV-2. Our solution, CoViT, places SARS-CoV-2 genome accessions onto SARS-CoV-2 phylogenetic tree with the accuracy of 94.2%. Since CoViT is a classification neural network, it provides more than one likely placement. Specifically, one of the two most likely placements suggested by CoViT is correct with the probability of 97.9%. The probability of the correct placement to be found among the five most likely placements generated by CoViT is 99.8%. The placement time is 0.055s per individual genome running on NVIDIAs GeForce RTX 2080 Ti GPU. We make CoViT available to research community through GitHub: https://github.com/zuherJahshan/covit.

Marcel Khalifa, Barak Hoffer, Orian Leitersdorf et al.

DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important. This paper introduces ClaPIM, a scalable DNA sequence classification architecture based on the emerging concept of hybrid in-crossbar and near-crossbar memristive processing-in-memory (PIM). We enable efficient and high-quality classification by uniting the filter and search stages within a single algorithm. Specifically, we propose a custom filtering technique that drastically narrows the search space and a search approach that facilitates approximate string matching through a distance function. ClaPIM is the first PIM architecture for scalable approximate string matching that benefits from the high density of memristive crossbar arrays and the massive computational parallelism of PIM. Compared with Kraken2, a state-of-the-art software classifier, ClaPIM provides significantly higher classification quality (up to 20x improvement in F1 score) and also demonstrates a 1.8x throughput improvement. Compared with EDAM, a recently-proposed SRAM-based accelerator that is restricted to small datasets, we observe both a 30.4x improvement in normalized throughput per area and a 7% increase in classification precision.

William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi et al.

Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. Therefore, there is a need for fast, energy-efficient, and cost-efficient technologies that enable genomics research without requiring data centers and cloud platforms. We recently launched the BioPIM Project to leverage emerging processing-in-memory (PIM) technologies to enable energy- and cost-efficient analysis of bioinformatics workloads. The BioPIM Project focuses on co-designing algorithms and data structures commonly used in genomics with several PIM architectures to achieve the highest cost, energy, and time savings.

Yuval Harary, Almog Sharoni, Esteban Garzón et al.

Binary Neural Networks (BNNs), where weights and activations are constrained to binary values (+1, -1), are a highly efficient alternative to traditional neural networks. Unfortunately, typical BNNs, while binarizing linear layers (matrix-vector multiplication), still implement other network layers (batch normalization, softmax, output layer, and sometimes the input layer of a convolutional neural network) in full precision. This limits the area and energy benefits and requires architectural support for full precision operations. We propose PiC-BNN, a true end-to-end binary in-approximate search (Hamming distance tolerant) Content Addressable Memory based BNN accelerator. PiC-BNN is designed and manufactured in a commercial 65nm process. PiC-BNN uses Hamming distance tolerance to apply the law of large numbers to enable accurate classification without implementing full precision operations. PiC-BNN achieves baseline software accuracy (95.2%) on the MNIST dataset and 93.5% on the Hand Gesture (HG) dataset, a throughput of 560K inferences/s, and presents a power efficiency of 703M inferences/s/W when implementing a binary MLP model for MNIST/HG dataset classification.

Zuher Jahshan, Ben Ben Ishay, Leonid Yavits

MANAR (Memory-augmented Attention with Navigational Abstract Conceptual Representation), contextualization layer generalizes standard multi-head attention (MHA) by instantiating the principles of Global Workspace Theory (GWT). While MHA enables unconstrained all-to-all communication, it lacks the functional bottleneck and global integration mechanisms hypothesized in cognitive models of consciousness. MANAR addresses this by implementing a central workspace through a trainable memory of abstract concepts and an Abstract Conceptual Representation (ACR). The architecture follows a two-stage logic that maps directly to GWT mechanics: (i) an integration phase, where retrieved memory concepts converge to form a collective "mental image" (the ACR) based on input stimuli; and (ii) a broadcasting phase, where this global state navigates and informs the contextualization of individual local tokens. We demonstrate that efficient linear-time scaling is a fundamental architectural byproduct of instantiating GWT functional bottleneck, as routing global information through a constant-sized ACR resolves the quadratic complexity inherent in standard attention. MANAR is a compatible re-parameterization of MHA with identical semantic roles for its projections, enabling knowledge transfer from pretrained transformers via weight-copy and thus overcoming the adoption barriers of structurally incompatible linear-time alternatives. MANAR enables non-convex contextualization, synthesizing representations that provably lie outside the convex hull of input tokens - a mathematical reflection of the creative synthesis described in GWT. Empirical evaluations confirm that MANAR matches or exceeds strong baselines across language (GLUE score of 85.1), vision (83.9% ImageNet-1K), and speech (2.7% WER on LibriSpeech), positioning it as an efficient and expressive alternative to quadratic attention.