Search for: All records

Signal peptides (SPs) play a crucial role in protein translocation in cells. The development of large protein language models (PLMs) and prompt-based learning provide a new opportunity for SP prediction, especially for the categories with limited annotated data. We present a parameter-efficient fine-tuning (PEFT) framework for SP prediction, PEFT-SP, to effectively utilize pretrained PLMs. We integrated low-rank adaptation (LoRA) into ESM-2 models to better leverage the protein sequence evolutionary knowledge of PLMs. Experiments show that PEFT-SP using LoRA enhances state-of-the-art results, leading to a maximum Matthews correlation coefficient (MCC) gain of 87.3% for SPs with small training samples and an overall MCC gain of 6.1%. Furthermore, we also employed two other PEFT methods, prompt tuning and adapter tuning, in ESM-2 for SP prediction. More elaborate experiments show that PEFT-SP using adapter tuning can also improve the state-of-the-art results by up to 28.1% MCC gain for SPs with small training samples and an overall MCC gain of 3.8%. LoRA requires fewer computing resources and less memory than the adapter tuning during the training stage, making it possible to adapt larger and more powerful protein models for SP prediction. 

Trapped-Ion (TI) technology offers potential breakthroughs for Noisy Intermediate Scale Quantum (NISQ) computing. TI qubits offer extended coherence times and high gate fidelity, making them appealing for large-scale NISQ computers. Constructing such computers demands a distributed architecture connecting Quantum Charge Coupled Devices (QCCDs) via quantum matter-links and photonic switches. However, current distributed TI NISQ computers face hardware and system challenges. Entangling qubits across a photonic switch introduces significant latency, while existing compilers generate suboptimal mappings due to their unawareness of the interconnection topology. In this paper, we introduce TITAN, a large-scale distributed TI NISQ computer, which employs an innovative photonic interconnection design to reduce entanglement latency and an advanced partitioning and mapping algorithm to optimize matter-link communications. Our evaluations show that TITAN greatly enhances quantum application performance by 56.6% and fidelity by 19.7% compared to existing systems. 

This paper presents \textit{OFHE}, an electro-optical accelerator designed to process Discretized TFHE (DTFHE) operations, which encrypt multi-bit messages and support homomorphic multiplications, lookup table operations and full-domain functional bootstrappings. While DTFHE is more efficient and versatile than other fully homomorphic encryption schemes, it requires 32-, 64-, and 128-bit polynomial multiplications, which can be time-consuming. Existing TFHE accelerators are not easily upgradable to support DTFHE operations due to limited datapaths, a lack of datapath bit-width reconfigurability, and power inefficiencies when processing FFT and inverse FFT (IFFT) kernels. Compared to prior TFHE accelerators, OFHE addresses these challenges by improving the DTFHE operation latency by 8.7\%, the DTFHE operation throughput by $$57\%$$, and the DTFHE operation throughput per Watt by $$94\%$$. 

The carbon footprint associated with large language models (LLMs) is a significant concern, encompassing emissions from their training, inference, experimentation, and storage processes, including operational and embodied carbon emissions. An essential aspect is accurately estimating the carbon impact of emerging LLMs even before their training, which heavily relies on GPU usage. Existing studies have reported the carbon footprint of LLM training, but only one tool, mlco2, can predict the carbon footprint of new neural networks prior to physical training. However, mlco2 has several serious limitations. It cannot extend its estimation to dense or mixture-of-experts (MoE) LLMs, disregards critical architectural parameters, focuses solely on GPUs, and cannot model embodied carbon footprints. Addressing these gaps, we introduce \textit{\carb}, an end-to-end carbon footprint projection model designed for both dense and MoE LLMs. Compared to mlco2, \carb~significantly enhances the accuracy of carbon footprint estimations for various LLMs. The source code is released at \url{https://github.com/SotaroKaneda/MLCarbon}. 

We propose a circuit-level backdoor attack, QTrojan, against Quantum Neural Networks (QNNs) in this paper. QTrojan is implemented by a few quantum gates inserted into the variational quantum circuit of the victim QNN. QTrojan is much stealthier than a prior Data-Poisoning-based Backdoor Attack (DPBA) since it does not embed any trigger in the inputs of the victim QNN or require access to original training datasets. Compared to a DPBA, QTrojan improves the clean data accuracy by 21% and the attack success rate by 19.9%. 

The evolution of oxygen cycles on Earth’s surface has been regulated by the balance between molecular oxygen production and consumption. The Neoproterozoic–Paleozoic transition likely marks the second rise in atmospheric and oceanic oxygen levels, widely attributed to enhanced burial of organic carbon. However, it remains disputed how marine organic carbon production and burial respond to global environmental changes and whether these feedbacks trigger global oxygenation during this interval. Here, we report a large lithium isotopic and elemental dataset from marine mudstones spanning the upper Neoproterozoic to middle Cambrian [~660 million years ago (Ma) to 500 Ma]. These data indicate a dramatic increase in continental clay formation after ~525 Ma, likely linked to secular changes in global climate and compositions of the continental crust. Using a global biogeochemical model, we suggest that intensified continental weathering and clay delivery to the oceans could have notably increased the burial efficiency of organic carbon and facilitated greater oxygen accumulation in the earliest Paleozoic oceans.