Implementasi IndoBERT-lite dan RoBERTa untuk Text Minng pada Aplikasi Chatbot Jacob

Jacob merupakan aplikasi chatbot yang memiliki kemampuan untuk memberikan informasi terkait program Joint Degree informatika Universitas Multimedia Nusantara. Jacob saat ini telah dirancang untuk dapat melakukan text mining secara daring, tetapi bahasa yang digunakan hanya tersedia dalam bahasa Inggris. Pada penelitian ini, dilakukan implementasi pre-trained model IndoBERT-lite dan RoBERTa melalui web service untuk melakukan text mining dalam Bahasa Indonesia. Selain itu, dilakukan juga pre-training dan fine-tuning pada model RoBERTa dengan TyDI QA dan SQuAD Bahasa Indonesia untuk mendapatkan model yang mampu memprediksi jawaban dalam Bahasa Indonesia. Pengujian dilakukan dengan menggunakan 5 pre-trained model dan evaluasi untuk melihat nilai akurasi/F-Score dari hasil pengujian. Hasil evaluasi menunjukkan indobert- lite-squad memiliki hasil sebesar 0,8/0,89, roberta-1.5gb-tydiqa sebesar 0,8/0,87, roberta-3gb-tydiqa sebesar 0,47/0,57, roberta-1.5gb-squad sebesar 0,47/0,64, dan roberta-3gb-squad sebesar 0,4/0,57

Pembuatan Fitur Custom Domain, Download Application, Ubah Password Dan Cek Status Transaksi Mobilepulsa

Mobilepulsa merupakan produk dari PT Indobest Artha Kreasi yang bertujuan untuk melayani kebutuhan bertransaksi bulanan masyarakat. Salah satu layanan dari Mobilepulsa adalah layanan Whitelabel, yang meyediakan aplikasi maupun website jualan pulsa dengan menggunakan label sendiri. Pada Whitelabel, website yang dimiliki masih menggunakan domain milik Whitelabel. Sehingga untuk merubah domain website, domain harus dibeli sendiri. Kemudian, website Whitelabel tidak menyediakan fitur untuk memasukkan dan megunduh aplikasi mobile sehingga jika ingin mengunduh aplikasi, end-user diharuskan untuk mengunjungi aplikasi third party yang digunakan oleh client. Selain itu, untuk memeriksa status transaksi pembelian dan mengubah password akun hanya dapat dilakukan melalui website Mobilepulsa. Hal ini tentunya menyulitkan bagi para agen pulsa yang tidak memiliki koneksi internet yang memadai. Berdasarkan permasalahan tersebut, dilakukan pembuatan fitur pada layanan Whitelabel yaitu fitur Custom Domain dan Download Application. Selain itu, dilakukan juga penambahan fitur Cek Status Transaksi dan Ubah Password pada chatbot Mobilepulsa. Selama kerja magang, fitur Custom Domain, Download Application, Cek Status Transaksi, dan Ubah Password, telah berhasil dirancang dan dibangun. Fitur Custom Domain dan Download Application telah diuji dan telah digunakan oleh karyawan Mobilepulsa melalui whitelabel.mobilepulsa.com. Fitur Cek Status Transaksi dan Ubah Password pada chatbot telah diuji, namun belum digunakan karena ada tambahan fitur lain yang dirancang oleh rekan kerja

Penerapan Konsep Non-Deterministic Finite Automata (NFA) pada Aplikasi Simulasi Mesin Kopi Vending

In this research, an application for the simulation of vending coffee machines will be discussed using the concept of Non-Deterministic Finite Automata (NFA). With the projected growth in coffee consumption in Indonesia, which increases every year, vending machines can be one of the innovations that can be applied to coffee machines. This coffee vending machine can make 6 coffee variants, with its temperature and desired glass size. There is also a system of cash payments that are applied to this vending coffee machine, where the change will be issued according to the excess balance that is available. The method used is the formal method, to link the design of formal specifications with the application flowchart. Based on the test results obtained, the concept of Non-Deterministic Finite Automata (NFA) can be used as an alternative in the design of vending coffee machines

Cambios fenológicos constantes en la creación de un hotspot de biodiversidad: la flora del cabo

The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record

The evolution of lung cancer and impact of subclonal selection in TRACERx

Lung cancer is the leading cause of cancer-associated mortality worldwide. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource

The evolution of non-small cell lung cancer metastases in TRACERx

Metastatic disease is responsible for the majority of cancer-related deaths. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse

Genomic–transcriptomic evolution in lung cancer and metastasis

Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic–transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary–metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis

Antibodies against endogenous retroviruses promote lung cancer immunotherapy

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS). Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response