Out to ‘re­think the drug de­sign process,’ AI star Daphne Koller is cre­at­ing a new ma­chine learn­ing ven­ture at in­sitro with some heavy­weight back­ers

Daphne Koller has been busy.

Just two months since the high pro­file AI ex­pert ex­it­ed Google’s an­ti-ag­ing biotech Cal­i­co Labs, where she was chief com­put­ing of­fi­cer, Koller has gath­ered a group of mar­quee in­vestors to back a tech up­start — in­sitro — with plans to de­vel­op a ma­chine learn­ing plat­form equipped with cus­tom-built datasets to cre­ate a new and far more ef­fi­cient ap­proach to drug dis­cov­ery and de­vel­op­ment.

AI cir­cles have been buzzing with spec­u­la­tion and queries about what the for­mer Stan­ford pro­fes­sor planned to do af­ter ex­it­ing Cal­i­co, where she had been de­vel­op­ing com­pu­ta­tion­al meth­ods for an­a­lyz­ing bi­o­log­i­cal da­ta sets. She an­swered at least some of those ques­tions with a blog post late Tues­day that spelled out her com­mit­ment to “in­vest heav­i­ly” in cre­at­ing new datasets that can ac­cel­er­ate the use of ma­chine learn­ing in bio­phar­ma.

Koller has some high rollers back­ing the start­up, in­clud­ing some ven­ture groups well known for block­buster fundrais­ing and a yen for trans­for­ma­tion­al ven­tures. They are: Arch Ven­ture Part­ners, Fore­site Cap­i­tal, a16z, GV (for­mer­ly Google Ven­tures) and Third Rock.

In­sitro, she says, will “col­lect and use a range of very large da­ta sets to train ML mod­els that will help ad­dress key prob­lems in the drug dis­cov­ery and de­vel­op­ment process. To en­able the ma­chine learn­ing, we will use high-qual­i­ty da­ta that has al­ready been col­lect­ed, but we will al­so in­vest heav­i­ly in the cre­ation of our own datasets us­ing high through­put ex­per­i­men­tal ap­proach­es, datasets that are de­signed ex­plic­it­ly with ma­chine learn­ing in mind from the very start. The ML mod­els that are de­vel­oped will then help guide sub­se­quent ex­per­i­ments, pro­vid­ing a tight, closed loop in­te­gra­tion of in sil­i­co and in vit­ro meth­ods (an in­sitro par­a­digm).”

Ac­cord­ing to Koller, the low hang­ing fruit in drug dis­cov­ery has been picked. Reach­ing high­er, go­ing for much bet­ter drugs, will re­quire “a dif­fer­ent ap­proach to drug de­vel­op­ment.” Spend­ing bil­lions to de­vel­op new drugs — and then pass­ing the cost to pa­tients — is not sus­tain­able.

In launch­ing in­sitro with a group of hy­per con­nect­ed back­ers, Koller is in­stant­ly mak­ing her­self a top play­er in a field that has Big Phar­ma’s rapt at­ten­tion. Stream­lin­ing R&D and im­prov­ing the odds of suc­cess find­ing high im­pact ther­a­pies are con­sid­ered keys to longterm prof­itabil­i­ty. But now the fo­cus is on which out­fits can ac­tu­al­ly de­liv­er.

There will be plen­ty of peo­ple watch­ing to see if Koller and the team she’s now re­cruit­ing can per­form. And she knows it won’t be easy. She writes:

There is a lot of hype to­day around ma­chine learn­ing, with hy­per­bol­ic promis­es that it will mag­i­cal­ly solve all of hu­mankind’s prob­lems (and dire warn­ings that it will lead to the de­struc­tion of hu­mankind). We at in­sitro don’t ex­pect ML to be the so­lu­tion to all of the prob­lems in drug de­vel­op­ment, nor to be the mag­ic bul­let that helps find a treat­ment for every dis­ease. How­ev­er, we do be­lieve that the time is right to re­think the drug de­sign process us­ing a dif­fer­ent and more mod­ern toolk­it, in the hope that a new par­a­digm may help us cure more peo­ple, soon­er, and at a much low­er cost.

I’d queried Koller re­cent­ly af­ter hear­ing word about in­sitro. For now, she tells me in a mes­sage, her blog post goes about as deep in­to this as she wants to go right now. But more is com­ing.


Im­age: Daphne Koller. STAN­FORD

Daniel O'Day [via AP Images]

UP­DAT­ED: Look­ing to re­solve lin­ger­ing doubts, Gilead un­leash­es a $5B late-stage cash al­liance with Gala­pa­gos

Daniel O’Day is executing his first major development deal since taking over as CEO of Gilead $GILD. And he’s going in deep to ally himself with a longstanding partner.

O’Day announced today that he is spending $5 billion in cash to add new late-stage drugs to Gilead’s pipeline, picking up rights to Galapagos’ $GLPG Phase III IPF drug GLPG1690 alongside adoption of the biotech’s Phase IIb drug GLPG1972 for osteoarthritis. And Gilead is also putting billions more on the table for milestones, gaining options for everything else in Galapagos’ pipeline, with a shot at all rights outside of Europe.

UP­DAT­ED: Am­gen, No­var­tis scrap Alzheimer's stud­ies -- is BACE fi­nal­ly dead or will Bio­gen and Ei­sai car­ry on?

The BACE theory of controlling Alzheimer’s died with failed pivotal projects at Merck, Eli Lilly and their partners at AstraZeneca. Now Amgen and Novartis have come along to bulldoze it under a mound of safety threats — leaving only Biogen and Eisai to carry on with a less than zero chance of success — with the notable addition that they may actually be doing harm to patients.

After the market closed Thursday, Amgen and Novartis announced that they were dumping two pivotal programs underway with the Banner Alzheimer’s Institute on their BACE drug CNP520 (umibecestat) after an independent review of the data indicated that patients’ cognitive abilities were actually worsening at a faster pace than the placebo arm.

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Christi Shaw at JP Morgan 2019. Jeff Rumans for Endpoints News

Fresh out of Eli Lil­ly, Christi Shaw sur­faces as Daniel O'­Day's new CEO at CAR-T pi­o­neer Kite

Well, that didn’t take long. 

We found out Thursday evening that Christi Shaw has given up her top post as the head of the Bio-Medicines group at Eli Lilly for the helm at CAR-T pioneer Kite. New Gilead CEO Daniel O’Day, a Roche veteran, had made finding a Kite CEO a top priority on his arrival at Gilead. And he went right for a headliner.

O’Day was clearly excited about the coup.

“We conducted an extensive search for a new leader at Kite and we believe that Christi’s unique set of skills will allow us to continue to build on our leadership position in cell therapy,” he said in a prepared statement. “Christi’s vast experience across complex therapeutic areas, and particularly in oncology, will serve Kite very well. She is clearly a leader who will bring teams and individuals together and I am confident she will build upon the entrepreneurial spirit at Kite as we seek to help more people with cancer around the world.”

Christi Shaw at JP Morgan 2019. Jeff Rumans for Endpoints News

Eli Lil­ly's Christi Shaw bows out of top post at the Bio-Med­i­cines unit

Less than 3 years after Eli Lilly CEO David Ricks recruited Novartis vet Christi Shaw to run their big Bio-Medicines business, she’s out.

In a statement put out Thursday morning, Lilly said that Shaw’s last day will come at the end of August. Patrik Jonsson, currently president and general manager of Lilly Japan, will succeed Shaw once he gets the paperwork sorted out.

Lilly’s shares dropped 4% on the news.

Jeff Poulton

Al­ny­lam’s Maraganore switch­es ‘per­haps the best CFO in mid-cap biotech’ with Shire vet Jeff Poul­ton

There’s a new CFO taking charge of the numbers at RNAi pioneer Alnylam.

Alnylam chief John Maraganore says that CFO Manmeet S. Soni is leaving in the proverbial pursuit of new opportunities. And he’s being replaced by ex-Shire CFO Jeff Poulton, not long after the Takeda takeover obliterated that position.

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Analy­sis: In most of the Big Phar­ma world, R&D spend­ing tow­ers over rev­enue from new drugs. Guess who beat the odds

It’s always been the case that there’s no medicine less useful than one that doesn’t make it to patients (unless you regard the task of R&D to be perpetually learning about swimming, while under water…). Yet, launching new medicines that physicians want, that payers will cover, and that patients will take, is a discipline that is unevenly distributed among the big players.

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President Donald Trump at State of the Union. AP Images

White House changes course to kill re­bate re­form

So what exactly is the White House’s plan to tackle rising drug prices? It doesn’t look like we will get definitive answers anytime soon. On the heels of President Donald Trump’s surprise revelation that an executive order is in the works to implement a “favored nations clause,” his administration is now putting out word that it has abandoned an earlier proposal to overhaul rebates.

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Janet Woodcock, AP Images

The FDA's Janet Wood­cock talks about some big changes she's push­ing for in drug de­vel­op­ment, and agency re­views

Janet Woodcock is perhaps the most influential regulator at the FDA. And when the head of CDER talks about the changes being made at the agency when it comes to clinical trial designs, or the need to reorganize for a specific disease arena, an assessment of the expansion of gene therapy or I/O, common development mistakes, and so on, you can be sure the industry pays attention to every word.

So it was with some eagerness that I opened up Geoffrey Porges’ summary of their recent conversation about the FDA. And I wasn’t disappointed. In a wide-ranging exchange with the SVB Leerink analyst, Woodcock discussed the growing importance of patient-reported outcomes in clinical trials, a campaign underway now to see if CROs would help spur more basket studies to compare drugs head-to-head, and much, much more.

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Ex-DARPA di­rec­tor pur­sues all-in-one can­cer pill as NED CEO; Karyopharm los­es com­mer­cial chief ahead of drug roll­out

“Why not try?”

That’s what Geoffrey Ling told me over the phone when asked about what led him to his journey to the position of CEO at NED Biosciences — a company with a lofty goal of creating an all-in-one oral drug to treat all types of cancer and making this drug available to not only developed nations, but also the developing world. 

Ling comes from an extensive background in medicine and the government. He is the co-leader of The Brain Health Project, a professor of neurology and an attending neurocritical care physician at John Hopkins University and Hospital, as well as the assistant director for Medical Innovation of the Science Division in president Obama’s White House Office of Science and Technology Policy (OSTP).